BLASTX 2.0.8 [Jan-05-1999]
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.
Query= 11VII-24F
(492 letters)
Database: Non-redundant GenBank CDS
translations+PDB+SwissProt+SPupdate+PIR
369,800 sequences; 113,023,754 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
gi|2920559 (AF019227) DNA-directed RNA polymerase II [Spraguea l... 108 4e-23
gi|421849|pir||S30229 DNA-directed RNA polymerase (EC 2.7.7.6) I... 66 1e-10
gi|4455279|emb|CAB36815| (AL035527) DNA-directed RNA polymerase ... 66 1e-10
gi|585914|sp|P38420|RPB2_ARATH DNA-DIRECTED RNA POLYMERASE II 13... 66 1e-10
gi|2129929|pir||S65068 DNA-directed RNA polymerase (EC 2.7.7.6) ... 66 2e-10
gi|401013|sp|Q02061|RPB2_SCHPO DNA-DIRECTED RNA POLYMERASE II 13... 59 2e-08
gi|4505941|oth|NP_000929|PPOLR2B polymerase (RNA) II (DNA direct... 59 3e-08
gi|2507348|sp|Q10578|RPB2_CAEEL DNA-DIRECTED RNA POLYMERASE II S... 55 4e-07
gi|157267 (M62975) RNA polymerase II [Drosophila melanogaster] 53 1e-06
gi|84936|pir||A27826 DNA-directed RNA polymerase (EC 2.7.7.6) II... 53 1e-06
gi|2133437|pir||S70415 RNA polymerase II second largest chain RP... 52 4e-06
gi|3257974|dbj|BAA30657| (AP000006) 1117aa long hypothetical DNA... 49 2e-05
gi|3845258 (AE001413) DNA-directed RNA polymerase subunit 2 [Pla... 48 4e-05
gi|172211 (M15693) RNA polymerase II 48 kd subunit [Saccharomyce... 47 7e-05
gi|2507349|sp|P08518|RPB2_YEAST DNA-DIRECTED RNA POLYMERASE II 1... 47 7e-05
gi|1877509 (U89650) RNA polymerase II second largest subunit [Eu... 46 2e-04
gi|401018|sp|P31814|RPOB_THECE DNA-DIRECTED RNA POLYMERASE SUBUN... 46 2e-04
gi|133422|sp|P11513|RPOB_SULAC DNA-DIRECTED RNA POLYMERASE SUBUN... 45 3e-04
gi|172383 (M38723) RNA polymerase III [Saccharomyces cerevisiae] 43 0.001
gi|2507350|sp|P22276|RPC2_YEAST DNA-DIRECTED RNA POLYMERASE III ... 43 0.001
gi|1710663|sp|Q10233|RPC2_SCHPO PUTATIVE DNA-DIRECTED RNA POLYME... 43 0.001
gi|2414583|emb|CAB16564| (Z99292) hypothetical protein [Schizosa... 41 0.005
gi|485110 (U00050) similarity across entire gene to DNA-directed... 39 0.026
gi|133361|sp|P25167|RPC2_DROME DNA-DIRECTED RNA POLYMERASE III 1... 37 0.10
gi|102039|pir||A25877 cytochrome-c oxidase (EC 1.9.3.1) chain II... 35 0.30
gi|1173133|sp|P41558|RPB2_METVA DNA-DIRECTED RNA POLYMERASE SUBU... 34 0.67
gi|2500641|sp|Q58444|RPB2_METJA DNA-DIRECTED RNA POLYMERASE SUBU... 34 0.87
gi|133463|sp|P09844|RPB2_METTW DNA-DIRECTED RNA POLYMERASE SUBUN... 33 1.5
gi|501027 (U01849) ORF2 [Trypanosoma brucei] 33 1.5
gi|2622148 (AE000876) DNA-dependent RNA polymerase, subunit B'' ... 33 1.5
gi|2833558|sp|Q58134|Y724_METJA HYPOTHETICAL PROTEIN MJ0724 >gi|... 32 2.6
gi|83989|pir||B30010 hypothetical ORF-5 protein - Sauroleishmani... 32 3.4
gi|340613 (L07545) A 'c' was inserted after nt 369 (=nt 10459 in... 31 4.4
gi|84041|pir||F22845 hypothetical protein 6 - Trypanosoma brucei... 31 7.6
gi|2146715|pir||S59078 hypothetical protein 262 - red alga (Chon... 31 7.6
gi|1890826 (U88510) NADH dehydrogenase 1 [Flexamia picta] 30 9.9
gi|548823|sp|Q03587|RPOB_THEAC DNA-DIRECTED RNA POLYMERASE SUBUN... 30 9.9
>gi|2920559 (AF019227) DNA-directed RNA polymerase II [Spraguea lophii]
Length = 52
Score = 108 bits (266), Expect = 4e-23
Identities = 51/51 (100%), Positives = 51/51 (100%)
Query: 155 MQTNKSDDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
MQTNKSDDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN
Sbjct: 1 MQTNKSDDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 51
>gi|421849|pir||S30229 DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain -
Arabidopsis thaliana >gi|16486|emb|CAA79528| (Z19121)
RNA polymerase II second largest subunit [Arabidopsis
thaliana]
Length = 1188
Score = 66.3 bits (159), Expect = 1e-10
Identities = 30/45 (66%), Positives = 38/45 (83%)
Query: 137 DDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
D+ I +ED W+VIS++FE KGLVRQQLDSFD F++ MQEIVDE+
Sbjct: 18 DEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDES 62
>gi|4455279|emb|CAB36815| (AL035527) DNA-directed RNA polymerase (EC 2.7.7.6) II second
largest chain [Arabidopsis thaliana]
Length = 1188
Score = 66.3 bits (159), Expect = 1e-10
Identities = 30/45 (66%), Positives = 38/45 (83%)
Query: 137 DDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
D+ I +ED W+VIS++FE KGLVRQQLDSFD F++ MQEIVDE+
Sbjct: 18 DEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDES 62
>gi|585914|sp|P38420|RPB2_ARATH DNA-DIRECTED RNA POLYMERASE II 135 KD POLYPEPTIDE (RNA POLYMERASE
II SUBUNIT 2) >gi|421848|pir||S30228 DNA-directed RNA
polymerase (EC 2.7.7.6) II second largest chain -
Arabidopsis thaliana >gi|16488|emb|CAA79527| (Z19120)
RNA polymerase II second largest subunit [Arabidopsis
thaliana]
Length = 1188
Score = 66.3 bits (159), Expect = 1e-10
Identities = 30/45 (66%), Positives = 38/45 (83%)
Query: 137 DDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
D+ I +ED W+VIS++FE KGLVRQQLDSFD F++ MQEIVDE+
Sbjct: 18 DEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDES 62
>gi|2129929|pir||S65068 DNA-directed RNA polymerase (EC 2.7.7.6) II chain RPB2 - tomato
>gi|1049068 (U28403) RNA polymerase II subunit 2
[Solanum lycopersicum]
Length = 1191
Score = 65.6 bits (157), Expect = 2e-10
Identities = 33/50 (66%), Positives = 40/50 (80%), Gaps = 2/50 (4%)
Query: 152 QTNKSDDT--IKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
Q N DD I +ED W+VIS++FE KGLVRQQLDSFD F++ MQEIVDE+
Sbjct: 10 QYNVDDDEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDES 61
>gi|401013|sp|Q02061|RPB2_SCHPO DNA-DIRECTED RNA POLYMERASE II 138 KD POLYPEPTIDE (RNA POLYMERASE
II SUBUNIT 2) >gi|479866|pir||S35548 DNA-directed RNA
polymerase (EC 2.7.7.6) II chain 2 - fission yeast
(Schizosaccharomyces pombe) >gi|218554|dbj|BAA02600|
(D13337) RNA polymerase II second largest subunit
[Schizosaccharomyces pombe]
Length = 1210
Score = 58.9 bits (140), Expect = 2e-08
Identities = 27/45 (60%), Positives = 35/45 (77%)
Query: 137 DDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
++T+ +EDCW+VISS FE L RQQL SFD FV+ MQEIVD++
Sbjct: 9 NETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDD 53
>gi|4505941|oth|NP_000929|PPOLR2B polymerase (RNA) II (DNA directed) polypeptide B (140kD)
>gi|401012|sp|P30876|RPB2_HUMAN DNA-DIRECTED RNA
POLYMERASE II 140 KD POLYPEPTIDE (RNA POLYMERASE II
SUBUNIT 2) (RPB2) >gi|346349|pir||S28976 DNA-directed
RNA polymerase (EC 2.7.7.6) II largest chain - human
>gi|254869|bbs|112657 RNA polymerase II second largest
subunit, RNA polymerase B second largest subunit [human,
HeLa cells, Peptide, 1174 aa] >gi|36122|emb|CAA45124|
(X63563) RNA polymerase II 140 kDa subunit [Homo
sapiens]
Length = 1174
Score = 58.6 bits (139), Expect = 3e-08
Identities = 29/50 (58%), Positives = 39/50 (78%), Gaps = 4/50 (8%)
Query: 155 MQTNKSDDTIK----KEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDE 6
MQ ++ DD I +E CW VISS+F+ KGLVRQQLDSFD F++ +Q IV++
Sbjct: 8 MQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVED 61
>gi|2507348|sp|Q10578|RPB2_CAEEL DNA-DIRECTED RNA POLYMERASE II SECOND LARGEST SUBUNIT (RNA
POLYMERASE I SUBUNIT 2) >gi|532805 (U13875) highly
similar to DNA-directed RNA polymerase II
[Caenorhabditis elegans]
Length = 1193
Score = 54.7 bits (129), Expect = 4e-07
Identities = 24/40 (60%), Positives = 33/40 (82%)
Query: 122 KEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
+E CW VIS++F+ KGLVRQQLDSFD FV+ +Q IV+++
Sbjct: 30 QEACWVVISAYFDEKGLVRQQLDSFDEFVQMNVQRIVEDS 69
>gi|157267 (M62975) RNA polymerase II [Drosophila melanogaster]
Length = 69
Score = 53.1 bits (125), Expect = 1e-06
Identities = 22/40 (55%), Positives = 33/40 (82%)
Query: 122 KEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
+E CW VI+++F+ KGLVRQQLDSFD F++ +Q IV+++
Sbjct: 24 QEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDS 63
>gi|84936|pir||A27826 DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain -
fruit fly (Drosophila melanogaster)
Length = 1176
Score = 53.1 bits (125), Expect = 1e-06
Identities = 22/40 (55%), Positives = 33/40 (82%)
Query: 122 KEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
+E CW VI+++F+ KGLVRQQLDSFD F++ +Q IV+++
Sbjct: 24 QEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDS 63
>gi|2133437|pir||S70415 RNA polymerase II second largest chain RPB2 - Euplotes
octocarinatus (SGC9) >gi|2654279|emb|CAA47069| (X66453)
DNA-directed RNA polymerase [Euplotes octocarinatus]
Length = 1194
Score = 51.5 bits (121), Expect = 4e-06
Identities = 23/45 (51%), Positives = 32/45 (71%)
Query: 137 DDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
DD I +ED W+VI ++F+ GLV QQ+ SFD F+ +Q+IV EN
Sbjct: 29 DDEITQEDAWAVIRAYFDQHGLVSQQISSFDRFLSYTVQDIVTEN 73
>gi|3257974|dbj|BAA30657| (AP000006) 1117aa long hypothetical DNA-directed RNA polymerase
subunit B [Pyrococcus horikoshii]
Length = 1117
Score = 48.8 bits (114), Expect = 2e-05
Identities = 20/41 (48%), Positives = 30/41 (72%)
Query: 128 IKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDE 6
+ +D W V+ S++E KGLVRQ LDS++ F+ +QE+VDE
Sbjct: 9 VTPDDLWIVMESYWEEKGLVRQHLDSYNAFIERGLQEVVDE 49
>gi|3845258 (AE001413) DNA-directed RNA polymerase subunit 2 [Plasmodium
falciparum]
Length = 1345
Score = 48.0 bits (112), Expect = 4e-05
Identities = 20/45 (44%), Positives = 32/45 (70%)
Query: 137 DDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
++ I ++D W VI S F GLV QQ++S++ F+ +MQEI+DE+
Sbjct: 33 NEQITEDDSWVVIGSFFGSHGLVNQQIESYNDFIEYRMQEIIDEH 77
>gi|172211 (M15693) RNA polymerase II 48 kd subunit [Saccharomyces cerevisiae]
Length = 1224
Score = 47.3 bits (110), Expect = 7e-05
Identities = 23/42 (54%), Positives = 30/42 (70%)
Query: 128 IKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
I ED W+VIS+ F KGLV QQLDSF+ FV +Q+I+ E+
Sbjct: 25 ITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICED 66
>gi|2507349|sp|P08518|RPB2_YEAST DNA-DIRECTED RNA POLYMERASE II 140 KD POLYPEPTIDE (B150) (RNA
POLYMERASE II SUBUNIT 2) >gi|82997|pir||A25884
DNA-directed RNA polymerase (EC 2.7.7.6) II 140K chain -
yeast (Saccharomyces cerevisiae) >gi|1293711 (U55020)
Rpb2p polymerase [Saccharomyces cerevisiae]
>gi|1420379|emb|CAA99357| (Z75059) ORF YOR151c
[Saccharomyces cerevisiae]
Length = 1224
Score = 47.3 bits (110), Expect = 7e-05
Identities = 23/42 (54%), Positives = 30/42 (70%)
Query: 128 IKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
I ED W+VIS+ F KGLV QQLDSF+ FV +Q+I+ E+
Sbjct: 25 ITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICED 66
>gi|1877509 (U89650) RNA polymerase II second largest subunit [Euplotes
crassus]
Length = 205
Score = 46.1 bits (107), Expect = 2e-04
Identities = 20/42 (47%), Positives = 30/42 (70%)
Query: 128 IKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
I +ED W++I ++F+ GLV QQ+ SFD F+ +Q+IV EN
Sbjct: 9 ITQEDAWALIKAYFQQHGLVSQQISSFDRFLSYTIQDIVAEN 50
>gi|401018|sp|P31814|RPOB_THECE DNA-DIRECTED RNA POLYMERASE SUBUNIT B >gi|280354|pir||S25563
DNA-directed RNA polymerase (EC 2.7.7.6) chain B -
Thermococcus celer >gi|48140|emb|CAA47722| (X67313)
Subunit B of DNA-dependent RNA polymerase [Thermococcus
celer]
Length = 1122
Score = 45.7 bits (106), Expect = 2e-04
Identities = 18/41 (43%), Positives = 30/41 (72%)
Query: 128 IKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDE 6
+ +D W V+ ++++ KGLVRQ LDS++ F+ MQE++DE
Sbjct: 11 VTPDDLWLVMEAYWKEKGLVRQHLDSYNAFIDHGMQEVIDE 51
>gi|133422|sp|P11513|RPOB_SULAC DNA-DIRECTED RNA POLYMERASE SUBUNIT B >gi|81108|pir||S04716
DNA-directed RNA polymerase (EC 2.7.7.6) chain B -
Sulfolobus acidocaldarius >gi|46669|emb|CAA32924|
(X14818) RNA polymerase subunit B (AA 1-1126)
[Sulfolobus acidocaldarius]
Length = 1126
Score = 45.3 bits (105), Expect = 3e-04
Identities = 18/38 (47%), Positives = 28/38 (73%)
Query: 119 EDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDE 6
E W++ S F+ +GLVRQ LDSF+ F+R K+Q+++ E
Sbjct: 5 ESRWAIAESFFKTRGLVRQHLDSFNDFLRNKLQQVIYE 42
>gi|172383 (M38723) RNA polymerase III [Saccharomyces cerevisiae]
Length = 1149
Score = 43.4 bits (100), Expect = 0.001
Identities = 18/57 (31%), Positives = 35/57 (60%)
Query: 173 IFSPLFMQTNKSDDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
+ P++ +D+ +D W ++ + ++KGLV+Q LDSF+ FV T +++I+ N
Sbjct: 24 LLKPVYKGKKLTDEINTAQDKWHLLPAFLKVKGLVKQHLDSFNYFVDTDLKKIIKAN 80
>gi|2507350|sp|P22276|RPC2_YEAST DNA-DIRECTED RNA POLYMERASE III 130 KD POLYPEPTIDE (C128) (RNA
POLYMERASE III SUBUNIT 2) >gi|2117916|pir||S67099
DNA-directed RNA polymerase (EC 2.7.7.6) III
second-largest chain - yeast (Saccharomyces cerevisiae)
>gi|1420485|emb|CAA99422| (Z75115) ORF YOR207c
[Saccharomyces cerevisiae]
Length = 1149
Score = 43.4 bits (100), Expect = 0.001
Identities = 18/57 (31%), Positives = 35/57 (60%)
Query: 173 IFSPLFMQTNKSDDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
+ P++ +D+ +D W ++ + ++KGLV+Q LDSF+ FV T +++I+ N
Sbjct: 24 LLKPVYKGKKLTDEINTAQDKWHLLPAFLKVKGLVKQHLDSFNYFVDTDLKKIIKAN 80
>gi|1710663|sp|Q10233|RPC2_SCHPO PUTATIVE DNA-DIRECTED RNA POLYMERASE III 130 KD POLYPEPTIDE (RNA
POLYMERASE III SUBUNIT 2) >gi|1204209|emb|CAA93558|
(Z69727) putative DNA-directed RNA polymerase III 130 kd
subunit [Schizosaccharomyces pombe]
Length = 1165
Score = 43.4 bits (100), Expect = 0.001
Identities = 19/57 (33%), Positives = 34/57 (59%)
Query: 173 IFSPLFMQTNKSDDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
+F P++ +D ED W ++ + ++KGLV+Q LDS++ FV +++IV N
Sbjct: 30 LFKPVYKGKKLADPVPTIEDKWQLLPAFLKVKGLVKQHLDSYNYFVDVDLKKIVQAN 86
>gi|2414583|emb|CAB16564| (Z99292) hypothetical protein [Schizosaccharomyces pombe]
Length = 300
Score = 41.0 bits (94), Expect = 0.005
Identities = 21/42 (50%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 282 LFFIFFYVLFYKLYITCLQLFFIFIYPLCSSTFYF-INFFSPL 157
LF IF+++LFY YIT L F F++ L S +F F +FF PL
Sbjct: 7 LFRIFYFILFYLFYITFLFFFIPFLFTLFSPSFLFHSSFFLPL 49
>gi|485110 (U00050) similarity across entire gene to DNA-directed RNA
polymerase [Caenorhabditis elegans]
Length = 1207
Score = 38.7 bits (88), Expect = 0.026
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 14/78 (17%)
Query: 236 LVFNYFLSSFILYVLLRFIL*IFSPLFMQT--------------NKSDDTIKKEDCWSVI 99
L+F+ F+ F + +L F IF+ F T K + ED W ++
Sbjct: 28 LLFSVFVPLFQIIFILEFQ--IFNTNFQMTIGQVNGRARIKSECGKDQKCMPLEDKWLLV 85
Query: 98 SSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
+ +++GLV+Q L SFD FV+ +++ I+ N
Sbjct: 86 PAFLKVRGLVKQHLVSFDHFVQEEIRSIMLSN 117
>gi|133361|sp|P25167|RPC2_DROME DNA-DIRECTED RNA POLYMERASE III 128 KD POLYPEPTIDE (RNA POLYMERASE
III SUBUNIT 2) >gi|66988|pir||RNFF32 DNA-directed RNA
polymerase (EC 2.7.7.6) III second-largest chain - fruit
fly (Drosophila melanogaster) >gi|10963|emb|CAA41631|
(X58826) RNA polymerase III second-largest subunit
[Drosophila melanogaster]
Length = 1135
Score = 36.7 bits (83), Expect = 0.10
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 110 WSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDEN 3
W ++ + ++KGLV+Q +DSF+ F+ +++IV N
Sbjct: 35 WKLVPAFLQVKGLVKQHIDSFNHFINVDIKKIVKAN 70
>gi|102039|pir||A25877 cytochrome-c oxidase (EC 1.9.3.1) chain III - Crithidia fasciculata
mitochondrion (SGC6) (fragment)
Length = 287
Score = 35.2 bits (79), Expect = 0.30
Identities = 20/48 (41%), Positives = 30/48 (61%), Gaps = 10/48 (20%)
Query: 300 VYSVIQLFFIFFYVLFYKLYITCLQLFFIFIYP------LCSSTF----YFINFFSPL 157
V S + LF FFYV+F + C++ F+F+ P +C F YFI+ F+ L
Sbjct: 93 VISELVLFISFFYVVFSLVLFVCVEFAFVFVIPVMFCCLICDYGFVFYWYFIDVFNLL 150
>gi|1173133|sp|P41558|RPB2_METVA DNA-DIRECTED RNA POLYMERASE SUBUNIT B" >gi|629374|pir||S47160
DNA-directed RNA polymerase (EC 2.7.7.6) - Methanococcus
vannielii >gi|505290|emb|CAA51726| (X73293) DNA-directed
RNA polymerase [Methanococcus vannielii]
Length = 499
Score = 34.0 bits (76), Expect = 0.67
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 104 VISSHFELKGLVRQQLDSFDGFVRTKMQEIVDE 6
++ + F LV+ +DS+D FV K+Q I+DE
Sbjct: 6 IVDAFFRENSLVKHHIDSYDDFVENKIQGIIDE 38
>gi|2500641|sp|Q58444|RPB2_METJA DNA-DIRECTED RNA POLYMERASE SUBUNIT B" >gi|2117911|pir||G64429
DNA-directed RNA polymerase (EC 2.7.7.6) subunit B'' -
Methanococcus jannaschii >gi|1591693 (U67546)
DNA-directed RNA polymerase, subunit B'' (rpoB2)
[Methanococcus jannaschii]
Length = 498
Score = 33.6 bits (75), Expect = 0.87
Identities = 11/33 (33%), Positives = 25/33 (75%)
Query: 104 VISSHFELKGLVRQQLDSFDGFVRTKMQEIVDE 6
++ ++F+ GL+ Q++S++ FV ++Q+I+DE
Sbjct: 7 LVDAYFKEHGLIDHQIESYNDFVENRLQKIIDE 39
>gi|133463|sp|P09844|RPB2_METTW DNA-DIRECTED RNA POLYMERASE SUBUNIT B" >gi|80919|pir||S02194
DNA-directed RNA polymerase (EC 2.7.7.6) chain B'' -
Methanobacterium thermoautotrophicum
>gi|44665|emb|CAA30836| (X08038) RNA polymerase subunit
B'' (AA 1-515) [Methanobacterium thermoautotrophicum]
Length = 515
Score = 32.8 bits (73), Expect = 1.5
Identities = 12/38 (31%), Positives = 23/38 (59%)
Query: 122 KEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVD 9
K+ W ++ + F+ LV + S++ FV ++QEI+D
Sbjct: 2 KKSAWGLVDAFFDKYDLVDHHIHSYNDFVSNRIQEIID 39
>gi|501027 (U01849) ORF2 [Trypanosoma brucei]
Length = 141
Score = 32.8 bits (73), Expect = 1.5
Identities = 19/42 (45%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 291 VIQLFFIFFYV----LFYKLYITCLQLFFIFIYPLCSSTFYFINFF 166
VI LF FFY L+ Y+ CL F IF LC YF+ F
Sbjct: 70 VIILFIFFFYFVLCFLYCCFYLVCLVFFCIFCCVLCYFLIYFLCCF 115
>gi|2622148 (AE000876) DNA-dependent RNA polymerase, subunit B''
[Methanobacterium thermoautotrophicum]
Length = 519
Score = 32.8 bits (73), Expect = 1.5
Identities = 12/38 (31%), Positives = 23/38 (59%)
Query: 122 KEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVD 9
K+ W ++ + F+ LV + S++ FV ++QEI+D
Sbjct: 8 KKSAWGLVDAFFDKYDLVDHHIHSYNDFVSNRIQEIID 45
>gi|2833558|sp|Q58134|Y724_METJA HYPOTHETICAL PROTEIN MJ0724 >gi|2128462|pir||D64390 hypothetical
protein MJ0724 - Methanococcus jannaschii >gi|1499541
(U67519) conserved hypothetical protein [Methanococcus
jannaschii]
Length = 207
Score = 32.1 bits (71), Expect = 2.6
Identities = 14/47 (29%), Positives = 30/47 (63%)
Query: 146 NKSDDTIKKEDCWSVISSHFELKGLVRQQLDSFDGFVRTKMQEIVDE 6
NKS++ KE C+ +++++F +G +R Q + DGF+ +E+ ++
Sbjct: 31 NKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEK 77
>gi|83989|pir||B30010 hypothetical ORF-5 protein - Sauroleishmania tarentolae
mitochondrion (SGC6)
Length = 105
Score = 31.7 bits (70), Expect = 3.4
Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 291 VIQLFFIFFYVLFYKLYITCLQLFFIFIYPLCSSTFYFINFFSPLYANK*IR*YYKERRL 112
V+ + FIF +VL + L++FF F++ L F+ + S LY I Y
Sbjct: 38 VVCITFIFVFVLGF-----FLRIFFSFVFVLLFIVFFGLFSLSFLYTGYFIY-YIYILYN 91
Query: 111 LVCYFFSFRIKRI 73
+CYFF F I I
Sbjct: 92 FICYFFCFSIAYI 104
>gi|340613 (L07545) A 'c' was inserted after nt 369 (=nt 10459 in genomic
sequence (M10126)) to correct -1 frameshift probably due
to gel compression [Leishmania tarentolae]
Length = 355
Score = 31.3 bits (69), Expect = 4.4
Identities = 23/70 (32%), Positives = 34/70 (47%)
Query: 291 VIQLFFIFFYVLFYKLYITCLQLFFIFIYPLCSSTFYFINFFSPLYANK*IR*YYKERRL 112
V+ + FIF +VL + L++FF F++ L F+ + S LY I Y
Sbjct: 48 VVCITFIFVFVLGF-----FLRIFFSFVFVLLFIVFFGLFSLSFLYTGYFIY-YIYILYN 101
Query: 111 LVCYFFSFRI 82
+CYFF F I
Sbjct: 102 FICYFFCFSI 111
>gi|84041|pir||F22845 hypothetical protein 6 - Trypanosoma brucei mitochondrion (SGC6)
Length = 347
Score = 30.5 bits (67), Expect = 7.6
Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 291 VIQLFFIFFYVLFYKLYITCLQLFFIFIYPLCSSTFYFINFFSPLYANK*IR*YYKERRL 112
V+ + FIF +VL + +++FF F++ L TF+ I + L+ I Y
Sbjct: 38 VVCITFIFIFVLGF-----FIRIFFSFVFVLLFITFFGICSLTMLFTGYYIY-YIYILYN 91
Query: 111 LVCYFFSFRI 82
+C+FF+F I
Sbjct: 92 FICFFFAFGI 101
>gi|2146715|pir||S59078 hypothetical protein 262 - red alga (Chondrus crispus)
mitochondrion (SGC3) >gi|1334477|emb|CAA87594| (Z47547)
Pwi=orf234.1;Mpo=orf244;Angio=orfx; no ATG start codon
[Chondrus crispus]
Length = 262
Score = 30.5 bits (67), Expect = 7.6
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 269 SFTFYFINCILLVFNYFLSSFILYVLLRFIL*IFSPLFMQT 147
SF FY + + F++ L+S I Y LL+F IF +F+ T
Sbjct: 180 SFLFYIVTFFICFFSFLLNSMIKYNLLKFHRKIF--IFLNT 218
>gi|1890826 (U88510) NADH dehydrogenase 1 [Flexamia picta]
Length = 310
Score = 30.1 bits (66), Expect = 9.9
Identities = 14/38 (36%), Positives = 24/38 (62%)
Query: 300 VYSVIQLFFIFFYVLFYKLYITCLQLFFIFIYPLCSST 187
V+S+IQ FI+ + + YI CL++ F++ LC S+
Sbjct: 76 VFSMIQSLFIW---VIFPYYINCLEMSLSFLFFLCCSS 110
>gi|548823|sp|Q03587|RPOB_THEAC DNA-DIRECTED RNA POLYMERASE SUBUNIT B >gi|280358|pir||S26722
DNA-directed RNA polymerase (EC 2.7.7.6) chain B -
Thermoplasma acidophilum >gi|809775|emb|CAA48280|
(X68198) DNA-directed RNA polymerase [Thermoplasma
acidophilum]
Length = 1195
Score = 30.1 bits (66), Expect = 9.9
Identities = 15/33 (45%), Positives = 23/33 (69%), Gaps = 6/33 (18%)
Query: 104 VISSHFELKGLVRQQLDSFDGFVRTK------MQEIVDE 6
++ ++F+ G+V QLDS + F T MQ+IVDE
Sbjct: 4 IVDAYFKKYGIVNHQLDSMNSFYATPDNPNSVMQQIVDE 42
Database: Non-redundant GenBank CDS
translations+PDB+SwissProt+SPupdate+PIR
Posted date: Apr 17, 1999 5:33 AM
Number of letters in database: 113,023,754
Number of sequences in database: 369,800
Lambda K H
0.318 0.135 0.00
Gapped
Lambda K H
0.270 0.0470 4.94e-324
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 72350716
Number of Sequences: 369800
Number of extensions: 1131361
Number of successful extensions: 3199
Number of sequences better than 10.0: 74
Number of HSP's better than 10.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 3152
Number of HSP's gapped (non-prelim): 56
length of query: 164
length of database: 113,023,754
effective HSP length: 52
effective length of query: 111
effective length of database: 93794154
effective search space: 10411151094
effective search space used: 10411151094
frameshift window, decay const: 50, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.7 bits)
S2: 66 (30.1 bits)