MedBlast Result

MedBlast(0.8) Results

Direct References
Indirect References
Options
BLASTN
BLASTX

Direct References:

Hit	Evalue	SeqType	References
Z75132	0.0	N
X53289	0.0	N	Genes Dev 1990 Mar;4(3):313-23
X92441	0.0	N	Yeast 1997 May;13(6):573-81 Yeast 1996 Jul;12(9):877-85 FEBS Lett 1997 May 5;407(3):249-52 Curr Genet 1997 Dec;32(6):384-8
NP_014867	2e-79	P
P20436	2e-79	P
C34588	2e-79	P
1A1D	2e-79	P	Leuk Res 1982;6(2):269-79 Cytogenet Cell Genet 1988;47(1-2):66-71 Nat Struct Biol 1998 Feb;5(2):110-4
1I3Q	2e-79	P	Science 2001 Jun 8;292(5523):1863-76
1I50	2e-79	P	Science 2001 Jun 8;292(5523):1863-76
1I6H	2e-79	P	Science 2001 Jun 8;292(5523):1876-82
1K83	2e-79	P	Proc Natl Acad Sci U S A 2002 Feb 5;99(3):1218-22
CAA37383	2e-79	P
CAA63187	2e-79	P
CAA99443	2e-79	P

References Summary:

Woychik NA, Liao SM, Kolodziej PA, Young RA
Subunits shared by eukaryotic nuclear RNA polymerases.
Genes Dev 1990 Mar;4(3):313-23
PMID: 2186966
el Moualij B, Duyckaerts C, Lamotte-Brasseur J, Sluse FE
Phylogenetic classification of the mitochondrial carrier family of Saccharomyces cerevisiae.
Yeast 1997 May;13(6):573-81
PMID: 9178508
Galisson F, Dujon B
Sequence and analysis of a 33 kb fragment from the right arm of chromosome XV of the yeast Saccharomyces cerevisiae.
Yeast 1996 Jul;12(9):877-85
PMID: 8840505
Schneider R, Brors B, Massow M, Weiss H
Mitochondrial fatty acid synthesis: a relic of endosymbiontic origin and a specialized means for respiration.
FEBS Lett 1997 May 5;407(3):249-52
PMID: 9175861
Schneider R, Brors B, Burger F, Camrath S, Weiss H
Two genes of the putative mitochondrial fatty acid synthase in the genome of Saccharomyces cerevisiae.
Curr Genet 1997 Dec;32(6):384-8
PMID: 9388293
Schwartz GN, Biegel JA, Boggs SS
A model to study drug effects on lymphoma and normal cell populations using the AKR/J mouse.
Leuk Res 1982;6(2):269-79
PMID: 7186089
Beechey CV, Searle AG
Effects of zero to four copies of chromosome 15 on mouse embryonic development.
Cytogenet Cell Genet 1988;47(1-2):66-71
PMID: 3356171
Krapp S, Kelly G, Reischl J, Weinzierl RO, Matthews S
Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family.
Nat Struct Biol 1998 Feb;5(2):110-4
PMID: 9461075
Cramer P, Bushnell DA, Kornberg RD
Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.
Science 2001 Jun 8;292(5523):1863-76
PMID: 11313498
Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD
Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.
Science 2001 Jun 8;292(5523):1876-82
PMID: 11313499
Bushnell DA, Cramer P, Kornberg RD
Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution.
Proc Natl Acad Sci U S A 2002 Feb 5;99(3):1218-22
PMID: 11805306

Indirect References:

Hit	Evalue	SeqType	References
Z75132	0.0	N	rpb8p Mol Cell Biol 2001 Sep;21(17):6056-65 rpb8 Gene 1997 Sep 1;196(1-2):165-74 J Mol Biol 2000 Feb 4;295(5):1119-27 Genes Cells 1996 Sep;1(9):843-54 Bioorg Khim 1999 Nov;25(11):828-37 Nat Struct Biol 1998 Feb;5(2):110-4 J Mol Biol 1998 Jun 19;279(4):703-12 Nucleic Acids Res 1999 Feb 15;27(4):1047-55 Yeast 1996 Jul;12(9):877-85 Eur J Biochem 2001 Feb;268(3):612-9 Genes Dev 1990 Mar;4(3):313-23 Nucleic Acids Res 1992 Oct 11;20(19):5231 Bioorg Khim 1998 Feb;24(2):119-25 Mol Cell Biol 1995 Sep;15(9):4702-10 Mol Cell Biol 2001 Sep;21(17):6056-65 J Biol Chem 1990 Oct 15;265(29):17816-9
X53289	0.0	N
X92441	0.0	N	rbp8 (-)
NP_014867	2e-79	P	rpb8p (...) rpb8 (...)
P20436	2e-79	P
C34588	2e-79	P
1A1D	2e-79	P
1I3Q	2e-79	P
1I50	2e-79	P
1I6H	2e-79	P
1K83	2e-79	P
CAA37383	2e-79	P
CAA63187	2e-79	P	rbp8 (-)
CAA99443	2e-79	P	rpb8p (...) rpb8 (...)

References Summary:

Briand JF, Navarro F, Rematier P, Boschiero C, Labarre S, Werner M, Shpakovski GV, Thuriaux P
Partners of Rpb8p, a small subunit shared by yeast RNA polymerases I, II and III.
Mol Cell Biol 2001 Sep;21(17):6056-65
PMID: 11486042
Sakurai H, Ishihama A
Gene organization and protein sequence of the small subunits of Schizosaccharomyces pombe RNA polymerase II.
Gene 1997 Sep 1;196(1-2):165-74
PMID: 9322754
Shpakovski GV, Gadal O, Labarre-Mariotte S, Lebedenko EN, Miklos I, Sakurai H, Proshkin SA, Van Mullem V, Ishihama A, Thuriaux P
Functional conservation of RNA polymerase II in fission and budding yeasts.
J Mol Biol 2000 Feb 4;295(5):1119-27
PMID: 10653691
Miyao T, Yasui K, Sakurai H, Yamagishi M, Ishihama A
Molecular assembly of RNA polymerase II from the fission yeast Schizosaccharomyces pombe: subunit-subunit contact network involving Rpb5.
Genes Cells 1996 Sep;1(9):843-54
PMID: 9077438
Shpakovskii GV, Lebedenko EN
[Molecular evolution and structure of eukaryotic nuclear RNA polymerase subunits in light of the exon-intron organization of their genes]
Bioorg Khim 1999 Nov;25(11):828-37
PMID: 10645488
Ishiguro A, Kimura M, Yasui K, Iwata A, Ueda S, Ishihama A
Two large subunits of the fission yeast RNA polymerase II provide platforms for the assembly of small subunits.
J Mol Biol 1998 Jun 19;279(4):703-12
PMID: 9642054
Voutsina A, Riva M, Carles C, Alexandraki D
Sequence divergence of the RNA polymerase shared subunit ABC14.5 (Rpb8) selectively affects RNA polymerase III assembly in Saccharomyces cerevisiae.
Nucleic Acids Res 1999 Feb 15;27(4):1047-55
PMID: 9927738
Kimura M, Sakurai H, Ishihama A
Intracellular contents and assembly states of all 12 subunits of the RNA polymerase II in the fission yeast Schizosaccharomyces pombe.
Eur J Biochem 2001 Feb;268(3):612-9
PMID: 11168400
Kontermann R, Bautz EK
Similarity between subunit 8 of yeast RNA polymerase II (RPB8) and the second-largest subunits of eukaryotic RNA polymerases.
Nucleic Acids Res 1992 Oct 11;20(19):5231
PMID: 1408842
Shpakovskii GV, Proshkin SA, Kaiushin AL, Korosteleva MD, Lebedenko EN
[Structural-functional characteristics of the Schizosaccharomyces pombe rpb8+ gene, coding the subunit of RNA polymerase I-III, specific only for eukaryotes]
Bioorg Khim 1998 Feb;24(2):119-25
PMID: 10335407
Shpakovski GV, Acker J, Wintzerith M, Lacroix JF, Thuriaux P, Vigneron M
Four subunits that are shared by the three classes of RNA polymerase are functionally interchangeable between Homo sapiens and Saccharomyces cerevisiae.
Mol Cell Biol 1995 Sep;15(9):4702-10
PMID: 7651387
Woychik NA, Young RA
RNA polymerase II subunit RPB10 is essential for yeast cell viability.
J Biol Chem 1990 Oct 15;265(29):17816-9
PMID: 2211663

Options:

Limit of E-value: 1e-20
Limit of Length: 100000
Limit of references returned each search: 40
Limit of retry times: 3
Direct references: Yes
Indirect references: Yes
Allow symbol with hyphen: Yes
Use stop word list: Yes
Thesaurus:
- Saccharomyces cerevisiae (Version: 20021123.0)




 
BLASTN 2.2.5 [Nov-16-2002]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.
RID: 1048251643-02094-24976
Query= ORFN:YOR224C RPB8 SGDID:S0005750, Chr XV from 760825-761265,
reverse complement
         (441 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
or phase 0, 1 or 2 HTGS sequences) 
           1,707,549 sequences; 7,931,913,529 total letters



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|1420517|emb|Z75132.1|SCYOR224C S.cerevisiae chromosome XV rea...   874   0.0  
gi|287825|emb|X53289.1|SCRPB8 S.cerevisiae DNA for RNA polymeras...   874   0.0  
gi|1050762|emb|X92441.1|SC33KB S.cerevisiae 33kb fragment from t...   874   0.0  
gi|23395641|emb|AL845417.3| Mouse DNA sequence from clone RP23-2...    42   0.69 
gi|20336733|ref|NM_138951.1| Mus musculus cDNA sequence BC021608...    40   2.7  
gi|28380692|gb|AE003786.4| Drosophila melanogaster chromosome 2R...    40   2.7  
gi|27597053|gb|AC115356.5| Mus musculus chromosome 15 clone RP23...    40   2.7  
gi|2804496|gb|AF043705.1| Caenorhabditis elegans cosmid Y73A3A, ...    40   2.7  
gi|23505531|gb|AC073590.5| Mus musculus chromosome 12 clone RP23...    40   2.7  
gi|20387450|gb|AC046136.12| Homo sapiens 3 BAC RP11-190P13 (Rosw...    40   2.7  
gi|19353922|gb|BC024432.1| Mus musculus, clone MGC:37247 IMAGE:4...    40   2.7  
gi|18204578|gb|BC021613.1| Mus musculus, clone MGC:37912 IMAGE:5...    40   2.7  
gi|18204569|gb|BC021608.1| Mus musculus, clone MGC:37838 IMAGE:5...    40   2.7  
gi|20070926|gb|BC026825.1| Mus musculus, clone MGC:25970 IMAGE:4...    40   2.7  
gi|17646876|gb|AC013450.5| Drosophila melanogaster, chromosome 2...    40   2.7  
gi|17530775|gb|AC061963.13| Mus musculus chromosome 9, clone RP2...    40   2.7  
gi|16414852|emb|AL596172.1| Listeria innocua Clip11262 complete ...    40   2.7  

ALIGNMENTS
>gi|1420517|emb|Z75132.1|SCYOR224C S.cerevisiae chromosome XV reading frame ORF YOR224c
          Length = 731

 Score =  874 bits (441), Expect = 0.0
 Identities = 441/441 (100%)
 Strand = Plus / Minus

                                                                       
Query: 1   atgtctaacactctatttgatgatatattccaagtctcggaagttgatcccggtcgttat 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 605 atgtctaacactctatttgatgatatattccaagtctcggaagttgatcccggtcgttat 546

                                                                       
Query: 61  aacaaagtctgccgtatcgaagccgcatctaccactcaggaccaatgcaaactaaccttg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 545 aacaaagtctgccgtatcgaagccgcatctaccactcaggaccaatgcaaactaaccttg 486

                                                                       
Query: 121 gatataaatgttgaattgtttcccgtcgccgcacaagattctttgacagtgactattgca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 485 gatataaatgttgaattgtttcccgtcgccgcacaagattctttgacagtgactattgca 426

                                                                       
Query: 181 tcctctttaaacctcgaagacaccccagctaacgactcttctgcgacaagaagctggaga 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 425 tcctctttaaacctcgaagacaccccagctaacgactcttctgcgacaagaagctggaga 366

                                                                       
Query: 241 cctccacaggctggtgacagatcccttgcagatgattatgattacgtcatgtatggtacc 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 365 cctccacaggctggtgacagatcccttgcagatgattatgattacgtcatgtatggtacc 306

                                                                       
Query: 301 gcttacaagtttgaggaagtaagcaaggatctaattgccgtttactactcattcggtggc 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 305 gcttacaagtttgaggaagtaagcaaggatctaattgccgtttactactcattcggtggc 246

                                                                       
Query: 361 ctcttaatgagattagaaggtaactatagaaatttgaataacttgaagcaagagaacgct 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 245 ctcttaatgagattagaaggtaactatagaaatttgaataacttgaagcaagagaacgct 186

                                
Query: 421 tatcttttgattcgtcgttag 441
           |||||||||||||||||||||
Sbjct: 185 tatcttttgattcgtcgttag 165


>gi|287825|emb|X53289.1|SCRPB8 S.cerevisiae DNA for RNA polymerase, subunit RPB8
          Length = 600

 Score =  874 bits (441), Expect = 0.0
 Identities = 441/441 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   atgtctaacactctatttgatgatatattccaagtctcggaagttgatcccggtcgttat 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 atgtctaacactctatttgatgatatattccaagtctcggaagttgatcccggtcgttat 180

                                                                       
Query: 61  aacaaagtctgccgtatcgaagccgcatctaccactcaggaccaatgcaaactaaccttg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 aacaaagtctgccgtatcgaagccgcatctaccactcaggaccaatgcaaactaaccttg 240

                                                                       
Query: 121 gatataaatgttgaattgtttcccgtcgccgcacaagattctttgacagtgactattgca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 gatataaatgttgaattgtttcccgtcgccgcacaagattctttgacagtgactattgca 300

                                                                       
Query: 181 tcctctttaaacctcgaagacaccccagctaacgactcttctgcgacaagaagctggaga 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 tcctctttaaacctcgaagacaccccagctaacgactcttctgcgacaagaagctggaga 360

                                                                       
Query: 241 cctccacaggctggtgacagatcccttgcagatgattatgattacgtcatgtatggtacc 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 cctccacaggctggtgacagatcccttgcagatgattatgattacgtcatgtatggtacc 420

                                                                       
Query: 301 gcttacaagtttgaggaagtaagcaaggatctaattgccgtttactactcattcggtggc 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 gcttacaagtttgaggaagtaagcaaggatctaattgccgtttactactcattcggtggc 480

                                                                       
Query: 361 ctcttaatgagattagaaggtaactatagaaatttgaataacttgaagcaagagaacgct 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 ctcttaatgagattagaaggtaactatagaaatttgaataacttgaagcaagagaacgct 540

                                
Query: 421 tatcttttgattcgtcgttag 441
           |||||||||||||||||||||
Sbjct: 541 tatcttttgattcgtcgttag 561


>gi|1050762|emb|X92441.1|SC33KB S.cerevisiae 33kb fragment from the right arm of chromosome XV
          Length = 33173

 Score =  874 bits (441), Expect = 0.0
 Identities = 441/441 (100%)
 Strand = Plus / Minus

                                                                         
Query: 1     atgtctaacactctatttgatgatatattccaagtctcggaagttgatcccggtcgttat 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 22049 atgtctaacactctatttgatgatatattccaagtctcggaagttgatcccggtcgttat 21990

                                                                         
Query: 61    aacaaagtctgccgtatcgaagccgcatctaccactcaggaccaatgcaaactaaccttg 120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21989 aacaaagtctgccgtatcgaagccgcatctaccactcaggaccaatgcaaactaaccttg 21930

                                                                         
Query: 121   gatataaatgttgaattgtttcccgtcgccgcacaagattctttgacagtgactattgca 180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21929 gatataaatgttgaattgtttcccgtcgccgcacaagattctttgacagtgactattgca 21870

                                                                         
Query: 181   tcctctttaaacctcgaagacaccccagctaacgactcttctgcgacaagaagctggaga 240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21869 tcctctttaaacctcgaagacaccccagctaacgactcttctgcgacaagaagctggaga 21810

                                                                         
Query: 241   cctccacaggctggtgacagatcccttgcagatgattatgattacgtcatgtatggtacc 300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21809 cctccacaggctggtgacagatcccttgcagatgattatgattacgtcatgtatggtacc 21750

                                                                         
Query: 301   gcttacaagtttgaggaagtaagcaaggatctaattgccgtttactactcattcggtggc 360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21749 gcttacaagtttgaggaagtaagcaaggatctaattgccgtttactactcattcggtggc 21690

                                                                         
Query: 361   ctcttaatgagattagaaggtaactatagaaatttgaataacttgaagcaagagaacgct 420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21689 ctcttaatgagattagaaggtaactatagaaatttgaataacttgaagcaagagaacgct 21630

                                  
Query: 421   tatcttttgattcgtcgttag 441
             |||||||||||||||||||||
Sbjct: 21629 tatcttttgattcgtcgttag 21609


>gi|23395641|emb|AL845417.3| Mouse DNA sequence from clone RP23-20I9 on chromosome 2, complete
             sequence
          Length = 144844

 Score = 42.1 bits (21), Expect = 0.69
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                  
Query: 316   gaagtaagcaaggatctaatt 336
             |||||||||||||||||||||
Sbjct: 81980 gaagtaagcaaggatctaatt 81960


>gi|20336733|ref|NM_138951.1| Mus musculus cDNA sequence BC021608 (BC021608), mRNA
          Length = 789

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 229 agaagctggagacctccaca 248
           ||||||||||||||||||||
Sbjct: 309 agaagctggagacctccaca 328


>gi|28380692|gb|AE003786.4| Drosophila melanogaster chromosome 2R, section 3 of 74 of the complete
              sequence
          Length = 280240

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                  
Query: 215    actcttctgcgacaagaagc 234
              ||||||||||||||||||||
Sbjct: 119034 actcttctgcgacaagaagc 119053


>gi|27597053|gb|AC115356.5| Mus musculus chromosome 15 clone RP23-47E9, complete sequence
          Length = 212177

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                  
Query: 85     gcatctaccactcaggacca 104
              ||||||||||||||||||||
Sbjct: 177919 gcatctaccactcaggacca 177938


>gi|2804496|gb|AF043705.1| Caenorhabditis elegans cosmid Y73A3A, complete sequence
          Length = 16070

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 385 tatagaaatttgaataactt 404
           ||||||||||||||||||||
Sbjct: 241 tatagaaatttgaataactt 260


>gi|23505531|gb|AC073590.5| Mus musculus chromosome 12 clone RP23-206K17, complete sequence
          Length = 204107

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 23/24 (95%)
 Strand = Plus / Minus

                                      
Query: 151    gcacaagattctttgacagtgact 174
              |||||||||||||||| |||||||
Sbjct: 160957 gcacaagattctttgagagtgact 160934


>gi|20387450|gb|AC046136.12| Homo sapiens 3 BAC RP11-190P13 (Roswell Park Cancer Institute Human BAC
             Library) complete sequence
          Length = 155827

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                 
Query: 124   ataaatgttgaattgtttcc 143
             ||||||||||||||||||||
Sbjct: 46800 ataaatgttgaattgtttcc 46819


>gi|19353922|gb|BC024432.1| Mus musculus, clone MGC:37247 IMAGE:4972715, mRNA, complete cds
          Length = 789

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 229 agaagctggagacctccaca 248
           ||||||||||||||||||||
Sbjct: 309 agaagctggagacctccaca 328


>gi|18204578|gb|BC021613.1| Mus musculus, clone MGC:37912 IMAGE:5102393, mRNA, complete cds
          Length = 787

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 229 agaagctggagacctccaca 248
           ||||||||||||||||||||
Sbjct: 315 agaagctggagacctccaca 334


>gi|18204569|gb|BC021608.1| Mus musculus, clone MGC:37838 IMAGE:5099426, mRNA, complete cds
          Length = 704

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 229 agaagctggagacctccaca 248
           ||||||||||||||||||||
Sbjct: 221 agaagctggagacctccaca 240


>gi|20070926|gb|BC026825.1| Mus musculus, clone MGC:25970 IMAGE:4240199, mRNA, complete cds
          Length = 742

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 229 agaagctggagacctccaca 248
           ||||||||||||||||||||
Sbjct: 256 agaagctggagacctccaca 275


>gi|17646876|gb|AC013450.5| Drosophila melanogaster, chromosome 2R, region 41E-41F, BAC clone
              BACR04B08, complete sequence
          Length = 196516

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                                  
Query: 215    actcttctgcgacaagaagc 234
              ||||||||||||||||||||
Sbjct: 161898 actcttctgcgacaagaagc 161879


>gi|17530775|gb|AC061963.13| Mus musculus chromosome 9, clone RP23-23P9, complete sequence
          Length = 201757

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                                 
Query: 229   agaagctggagacctccaca 248
             ||||||||||||||||||||
Sbjct: 23326 agaagctggagacctccaca 23307


>gi|16414852|emb|AL596172.1| Listeria innocua Clip11262 complete genome, segment 10/12
          Length = 248050

 Score = 40.1 bits (20), Expect = 2.7
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                  
Query: 127    aatgttgaattgtttcccgt 146
              ||||||||||||||||||||
Sbjct: 101403 aatgttgaattgtttcccgt 101422


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
  or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Mar 20, 2003 10:39 PM
  Number of letters in database: -658,021,059
  Number of sequences in database:  1,707,549
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 1,559,239
Number of Sequences: 1707549
Number of extensions: 1559239
Number of successful extensions: 27158
Number of sequences better than 10.0: 17
Number of HSP's better than 10.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 27133
Number of HSP's gapped (non-prelim): 25
length of query: 441
length of database: 7,931,913,529
effective HSP length: 21
effective length of query: 420
effective length of database: 7,896,055,000
effective search space: 3316343100000
effective search space used: 3316343100000
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 20 (40.1 bits)






 
BLASTX 2.2.5 [Nov-16-2002]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.
RID: 1048257130-02619-3754
Query= ORFN:YOR224C RPB8 SGDID:S0005750, Chr XV from 760825-761265,
reverse complement
         (441 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           1,376,251 sequences; 442,128,549 total letters



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|6324798|ref|NP_014867.1| 16-kDa RNA polymerase subunit (commo...   293   2e-79
gi|19112707|ref|NP_595915.1| dna-directed rna polymerases i, ii,...    97   6e-20
gi|28924311|gb|EAA33464.1| hypothetical protein [Neurospora crassa]    94   3e-19
gi|11359049|pir||T45232 DNA-directed RNA polymerase (EC 2.7.7.6)...    91   3e-18
gi|15221759|ref|NP_175827.1| RNA polymerase II subunit, putative...    86   1e-16
gi|15231714|ref|NP_191519.1| putative protein; protein id: At3g5...    85   2e-16
gi|14589953|ref|NP_006223.2| RNA polymerase II, polypeptide H [H...    84   3e-16
gi|1017823|gb|AAA91458.1| RNA polymerase II subunit                    84   3e-16
gi|21358365|ref|NP_649352.1| CG11246-PA [Drosophila melanogaster...    81   3e-15
gi|21288037|gb|EAA00358.1| agCP9744 [Anopheles gambiae str. PEST]      79   2e-14
gi|27685635|ref|XP_226176.1| similar to RNA polymerase II, polyp...    77   6e-14
gi|17553210|ref|NP_498036.1| RNA polymerase Rpb8 (17.0 kD) [Caen...    75   2e-13
gi|23508830|ref|NP_701498.1| RNA polymerase subunit 8c, putative...    73   7e-13
gi|23488908|gb|EAA21430.1| DNA-directed RNA polymerases i, ii, a...    70   8e-12
gi|13094965|gb|AAK12101.1|AF323605_1 RNA polymerase I, II and II...    69   1e-11
gi|21842223|gb|AAM77739.1|AF510647_1 RNA polymerase II subunit R...    58   2e-08
gi|14193247|gb|AAK55847.1|AF266463_1 RNA polymerase subunit [Man...    55   1e-07
gi|1401210|gb|AAD05371.1| putative RNA polymerase II subunit [Ch...    47   5e-05
gi|4406232|gb|AAD19908.1| RPB17 [Rattus norvegicus]                    46   1e-04
gi|13811973|ref|NP_113102.1| putative RNA polymerase II subunit ...    36   0.093
gi|19554208|ref|NP_602210.1| hypothetical membrane protein [Cory...    36   0.093
gi|6324157|ref|NP_014227.1| anaphase-promoting complex component...    35   0.21 
gi|2665790|gb|AAB88491.1| thymocyte activation and developmental...    33   0.79 
gi|11466113|ref|NP_047046.1| L2602.6 [Leishmania major] >gi|7494...    33   1.0  
gi|18310171|ref|NP_562105.1| probable cobyric acid synthase [Clo...    32   1.3  
gi|27378024|ref|NP_769553.1| blr2913 [Bradyrhizobium japonicum] ...    32   1.8  
gi|484448|pir||JN0729 hypothetical 16.2K protein - phage SPP1 >g...    31   3.9  
gi|22855132|ref|NP_690738.1| non-essential protein [Bacteriophag...    31   3.9  
gi|4502779|ref|NP_001803.1| centromere protein C 1; Centromere a...    30   5.1  
gi|26996556|gb|AAH41117.1| centromere protein C 1 [Homo sapiens]       30   5.1  
gi|23003197|ref|ZP_00046865.1| hypothetical protein [Lactobacill...    30   5.1  
gi|17564202|ref|NP_507025.1| Bacterial regulatory protein UHPC l...    30   6.7  
gi|17564204|ref|NP_507026.1| Sugar transporter family member [Ca...    30   6.7  
gi|28828829|gb|AAO51424.1| similar to Plasmodium falciparum. Hyp...    30   6.7  
gi|23490309|gb|EAA22118.1| hypothetical protein [Plasmodium yoel...    30   6.7  
gi|15800622|ref|NP_286636.1| Z1097 gene product [Escherichia col...    30   6.7  
gi|28378257|ref|NP_785149.1| exonuclease SbcC [Lactobacillus pla...    30   8.7  
gi|15599875|ref|NP_253369.1| hypothetical protein [Pseudomonas a...    30   8.7  
gi|23038011|gb|ZP_00070201.1| hypothetical protein [Oenococcus o...    30   8.7  

ALIGNMENTS
>gi|6324798|ref|NP_014867.1| 16-kDa RNA polymerase subunit (common to polymerases I, II and
           III); Rpb8p [Saccharomyces cerevisiae]
 gi|133340|sp|P20436|RPB8_YEAST DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KD POLYPEPTIDE
           (ABC14.4)
 gi|101298|pir||C34588 DNA-directed RNA polymerase (EC 2.7.7.6) chain RPB8 - yeast
           (Saccharomyces cerevisiae)
 gi|4557901|pdb|1A1D|  Yeast Rna Polymerase Subunit Rpb8, Nmr, Minimized Average
           Structure, Alpha Carbons Only
 gi|14278329|pdb|1I3Q|H Chain H, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 gi|14278340|pdb|1I50|H Chain H, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 gi|14278370|pdb|1I6H|H Chain H, Rna Polymerase Ii Elongation Complex
 gi|20150718|pdb|1K83|H Chain H, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 gi|287826|emb|CAA37383.1| RNA polymerase subunit RPB8 [Saccharomyces cerevisiae]
 gi|1050776|emb|CAA63187.1| YOR50-14 [Saccharomyces cerevisiae]
 gi|1420518|emb|CAA99443.1| ORF YOR224c [Saccharomyces cerevisiae]
          Length = 146

 Score =  293 bits (751), Expect = 2e-79
 Identities = 146/146 (100%), Positives = 146/146 (100%)
 Frame = +1

Query: 1   MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA 180
           MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
Sbjct: 1   MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA 60

Query: 181 SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG 360
           SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
Sbjct: 61  SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG 120

Query: 361 LLMRLEGNYRNLNNLKQENAYLLIRR 438
           LLMRLEGNYRNLNNLKQENAYLLIRR
Sbjct: 121 LLMRLEGNYRNLNNLKQENAYLLIRR 146


>gi|19112707|ref|NP_595915.1| dna-directed rna polymerases i, ii, and iii 14.5 kd polypeptide (ec
           2.7.7.6). [Schizosaccharomyces pombe]
 gi|3334495|sp|Q92399|RPB8_SCHPO DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
 gi|11359048|pir||T43540 DNA-directed RNA polymerase (EC 2.7.7.6) I/II/III 14.5K chain -
           fission yeast (Schizosaccharomyces pombe)
 gi|2529243|dbj|BAA22803.1| RNA polymerase II subunit Rpb8 [Schizosaccharomyces pombe]
 gi|2731566|gb|AAB93482.1| RNA polymerase I, II and III subunit Rpb8 [Schizosaccharomyces
           pombe]
 gi|2792200|gb|AAC39321.1| Rpb8 [Schizosaccharomyces pombe]
 gi|3006170|emb|CAA18430.1| dna-directed rna polymerases i, ii, and iii 14.5 kd polypeptide (ec
           2.7.7.6). [Schizosaccharomyces pombe]
 gi|3869135|dbj|BAA34367.1| RNA polymerase II subunit Rpb8 [Schizosaccharomyces pombe]
          Length = 125

 Score = 96.7 bits (239), Expect = 6e-20
 Identities = 54/144 (37%), Positives = 79/144 (54%)
 Frame = +1

Query: 7   NTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASS 186
           + L D+IF V+ VD  +Y +V RI A S   D   LTLDIN +++P+    + ++ I S+
Sbjct: 4   SVLLDEIFTVTSVDKQKYQRVSRITAVSGQNDM-NLTLDINSQIYPLEKDATFSLQITSN 62

Query: 187 LNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLL 366
           LN  D                     L +  DY+MYG  Y+ EE   + ++VY SFGGLL
Sbjct: 63  LNSPD---------------------LKEAADYIMYGKVYRVEEAKDEKVSVYVSFGGLL 101

Query: 367 MRLEGNYRNLNNLKQENAYLLIRR 438
           M +EG++R L  L  ++ YLL+RR
Sbjct: 102 MAIEGSHRKLYRLSLDHVYLLLRR 125


>gi|28924311|gb|EAA33464.1| hypothetical protein [Neurospora crassa]
          Length = 152

 Score = 94.4 bits (233), Expect = 3e-19
 Identities = 56/147 (38%), Positives = 86/147 (58%), Gaps = 5/147 (3%)
 Frame = +1

Query: 13  LFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLN 192
           LF+D F+V  +   +Y++V R+   S    Q  + LD+N ELFPV   + L + +A+SL+
Sbjct: 10  LFEDEFKVERISDPKYDRVDRLYCTSV-DGQTSMQLDVNKELFPVKVGEYLRIALATSLS 68

Query: 193 LEDTPANDSSATRSWRPPQ---AGDRSLADDYDYVMYGTAYKFEEVSKD--LIAVYYSFG 357
           L+ +  ++    R WR      + +++LAD Y+YV +G  YKFE+  KD   I  Y S+G
Sbjct: 69  LDGSKDDE----RGWRDAAKLGSVEQTLADSYEYVCHGKVYKFED-GKDGQTIKAYMSYG 123

Query: 358 GLLMRLEGNYRNLNNLKQENAYLLIRR 438
           GLLM L+G Y+ L  L+ +  YLL  R
Sbjct: 124 GLLMALDGPYKKLTPLRVDYVYLLANR 150


>gi|11359049|pir||T45232 DNA-directed RNA polymerase (EC 2.7.7.6) I/II/III chain RPB8 -
           fission yeast (Schizosaccharomyces pombe)
 gi|1515321|emb|CAA68926.1| RPB8 [Schizosaccharomyces pombe]
 gi|1515323|emb|CAA68927.1| RPB8 [Schizosaccharomyces pombe]
          Length = 126

 Score = 90.9 bits (224), Expect = 3e-18
 Identities = 51/142 (35%), Positives = 76/142 (53%)
 Frame = +1

Query: 7   NTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASS 186
           + L D+IF V+ VD  +Y +V RI A S   D   LTLDIN +++P+    + ++ I S+
Sbjct: 4   SVLLDEIFTVTSVDKQKYQRVSRITAVSGQNDM-NLTLDINSQIYPLEKDATFSLQITSN 62

Query: 187 LNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLL 366
           LN  D                     L +  DY+MYG  Y+ EE   + ++VY SFGGLL
Sbjct: 63  LNSPD---------------------LKEAADYIMYGKVYRVEEAKDEKVSVYVSFGGLL 101

Query: 367 MRLEGNYRNLNNLKQENAYLLI 432
           M +EG++R L  L  ++ YL +
Sbjct: 102 MAIEGSHRKLYRLSLDHVYLYL 123


>gi|15221759|ref|NP_175827.1| RNA polymerase II subunit, putative; protein id: At1g54250.1,
           supported by cDNA: 29173., supported by cDNA: gi_3372229
           [Arabidopsis thaliana]
 gi|25288519|pir||T52270 DNA-directed RNA polymerase (EC 2.7.7.6) 16.5 K chain [imported] -
           Arabidopsis thaliana
 gi|3372230|gb|AAC28252.1| RNA polymerase I, II and III 16.5 kDa subunit [Arabidopsis
           thaliana]
 gi|4585968|gb|AAD25604.1|AC005287_6 RNA polymerase I, II and III 16.5 kDa subunit [Arabidopsis
           thaliana]
 gi|21555812|gb|AAM63939.1| RNA polymerase II subunit, putative [Arabidopsis thaliana]
 gi|28466897|gb|AAO44057.1| At1g54250 [Arabidopsis thaliana]
          Length = 146

 Score = 85.5 bits (210), Expect = 1e-16
 Identities = 51/146 (34%), Positives = 85/146 (58%), Gaps = 4/146 (2%)
 Frame = +1

Query: 13  LFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASS 186
           LF+DIF V ++DP   +++KV R++A S   +   + LD+N E++P+A  D  T+ +A +
Sbjct: 7   LFEDIFVVDQLDPDGKKFDKVTRVQATSHNLEMF-MHLDVNTEVYPLAVGDKFTLALAPT 65

Query: 187 LNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEE--VSKDLIAVYYSFGG 360
           LNL+ TP      T  + P     ++LAD Y+Y+M+G  YK  E         +Y SFGG
Sbjct: 66  LNLDGTP-----DTGYFTP--GAKKTLADKYEYIMHGKLYKISERDGKTPKAELYVSFGG 118

Query: 361 LLMRLEGNYRNLNNLKQENAYLLIRR 438
           LLM L+G+  ++++ + +    L+ R
Sbjct: 119 LLMLLKGDPAHISHFELDQRLFLLMR 144


>gi|15231714|ref|NP_191519.1| putative protein; protein id: At3g59600.1, supported by cDNA:
           20583. [Arabidopsis thaliana]
 gi|11261459|pir||T49301 hypothetical protein T16L24.150 - Arabidopsis thaliana
 gi|6996296|emb|CAB75457.1| putative protein [Arabidopsis thaliana]
 gi|21554131|gb|AAM63211.1| RNA polymerase II subunit, putative [Arabidopsis thaliana]
 gi|26453032|dbj|BAC43592.1| unknown protein [Arabidopsis thaliana]
          Length = 146

 Score = 85.1 bits (209), Expect = 2e-16
 Identities = 51/146 (34%), Positives = 85/146 (58%), Gaps = 4/146 (2%)
 Frame = +1

Query: 13  LFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASS 186
           +F+DIF V ++DP   +++KV R+EA S   +   + LD+N E++P+A  D  T+ +A +
Sbjct: 7   MFEDIFVVDKLDPDGKKFDKVTRVEARSHNLEMF-MHLDVNTEVYPLAVGDKFTLAMAPT 65

Query: 187 LNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEE--VSKDLIAVYYSFGG 360
           LNL+ TP      T  + P     ++LAD Y+Y+M+G  YK  E         +Y SFGG
Sbjct: 66  LNLDGTP-----DTGYFTP--GAKKTLADKYEYIMHGKLYKISERDGKTPKAELYVSFGG 118

Query: 361 LLMRLEGNYRNLNNLKQENAYLLIRR 438
           LLM L+G+  ++++ + +    L+ R
Sbjct: 119 LLMLLQGDPAHISHFELDQRLFLLMR 144


>gi|14589953|ref|NP_006223.2| RNA polymerase II, polypeptide H [Homo sapiens]
 gi|20892063|ref|XP_148128.1| similar to PROBABLE DNA-DIRECTED RNA POLYMERASES I, II, AND III
           17.1 KD POLYPEPTIDE (RPB17) (RPB8) [Mus musculus]
 gi|21704118|ref|NP_663607.1| polymerase (RNA) II (DNA directed) polypeptide H [Mus musculus]
 gi|27665258|ref|XP_213574.1| similar to RNA polymerase II, polypeptide H [Homo sapiens] [Rattus
           norvegicus]
 gi|27690884|ref|XP_221194.1| similar to RNA polymerase II, polypeptide H [Homo sapiens] [Rattus
           norvegicus]
 gi|20178325|sp|P52434|RPB8_HUMAN DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide
           (RPB17) (RPB8)
 gi|1082772|pir||S55370 RNA polymerase II chain hRPB17 - human
 gi|854177|emb|CAA89060.1| RNA polymerase II subunit hRPB17 [Homo sapiens]
 gi|8052523|emb|CAB92189.1| RPB8 [Homo sapiens]
 gi|12653893|gb|AAH00739.1|AAH00739 Similar to CG11246 gene product [Homo sapiens]
 gi|12805649|gb|AAH02306.1| Similar to CG11246 gene product [Mus musculus]
          Length = 150

 Score = 84.3 bits (207), Expect = 3e-16
 Identities = 54/154 (35%), Positives = 89/154 (57%), Gaps = 8/154 (5%)
 Frame = +1

Query: 1   MSNTLFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVT 174
           M+  LF+DIF V ++DP   ++++V R+   S +  +  L LD+N++++PV   D   + 
Sbjct: 1   MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESF-KMDLILDVNIQIYPVDLGDKFRLV 59

Query: 175 IASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFE--EVSKDL---IA 339
           IAS+L  ED   +D         P     S AD ++YVMYG  Y+ E  E S +    ++
Sbjct: 60  IASTL-YEDGTLDDGEYN-----PTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLS 113

Query: 340 VYYSFGGLLMRLEGNYRNLNNLKQEN-AYLLIRR 438
            Y S+GGLLMRL+G+  NL+  + ++  YLL+++
Sbjct: 114 AYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKK 147


>gi|1017823|gb|AAA91458.1| RNA polymerase II subunit
          Length = 150

 Score = 84.3 bits (207), Expect = 3e-16
 Identities = 54/154 (35%), Positives = 89/154 (57%), Gaps = 8/154 (5%)
 Frame = +1

Query: 1   MSNTLFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVT 174
           M+  LF+DIF V ++DP   ++++V R+   S +  +  L LD+N++++PV   D   + 
Sbjct: 1   MAGILFEDIFDVKDIDPEAKKFDRVSRLHCESESF-KMDLILDVNIQIYPVDLGDKFRLV 59

Query: 175 IASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFE--EVSKDL---IA 339
           IAS+L  ED   +D         P     S AD ++YVMYG  Y+ E  E S +    ++
Sbjct: 60  IASTL-YEDGTLDDGEYN-----PTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLS 113

Query: 340 VYYSFGGLLMRLEGNYRNLNNLKQEN-AYLLIRR 438
            Y S+GGLLMRL+G+  NL+  + ++  YLL+++
Sbjct: 114 AYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKK 147


>gi|21358365|ref|NP_649352.1| CG11246-PA [Drosophila melanogaster]
 gi|7296484|gb|AAF51770.1| CG11246-PA [Drosophila melanogaster]
 gi|16768368|gb|AAL28403.1| GM03174p [Drosophila melanogaster]
          Length = 149

 Score = 81.3 bits (199), Expect = 3e-15
 Identities = 54/155 (34%), Positives = 88/155 (56%), Gaps = 9/155 (5%)
 Frame = +1

Query: 1   MSNTLFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVT 174
           M+  LF+DIF V ++DP   ++++V R+   S +  +  L LDIN  L+P+   D   + 
Sbjct: 1   MAGVLFEDIFNVKDMDPEGKKFDRVSRLHCESESF-KMDLILDINSWLYPMELGDKFRLV 59

Query: 175 IASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFE------EVSKDLI 336
           +A++L  +  P  DS        P   + + AD ++YVMYG  Y+ E      E S+  +
Sbjct: 60  LATTLREDGCP--DSGEYN----PMEHEGTRADSFEYVMYGKIYRIEGDEAHNEASR--L 111

Query: 337 AVYYSFGGLLMRLEGNYRNLNNLK-QENAYLLIRR 438
           + Y SFGGLLMRL+G+  NL+  +  ++ YLL++R
Sbjct: 112 SAYVSFGGLLMRLQGDANNLHGFEVDQHMYLLMKR 146


>gi|21288037|gb|EAA00358.1| agCP9744 [Anopheles gambiae str. PEST]
          Length = 164

 Score = 78.6 bits (192), Expect = 2e-14
 Identities = 50/154 (32%), Positives = 90/154 (58%), Gaps = 8/154 (5%)
 Frame = +1

Query: 1   MSNTLFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVT 174
           MS  LF+DIF V ++DP   ++++V R+   S +  +  L LDIN  L+P+   D   + 
Sbjct: 15  MSGILFEDIFNVKDMDPEGKKFDRVSRLHCESESF-KMDLILDINSWLYPLELGDKFRLV 73

Query: 175 IASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFE-----EVSKDLIA 339
           +A++L+ + T     +A+  +   +  + S AD ++YVM+G  Y+ E       S + ++
Sbjct: 74  LATTLHEDGT-----AASMEYNAAEI-EGSRADSFEYVMFGKVYRIEGDDSQTESSNRLS 127

Query: 340 VYYSFGGLLMRLEGNYRNLNNLK-QENAYLLIRR 438
            Y SFGGLLMRL+G+  NL+  +  ++ +LL+++
Sbjct: 128 AYVSFGGLLMRLQGDANNLHGFEIDQHMFLLMKK 161


>gi|27685635|ref|XP_226176.1| similar to RNA polymerase II, polypeptide H [Homo sapiens] [Rattus
           norvegicus]
          Length = 151

 Score = 76.6 bits (187), Expect = 6e-14
 Identities = 50/149 (33%), Positives = 85/149 (57%), Gaps = 7/149 (4%)
 Frame = +1

Query: 13  LFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASS 186
           LF+DIF V ++DP   ++++V ++   S +  +  L LDIN++++PV   D   + IAS+
Sbjct: 6   LFEDIFDVKDIDPEGKKFDRVSQLHCESESF-KVDLILDINIQIYPVDLGDKFRLVIAST 64

Query: 187 LNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFE--EVSKD---LIAVYYS 351
           L  +DT  +D         P  G  S AD ++YVMYG  Y+ E  E S +    ++   S
Sbjct: 65  LYDDDT-LDDGEYN-----PTDGRPSRADQFEYVMYGKVYRIEGDESSTEAATCLSACVS 118

Query: 352 FGGLLMRLEGNYRNLNNLKQENAYLLIRR 438
           +GGLLMR +G+  NL+  + ++   L+++
Sbjct: 119 YGGLLMRPQGDANNLHEFEVDSRVYLLKK 147


>gi|17553210|ref|NP_498036.1| RNA polymerase Rpb8 (17.0 kD) [Caenorhabditis elegans]
 gi|2833302|sp|Q19826|RPB8_CAEEL PROBABLE DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KD
           POLYPEPTIDE (RPB17) (RPB8)
 gi|7434790|pir||T16177 hypothetical protein F26F4.11 - Caenorhabditis elegans
 gi|1213454|gb|AAA91226.1| Hypothetical protein F26F4.11 [Caenorhabditis elegans]
          Length = 148

 Score = 75.1 bits (183), Expect = 2e-13
 Identities = 49/153 (32%), Positives = 82/153 (53%), Gaps = 7/153 (4%)
 Frame = +1

Query: 1   MSNTLFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVT 174
           M+  +FDD+F+V  VDP   ++++V R         + +L +DIN +++P+   D + + 
Sbjct: 1   MAGIIFDDMFKVKSVDPDGKKFDRVSRY-FCDAESFKMELIIDINSQIYPLKQNDKVRLV 59

Query: 175 IASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEE----VSKDLIAV 342
           +A++L        D  A      P+A +      Y+YVMYG  Y+ E+         +A 
Sbjct: 60  LATTLR------EDGLADEGEYDPKA-EYPRIKQYEYVMYGKVYRLEDDDTGTDGGKLAA 112

Query: 343 YYSFGGLLMRLEGNYRNLNNLKQE-NAYLLIRR 438
           Y SFGGLLMRL+G   NL+  + + N YLL+++
Sbjct: 113 YASFGGLLMRLKGEAINLHGFEVDMNLYLLMKK 145


>gi|23508830|ref|NP_701498.1| RNA polymerase subunit 8c, putative [Plasmodium falciparum 3D7]
 gi|23496666|gb|AAN36222.1|AE014846_21 RNA polymerase subunit 8c, putative [Plasmodium falciparum 3D7]
          Length = 145

 Score = 73.2 bits (178), Expect = 7e-13
 Identities = 49/145 (33%), Positives = 80/145 (55%), Gaps = 1/145 (0%)
 Frame = +1

Query: 4   SNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIAS 183
           SN LF+D F +S VD  ++ KV RI+A ST  D  +L LD++ ELF V  + ++ + +  
Sbjct: 3   SNILFEDRFVISSVDNSKFEKVSRIKAKSTGYD-AELILDVHSELFKVEEKKAIYLALQD 61

Query: 184 SLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGL 363
            L       ND    + W   +  +    ++ +Y+M G  +KFEE+S +   VY SFGGL
Sbjct: 62  KL----LNRNDE---KGW---EQNENVPLNNIEYIMSGRIFKFEELSSERRTVYASFGGL 111

Query: 364 LMRLEGNYRNLNNLKQE-NAYLLIR 435
           +M L  + + + +L+ +   YLL +
Sbjct: 112 MMALTTDKQFIGDLEIDMKIYLLTK 136


>gi|23488908|gb|EAA21430.1| DNA-directed RNA polymerases i, ii, and iii 17.1 kDa polypeptide
           [Plasmodium yoelii yoelii]
          Length = 160

 Score = 69.7 bits (169), Expect = 8e-12
 Identities = 53/156 (33%), Positives = 84/156 (53%), Gaps = 12/156 (7%)
 Frame = +1

Query: 4   SNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQD-------- 159
           SN LF+D F +S VD  ++ KV RI+A ST  D  +L LD++ ELF V  +         
Sbjct: 3   SNILFEDRFVISNVDNSKFEKVSRIKAKSTGYD-AELILDVHSELFKVEEKKVAQIIKKR 61

Query: 160 ---SLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKD 330
               L    A  L L+D     +   ++W   Q  ++SL ++ +Y+M G  +KFEE+S +
Sbjct: 62  EKKKLNHHHAIYLALQDNFMGKNDE-KTWE--QTDNKSL-NNIEYIMSGRIFKFEELSSE 117

Query: 331 LIAVYYSFGGLLMRLEGNYRNLNNLKQE-NAYLLIR 435
              VY S+GGL+M L  + + + +L+ +   YLL +
Sbjct: 118 RRTVYASYGGLMMALTADKQFIGDLEIDMKIYLLAK 153


>gi|13094965|gb|AAK12101.1|AF323605_1 RNA polymerase I, II and III subunit RPB8 [Manihot esculenta]
          Length = 110

 Score = 69.3 bits (168), Expect = 1e-11
 Identities = 38/111 (34%), Positives = 63/111 (56%), Gaps = 4/111 (3%)
 Frame = +1

Query: 118 LDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYG 297
           LD+N E++P+A  D  T+ +A +LNL+ TP             Q   ++LAD Y+Y+M+G
Sbjct: 6   LDVNTEIYPMAVGDKFTMALAHTLNLDGTPDTGYYI-------QGARKTLADKYEYIMHG 58

Query: 298 TAYKFEEVSKDLIA---VYYSFGGLLMRLEGNYRNLNNLK-QENAYLLIRR 438
             YK  E          +Y S+GGLLM L+G+  ++++ +  +  +LLIR+
Sbjct: 59  KLYKISEEGSGKAVKAEIYVSYGGLLMMLKGDPSHVSHFELDQRLFLLIRK 109


>gi|21842223|gb|AAM77739.1|AF510647_1 RNA polymerase II subunit Rpb8 [Giardia intestinalis]
          Length = 150

 Score = 58.2 bits (139), Expect = 2e-08
 Identities = 43/139 (30%), Positives = 71/139 (51%), Gaps = 6/139 (4%)
 Frame = +1

Query: 10  TLFDDIFQVSEVDPG---RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQD--SLTVT 174
           +L+   F ++  DP     Y+ + R+   ST      LTLD N+EL+P   ++  SL V 
Sbjct: 2   SLYSSRFSIASFDPECVKYYDNIGRVLLESTDDPDVFLTLDYNLELYPKLNKNARSLEVQ 61

Query: 175 IASSLNLEDTPANDSSATRSWRPPQAGD-RSLADDYDYVMYGTAYKFEEVSKDLIAVYYS 351
           I SS++ +D   N S+ + ++ P  +        D DY M+GT ++F  V  D + ++ S
Sbjct: 62  ILSSISYQD--FNVSADSPNYDPKLSEILHDAYPDLDYAMHGTVFEFRAVG-DKVDMFIS 118

Query: 352 FGGLLMRLEGNYRNLNNLK 408
           FGGL+ +L+     L   K
Sbjct: 119 FGGLIAKLQAPAFRLERFK 137


>gi|14193247|gb|AAK55847.1|AF266463_1 RNA polymerase subunit [Manihot esculenta]
          Length = 96

 Score = 55.5 bits (132), Expect = 1e-07
 Identities = 33/102 (32%), Positives = 55/102 (53%), Gaps = 4/102 (3%)
 Frame = +1

Query: 145 VAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVS 324
           +A  D  T+ +A +LNL+ TP             Q   ++LAD Y+Y+M+G  YK  E  
Sbjct: 1   MAVGDKFTMALAHTLNLDGTPDTGYYI-------QGARKTLADKYEYIMHGKLYKISEEG 53

Query: 325 KDLIA---VYYSFGGLLMRLEGNYRNLNNLK-QENAYLLIRR 438
                   +Y S+GGLLM L+G+  ++++ +  +  +LLIR+
Sbjct: 54  SGKAVKAEIYVSYGGLLMMLKGDPSHVSHFELDQRLFLLIRK 95


>gi|1401210|gb|AAD05371.1| putative RNA polymerase II subunit [Chlorarachnion CCMP621]
          Length = 147

 Score = 47.0 bits (110), Expect = 5e-05
 Identities = 42/127 (33%), Positives = 59/127 (46%), Gaps = 7/127 (5%)
 Frame = +1

Query: 19  DDIFQVSEVDPGR--YNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLN 192
           +DI ++   DP    Y KV RI A S   +  +L  DIN  LFP+   DSL ++I     
Sbjct: 11  NDIIKILSKDPDGKLYEKVSRIIAQSYYLNM-ELWFDINSHLFPIYVGDSLNLSI---YT 66

Query: 193 LEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKF-----EEVSKDLIAVYYSFG 357
           + D   N +     +         L D Y+Y M G  +        E S +LI  Y SFG
Sbjct: 67  ISDESFNSTIKDNQF-------SYLVDKYEYFMIGKVFNIITSIERETSFNLI--YASFG 117

Query: 358 GLLMRLE 378
           GLL++L+
Sbjct: 118 GLLLKLK 124


>gi|4406232|gb|AAD19908.1| RPB17 [Rattus norvegicus]
          Length = 83

 Score = 45.8 bits (107), Expect = 1e-04
 Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 2/70 (2%)
 Frame = +1

Query: 1   MSNTLFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVT 174
           M+  LF+DIF V ++DP   ++++V R+   S +  +  L LD+N++++PV   D   + 
Sbjct: 1   MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESF-KMDLILDVNIQIYPVDLGDKFRLV 59

Query: 175 IASSLNLEDT 204
           IAS+L  + T
Sbjct: 60  IASTLYEDGT 69


>gi|13811973|ref|NP_113102.1| putative RNA polymerase II subunit [Guillardia theta]
 gi|25375611|pir||F90122 putative RNA polymerase II subunit [imported] - Guillardia theta
           nucleomorph
 gi|13794298|gb|AAK39675.1|AF083031_32 putative RNA polymerase II subunit [Guillardia theta]
          Length = 176

 Score = 36.2 bits (82), Expect = 0.093
 Identities = 32/121 (26%), Positives = 54/121 (44%), Gaps = 9/121 (7%)
 Frame = +1

Query: 103 QCKLTLDINVELFPVAAQDSLTVTIA------SSLNLEDTPANDSSATRSWRPPQAGDRS 264
           Q +  LD N E++ +  +D L V I       S  N  +  +N+ +            + 
Sbjct: 63  QSEFFLDYNSEIYKIQNEDILDVLIIGFSNQISDFNSFELESNNENINLI--------KE 114

Query: 265 LADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNN---LKQENAYLLIR 435
              +++YVM G  +    + K+L   Y SFGGL+++   N RN +    L   N +L IR
Sbjct: 115 YIREFEYVMQGMIFH-TGLEKNLFFFYTSFGGLILKFYSN-RNYSKDPLLMDYNIFLFIR 172

Query: 436 R 438
           +
Sbjct: 173 K 173


>gi|19554208|ref|NP_602210.1| hypothetical membrane protein [Corynebacterium glutamicum ATCC
           13032]
 gi|21325788|dbj|BAC00409.1| Hypothetical membrane protein [Corynebacterium glutamicum ATCC
           13032]
          Length = 107

 Score = 36.2 bits (82), Expect = 0.093
 Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
 Frame = +1

Query: 160 SLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIA 339
           S+ +  A +L L  TPA   S T S    Q GD   A DY+  ++G++  F++V+    A
Sbjct: 8   SVALLTAGALALTATPAMAQSTTGSSASSQVGDALGASDYERDIWGSSKDFDDVTPFGSA 67

Query: 340 VY-YSFGGLLMRLEG-NYRNLNNLKQENA 420
            Y Y+     + + G  Y NL  ++Q  A
Sbjct: 68  WYGYTLAATAVAISGLVYANLPAIEQAAA 96


>gi|6324157|ref|NP_014227.1| anaphase-promoting complex component; Apc1p [Saccharomyces
            cerevisiae]
 gi|1730803|sp|P53886|YNR2_YEAST HYPOTHETICAL 196.1 KD PROTEIN IN RPS3-PSD1 INTERGENIC REGION
 gi|2132761|pir||S63127 probable membrane protein YNL172w - yeast (Saccharomyces cerevisiae)
 gi|1302144|emb|CAA96060.1| ORF YNL172w [Saccharomyces cerevisiae]
          Length = 1748

 Score = 35.0 bits (79), Expect = 0.21
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
 Frame = +1

Query: 229  RSWRPPQAGDRSLADDYDYVMYGT--AYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNN 402
            R W         + DD  ++M       KF E++ DL+ +YY+  G ++ +   + +  N
Sbjct: 1289 REWASNMILWEFIGDDLSFIMKDVDIGVKFSELNTDLLPIYYTMAGRILAMGIRFASTGN 1348

Query: 403  LKQENAYL 426
            LK  N  L
Sbjct: 1349 LKIRNILL 1356


>gi|2665790|gb|AAB88491.1| thymocyte activation and developmental protein [Gallus gallus]
          Length = 439

 Score = 33.1 bits (74), Expect = 0.79
 Identities = 24/84 (28%), Positives = 39/84 (46%)
 Frame = +1

Query: 139 FPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEE 318
           FP A  +++TV     LNL  T   DS AT+ W  P+     L  D  + +    Y+   
Sbjct: 19  FPGAGSETITVQEGEDLNLRCTFTGDSRATKQWLNPRGFTIFL--DNHWGLKDQRYRLIH 76

Query: 319 VSKDLIAVYYSFGGLLMRLEGNYR 390
            S+D +++  S   + +  EG Y+
Sbjct: 77  YSEDELSIRLS--NITVHDEGVYK 98


>gi|11466113|ref|NP_047046.1| L2602.6 [Leishmania major]
 gi|7494013|pir||T02808 conserved hypothetical protein YPL199c, L2602.6 [imported] -
           Leishmania major (strain Friedlin)
 gi|2995584|gb|AAC24631.1| L2602.6 [Leishmania major]
          Length = 897

 Score = 32.7 bits (73), Expect = 1.0
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 3/96 (3%)
 Frame = +1

Query: 151 AQDSLTVTIASSLNLEDTPANDSSA-TRSWRPPQAGDRSLAD--DYDYVMYGTAYKFEEV 321
           A ++LT  + S  + E TPA  ++A T  WRPP     + AD  D      G     EE 
Sbjct: 661 ALNALTQELLSLDSAEATPAKTAAAATVEWRPPHPATATTADAGDDGSGAGGVQRTREET 720

Query: 322 SKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLL 429
           S ++ + Y +    ++ L G++R +    +E AYL+
Sbjct: 721 SAEVYSAYRAAENEILEL-GDWRRV----RERAYLM 751


>gi|18310171|ref|NP_562105.1| probable cobyric acid synthase [Clostridium perfringens]
 gi|18144850|dbj|BAB80895.1| probable cobyric acid synthase [Clostridium perfringens str. 13]
          Length = 243

 Score = 32.3 bits (72), Expect = 1.3
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
 Frame = +1

Query: 253 GDRSLADDYDYVMYGTAYKFEE---------VSKDLIAVYYSFGGLLMRLEGNYRNLNN 402
           GD+   D+YD V +G    FE+         + KD++  Y   G +L+ + G Y+ L N
Sbjct: 44  GDKFDKDNYDIVFFGGGQDFEQSIVSDDLINLKKDVLKEYVEEGKVLLAICGGYQLLGN 102


>gi|27378024|ref|NP_769553.1| blr2913 [Bradyrhizobium japonicum]
 gi|27351170|dbj|BAC48178.1| blr2913 [Bradyrhizobium japonicum]
          Length = 368

 Score = 32.0 bits (71), Expect = 1.8
 Identities = 18/47 (38%), Positives = 29/47 (61%)
 Frame = +1

Query: 202 TPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAV 342
           TPANDSSA R+ R   A    + + Y ++++GT Y F+E  +  ++V
Sbjct: 67  TPANDSSACRAVRGFGACWAIIPEKYRFILFGT-YPFDEQWRPALSV 112


>gi|484448|pir||JN0729 hypothetical 16.2K protein - phage SPP1
 gi|14844|emb|CAA46744.1| orf42 [Bacteriophage SPP1]
          Length = 133

 Score = 30.8 bits (68), Expect = 3.9
 Identities = 25/81 (30%), Positives = 35/81 (43%), Gaps = 2/81 (2%)
 Frame = +1

Query: 190 NLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGT--AYKFEEVSKDLIAVYYSFGGL 363
           N  D P N +     W   Q  D  L ++YD  +YG   A+K EE    L A+      L
Sbjct: 41  NKYDKPFNPND----WTAEQLKDHFLQENYDQKVYGVALAWKLEEYEDKLKALEEENEDL 96

Query: 364 LMRLEGNYRNLNNLKQENAYL 426
              L+     +++LK EN  L
Sbjct: 97  KNELKEMSERVHDLKFENRNL 117


>gi|22855132|ref|NP_690738.1| non-essential protein [Bacteriophage SPP1]
 gi|2764924|emb|CAA66501.1| gene 42 [Bacteriophage SPP1]
          Length = 131

 Score = 30.8 bits (68), Expect = 3.9
 Identities = 25/81 (30%), Positives = 35/81 (43%), Gaps = 2/81 (2%)
 Frame = +1

Query: 190 NLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGT--AYKFEEVSKDLIAVYYSFGGL 363
           N  D P N +     W   Q  D  L ++YD  +YG   A+K EE    L A+      L
Sbjct: 39  NKYDKPFNPND----WTAEQLKDHFLQENYDQKVYGVALAWKLEEYEDKLKALEEENEDL 94

Query: 364 LMRLEGNYRNLNNLKQENAYL 426
              L+     +++LK EN  L
Sbjct: 95  KNELKEMSERVHDLKFENRNL 115


>gi|4502779|ref|NP_001803.1| centromere protein C 1; Centromere autoantigen C1 [Homo sapiens]
 gi|416784|sp|Q03188|CENC_HUMAN Centromere protein C (CENP-C) (Centromere autoantigen C)
 gi|420024|pir||A42681 centromere protein C - human
 gi|180247|gb|AAA51974.1| centromere autoantigen C
          Length = 943

 Score = 30.4 bits (67), Expect = 5.1
 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 16/55 (29%)
 Frame = +1

Query: 313  EEVSKDLIAVYYSFGGLLMRLE----------------GNYRNLNNLKQENAYLL 429
            + V +D++  Y +FG LL  L                 GNY N+ NL+ E + LL
Sbjct: 883  QHVGQDILVFYVNFGDLLCTLHETPYILSTGDSFYVPSGNYYNIKNLRNEESVLL 937


>gi|26996556|gb|AAH41117.1| centromere protein C 1 [Homo sapiens]
          Length = 943

 Score = 30.4 bits (67), Expect = 5.1
 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 16/55 (29%)
 Frame = +1

Query: 313  EEVSKDLIAVYYSFGGLLMRLE----------------GNYRNLNNLKQENAYLL 429
            + V +D++  Y +FG LL  L                 GNY N+ NL+ E + LL
Sbjct: 883  QHVGQDILVFYVNFGDLLCTLHETPYILSTGDSFYVPSGNYYNIKNLRNEESVLL 937


>gi|23003197|ref|ZP_00046865.1| hypothetical protein [Lactobacillus gasseri]
          Length = 227

 Score = 30.4 bits (67), Expect = 5.1
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 8/68 (11%)
 Frame = +1

Query: 256 DRSLADDYDYVMYGTAYKFEE--VSKDL------IAVYYSFGGLLMRLEGNYRNLNNLKQ 411
           D+  A+DYD++ +G    FE+  V+KDL      I  Y + G  ++ + G Y+ + +  +
Sbjct: 48  DKFDANDYDFLFFGGGQDFEQTVVAKDLPRHKETIENYINAGNPMLCICGGYQLMGDYYK 107

Query: 412 ENAYLLIR 435
            N+ + I+
Sbjct: 108 TNSGITIK 115


>gi|17564202|ref|NP_507025.1| Bacterial regulatory protein UHPC like family member (49.5 kD)
           [Caenorhabditis elegans]
 gi|7507605|pir||T24796 hypothetical protein T10C6.6a - Caenorhabditis elegans
 gi|3879741|emb|CAB07662.1| Hypothetical protein T10C6.6a [Caenorhabditis elegans]
          Length = 456

 Score = 30.0 bits (66), Expect = 6.7
 Identities = 11/29 (37%), Positives = 19/29 (65%)
 Frame = +1

Query: 301 AYKFEEVSKDLIAVYYSFGGLLMRLEGNY 387
           AY +EE   D ++++Y FGG++  + G Y
Sbjct: 272 AYHWEESQADQLSIWYDFGGIIGSVLGGY 300


>gi|17564204|ref|NP_507026.1| Sugar transporter family member [Caenorhabditis elegans]
 gi|6425203|emb|CAB60295.1| Hypothetical protein T10C6.6b [Caenorhabditis elegans]
          Length = 387

 Score = 30.0 bits (66), Expect = 6.7
 Identities = 11/29 (37%), Positives = 19/29 (65%)
 Frame = +1

Query: 301 AYKFEEVSKDLIAVYYSFGGLLMRLEGNY 387
           AY +EE   D ++++Y FGG++  + G Y
Sbjct: 203 AYHWEESQADQLSIWYDFGGIIGSVLGGY 231


>gi|28828829|gb|AAO51424.1| similar to Plasmodium falciparum. Hypothetical protein
           [Dictyostelium discoideum]
          Length = 1380

 Score = 30.0 bits (66), Expect = 6.7
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
 Frame = +1

Query: 208 ANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLM-RLEGN 384
           AN+ +A + +     GD    D Y   +Y +  K   +SKDL  + Y F  L++  +E N
Sbjct: 141 ANNFTAVKFF---SGGDNEENDGYQLQIYPSTLKCALLSKDLEIIKYIFNNLILYNIENN 197

Query: 385 YRNL 396
           ++ +
Sbjct: 198 FKGI 201


>gi|23490309|gb|EAA22118.1| hypothetical protein [Plasmodium yoelii yoelii]
          Length = 217

 Score = 30.0 bits (66), Expect = 6.7
 Identities = 22/97 (22%), Positives = 48/97 (49%), Gaps = 4/97 (4%)
 Frame = +1

Query: 61  NKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR 240
           +++  +E      DQ K T D+N   +  +   SLT++ +  LN+ +   ND+S  + + 
Sbjct: 110 SELSELEEGELFDDQDKNTEDLNSSEYTYS---SLTLSFSEYLNIREAYYNDNSYEKIFY 166

Query: 241 P--PQAGDRSLAD--DYDYVMYGTAYKFEEVSKDLIA 339
           P  P+     + D  D+ ++  G   + + + K+L++
Sbjct: 167 PKDPKMNVTYIYDTVDFYHISKGKVIRKKNIMKNLVS 203


>gi|15800622|ref|NP_286636.1| Z1097 gene product [Escherichia coli O157:H7 EDL933]
 gi|15830203|ref|NP_308976.1| hypothetical protein [Escherichia coli O157:H7]
 gi|25376654|pir||E90747 hypothetical protein ECs0949 [imported] - Escherichia coli  (strain
           O157:H7, substrain RIMD 0509952)
 gi|25376655|pir||B85598 hypothetical protein Z1097 [imported] - Escherichia coli  (strain
           O157:H7, substrain EDL933)
 gi|12513888|gb|AAG55246.1|AE005267_11 Z1097 gene product [Escherichia coli O157:H7 EDL933]
 gi|13360408|dbj|BAB34372.1| hypothetical protein [Escherichia coli O157:H7]
          Length = 413

 Score = 30.0 bits (66), Expect = 6.7
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
 Frame = +1

Query: 19  DDIFQV-SEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELF---PVAAQDSLTVTIASS 186
           D +F +  E+    YN +C +    T   QC + L +N E+F   PV     +    ++ 
Sbjct: 292 DTVFNLFPEMHSSHYNDICSVSVDMTKGTQCMIHLMVNEEVFMSLPVPVATMVREDASNL 351

Query: 187 LNLEDTPAND 216
           +NL+ T  ND
Sbjct: 352 INLK-TLLND 360


>gi|28378257|ref|NP_785149.1| exonuclease SbcC [Lactobacillus plantarum WCFS1]
 gi|28271092|emb|CAD63997.1| exonuclease SbcC [Lactobacillus plantarum WCFS1]
          Length = 1061

 Score = 29.6 bits (65), Expect = 8.7
 Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
 Frame = +1

Query: 73  RIEAASTTQDQCKLTL--------DINVELFPV-AAQDSLTVTIASSLNLEDTPANDSSA 225
           R+EAA  T    +LTL        D+N  L    A +  L  TIA +L   + P +D + 
Sbjct: 719 RLEAAQATVQTSQLTLSKHQTKLDDLNDRLKTTQATRTQLEQTIAQALAAPEAPTHDQTV 778

Query: 226 TRSWRPPQAGDRSLA 270
             +W    A  R  A
Sbjct: 779 LENWLEELANGRLTA 793


>gi|15599875|ref|NP_253369.1| hypothetical protein [Pseudomonas aeruginosa PA01]
 gi|11350246|pir||H83061 hypothetical protein PA4680 [imported] - Pseudomonas aeruginosa
           (strain PAO1)
 gi|9950936|gb|AAG08067.1|AE004881_10 hypothetical protein [Pseudomonas aeruginosa PAO1]
          Length = 178

 Score = 29.6 bits (65), Expect = 8.7
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
 Frame = +1

Query: 169 VTIASSLNLEDTP-----ANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDL 333
           ++I++SLNL++ P     A    A  + +P  +G+  L  D         + F+EV+ D+
Sbjct: 47  ISISASLNLQENPSQTRCAGGCGARLAIQPAGSGNNYLVIDD----ISGKFSFDEVTLDV 102

Query: 334 IAVYYSFGG 360
           + +   FGG
Sbjct: 103 VTIKDGFGG 111


>gi|23038011|gb|ZP_00070201.1| hypothetical protein [Oenococcus oeni MCW]
          Length = 244

 Score = 29.6 bits (65), Expect = 8.7
 Identities = 14/29 (48%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
 Frame = +1

Query: 253 GDRSLADDYDYVMYGTAYKFEE--VSKDL 333
           GD   ADDYD+V++G    +EE   +KDL
Sbjct: 47  GDSFKADDYDFVIFGGGQDYEESVTAKDL 75


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Mar 20, 2003 11:48 PM
  Number of letters in database: 442,128,549
  Number of sequences in database:  1,376,251
  
Lambda     K      H
   0.318    0.135    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 331,471,683
Number of Sequences: 1376251
Number of extensions: 6332812
Number of successful extensions: 16566
Number of sequences better than 10.0: 78
Number of HSP's better than 10.0 without gapping: 16091
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 16523
length of database: 442,128,549
effective HSP length: 122
effective length of database: 274,225,927
effective search space used: 6581422248
frameshift window, decay const: 50,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)