Psyllid ID: psy3015
Local Sequence Feature Prediction
| Prediction and (Method) | Result |
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Close Homologs for Annotation Transfer
Close Homologs in SWISS-PROT Database Detected by BLAST 
Original result of BLAST against SWISS-PROT Database
| ID | Alignment graph | Length |
Definition |
RBH(Q2H) |
RBH(H2Q) |
Q cover |
H cover |
Identity |
E-value |
| Query | 1791 | 2.2.26 [Sep-21-2011] | |||||||
| P04052 | 1887 | DNA-directed RNA polymera | yes | N/A | 0.268 | 0.254 | 0.734 | 0.0 | |
| P08775 | 1970 | DNA-directed RNA polymera | yes | N/A | 0.255 | 0.231 | 0.623 | 1e-178 | |
| P24928 | 1970 | DNA-directed RNA polymera | yes | N/A | 0.255 | 0.231 | 0.623 | 1e-178 | |
| P35074 | 1853 | DNA-directed RNA polymera | N/A | N/A | 0.209 | 0.202 | 0.672 | 1e-167 | |
| P16356 | 1856 | DNA-directed RNA polymera | yes | N/A | 0.209 | 0.202 | 0.668 | 1e-166 | |
| P35084 | 1727 | DNA-directed RNA polymera | yes | N/A | 0.201 | 0.208 | 0.562 | 1e-124 | |
| P18616 | 1839 | DNA-directed RNA polymera | yes | N/A | 0.214 | 0.208 | 0.519 | 1e-123 | |
| P36594 | 1752 | DNA-directed RNA polymera | yes | N/A | 0.201 | 0.205 | 0.530 | 1e-116 | |
| Q75A34 | 1745 | DNA-directed RNA polymera | yes | N/A | 0.199 | 0.204 | 0.516 | 1e-112 | |
| P04050 | 1733 | DNA-directed RNA polymera | yes | N/A | 0.203 | 0.210 | 0.495 | 1e-109 |
| >sp|P04052|RPB1_DROME DNA-directed RNA polymerase II subunit RPB1 OS=Drosophila melanogaster GN=RpII215 PE=3 SV=4 | Back alignment and function desciption |
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Score = 721 bits (1862), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 370/504 (73%), Positives = 401/504 (79%), Gaps = 24/504 (4%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVI 1012
V G D++SKQANENATLLFQCL+RSTLCTK V+E +RLS+EAFEWLVGEIE RFQQAQ
Sbjct: 1015 VTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQAQAN 1074
Query: 1013 A--CVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLT-----PSEFFF 1065
VG + P HF + G + ++ PS F
Sbjct: 1075 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVF 1134
Query: 1066 HAMGGREGLIDTAVKTAETV-NVL-----VFLFQVTANTAIYYDPDPQNTVIPEDQEFVN 1119
L A + AE NVL L +VTANTAIYYDPDPQ TVI EDQEFVN
Sbjct: 1135 --------LTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVN 1186
Query: 1120 VYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEK 1179
VYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTME I+EKIN GFG+DLNCIFNDDNA+K
Sbjct: 1187 VYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADK 1246
Query: 1180 LVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQT 1239
LVLRIRIMN++++K QDE++AVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQT
Sbjct: 1247 LVLRIRIMNNEENKFQDEDEAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQT 1306
Query: 1240 DSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAV 1299
DSKKRI+ITE+GEFKAI +WLLETDGTS+MKVLSERDVDP+RT SNDICEIFQVLGIEAV
Sbjct: 1307 DSKKRIVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAV 1366
Query: 1300 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 1359
RKSVEKEMN VLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE
Sbjct: 1367 RKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 1426
Query: 1360 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIP--LATGM 1417
TVDVLMDAAAHAE DPMRGVSENIIMGQLP+MGTGCFDLLLDAEKC+ GIEIP L M
Sbjct: 1427 TVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGCFDLLLDAEKCRFGIEIPNTLGNSM 1486
Query: 1418 MGGPAGMFFGSAATPSSIPGPPAW 1441
+GG A MF G +TPS P W
Sbjct: 1487 LGG-AAMFIGGGSTPSMTPPMTPW 1509
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DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Drosophila melanogaster (taxid: 7227) EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6 |
| >sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II subunit RPB1 OS=Mus musculus GN=Polr2a PE=1 SV=3 | Back alignment and function description |
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| >sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens GN=POLR2A PE=1 SV=2 | Back alignment and function description |
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| >sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis briggsae GN=rpb-1 PE=3 SV=2 | Back alignment and function description |
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| >sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis elegans GN=ama-1 PE=1 SV=3 | Back alignment and function description |
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| >sp|P35084|RPB1_DICDI DNA-directed RNA polymerase II subunit rpb1 OS=Dictyostelium discoideum GN=polr2a PE=2 SV=2 | Back alignment and function description |
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| >sp|P18616|RPB1_ARATH DNA-directed RNA polymerase II subunit RPB1 OS=Arabidopsis thaliana GN=RPB205 PE=1 SV=3 | Back alignment and function description |
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| >sp|P36594|RPB1_SCHPO DNA-directed RNA polymerase II subunit rpb1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb1 PE=1 SV=1 | Back alignment and function description |
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| >sp|Q75A34|RPB1_ASHGO DNA-directed RNA polymerase II subunit RPB1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB1 PE=3 SV=2 | Back alignment and function description |
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| >sp|P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPO21 PE=1 SV=2 | Back alignment and function description |
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Close Homologs in the Non-Redundant Database Detected by BLAST
Original result of BLAST against Nonredundant Database
| GI | Alignment Graph | Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 1791 | ||||||
| 324120564 | 1793 | RNA polymerase II largest subunit [Bemis | 0.268 | 0.267 | 0.785 | 0.0 | |
| 324120548 | 1862 | RNA polymerase II largest subunit [Zorot | 0.268 | 0.257 | 0.767 | 0.0 | |
| 324120540 | 1909 | RNA polymerase II largest subunit [Teleo | 0.268 | 0.251 | 0.763 | 0.0 | |
| 324120572 | 1708 | RNA polymerase II largest subunit [Vespa | 0.268 | 0.281 | 0.765 | 0.0 | |
| 383857287 | 1904 | PREDICTED: DNA-directed RNA polymerase I | 0.268 | 0.252 | 0.765 | 0.0 | |
| 380029407 | 1893 | PREDICTED: LOW QUALITY PROTEIN: DNA-dire | 0.268 | 0.254 | 0.761 | 0.0 | |
| 340722779 | 1902 | PREDICTED: DNA-directed RNA polymerase I | 0.268 | 0.252 | 0.759 | 0.0 | |
| 322801476 | 1905 | hypothetical protein SINV_09846 [Solenop | 0.265 | 0.249 | 0.767 | 0.0 | |
| 307181433 | 1906 | DNA-directed RNA polymerase II subunit R | 0.261 | 0.245 | 0.775 | 0.0 | |
| 324120558 | 1687 | RNA polymerase II largest subunit [Gynai | 0.268 | 0.284 | 0.758 | 0.0 |
| >gi|324120564|dbj|BAJ78673.1| RNA polymerase II largest subunit [Bemisia tabaci] | Back alignment and taxonomy information |
|---|
Score = 763 bits (1969), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 396/504 (78%), Positives = 412/504 (81%), Gaps = 24/504 (4%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVI 1012
VAGEDQLSKQANENATLLFQCLVRSTLCTKLV+E +RLSSEAFEWLVGEIENRFQQAQ
Sbjct: 1017 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVSEKFRLSSEAFEWLVGEIENRFQQAQCS 1076
Query: 1013 A--CVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLT-----PSEFFF 1065
VG + P HF + G + ++ PS F
Sbjct: 1077 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVF 1136
Query: 1066 HAMGGREGLIDTAVKTAETV-NVL-----VFLFQVTANTAIYYDPDPQNTVIPEDQEFVN 1119
L A + AE NVL L +VTANTAIYYDPDPQNTVI EDQEFVN
Sbjct: 1137 --------LTGAAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQNTVIREDQEFVN 1188
Query: 1120 VYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEK 1179
VYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEK
Sbjct: 1189 VYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEK 1248
Query: 1180 LVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQT 1239
LVLRIRIMNSDD+K+QDEED VDKMEDDMFLRCIEANMLSDMTLQGIEAI KVYMHLPQT
Sbjct: 1249 LVLRIRIMNSDDNKLQDEEDTVDKMEDDMFLRCIEANMLSDMTLQGIEAISKVYMHLPQT 1308
Query: 1240 DSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAV 1299
DSKKRI++TE+GEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIF VLGIEAV
Sbjct: 1309 DSKKRIVVTETGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFAVLGIEAV 1368
Query: 1300 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 1359
RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE
Sbjct: 1369 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 1428
Query: 1360 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPL--ATGM 1417
TVDVLMDAA+HAE DPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK GIEIP+ GM
Sbjct: 1429 TVDVLMDAASHAEVDPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKAGIEIPMNIGAGM 1488
Query: 1418 MGGPAGMFFGSAATPSSIPGPPAW 1441
M G AGMFFGS ATPS P W
Sbjct: 1489 MSG-AGMFFGSMATPSMSPQMTPW 1511
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Source: Bemisia tabaci Species: Bemisia tabaci Genus: Bemisia Family: Aleyrodidae Order: Hemiptera Class: Insecta Phylum: Arthropoda Superkingdom: Eukaryota |
| >gi|324120548|dbj|BAJ78665.1| RNA polymerase II largest subunit [Zorotypus sp. 154-1] | Back alignment and taxonomy information |
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| >gi|324120540|dbj|BAJ78661.1| RNA polymerase II largest subunit [Teleogryllus emma] | Back alignment and taxonomy information |
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| >gi|324120572|dbj|BAJ78677.1| RNA polymerase II largest subunit [Vespa analis insularis] | Back alignment and taxonomy information |
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| >gi|383857287|ref|XP_003704136.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Megachile rotundata] | Back alignment and taxonomy information |
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| >gi|380029407|ref|XP_003698365.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase II subunit RPB1-like [Apis florea] | Back alignment and taxonomy information |
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| >gi|340722779|ref|XP_003399779.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Bombus terrestris] gi|350424170|ref|XP_003493710.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Bombus impatiens] | Back alignment and taxonomy information |
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| >gi|322801476|gb|EFZ22137.1| hypothetical protein SINV_09846 [Solenopsis invicta] | Back alignment and taxonomy information |
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| >gi|307181433|gb|EFN69028.1| DNA-directed RNA polymerase II subunit RPB1 [Camponotus floridanus] | Back alignment and taxonomy information |
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| >gi|324120558|dbj|BAJ78670.1| RNA polymerase II largest subunit [Gynaikothrips ficorum] | Back alignment and taxonomy information |
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Prediction of Gene Ontology (GO) Terms
Close Homologs with Gene Ontology terms Detected by BLAST
Original result of BLAST against Gene Ontology (AMIGO)
| ID |
Alignment graph |
Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 1791 | ||||||
| FB|FBgn0003277 | 1887 | RpII215 "RNA polymerase II 215 | 0.271 | 0.257 | 0.722 | 0.0 | |
| UNIPROTKB|J9NW09 | 1789 | POLR2A "DNA-directed RNA polym | 0.197 | 0.197 | 0.742 | 4.4e-293 | |
| ZFIN|ZDB-GENE-041008-78 | 1965 | polr2a "polymerase (RNA) II (D | 0.270 | 0.246 | 0.625 | 2.4e-292 | |
| UNIPROTKB|P24928 | 1970 | POLR2A "DNA-directed RNA polym | 0.197 | 0.179 | 0.742 | 6.6e-291 | |
| MGI|MGI:98086 | 1970 | Polr2a "polymerase (RNA) II (D | 0.197 | 0.179 | 0.742 | 6.6e-291 | |
| UNIPROTKB|F1PGS0 | 1969 | POLR2A "DNA-directed RNA polym | 0.197 | 0.179 | 0.742 | 8e-291 | |
| RGD|1587326 | 1970 | Polr2a "polymerase (RNA) II (D | 0.197 | 0.179 | 0.742 | 8.5e-291 | |
| UNIPROTKB|G3MZY8 | 1970 | POLR2A "DNA-directed RNA polym | 0.197 | 0.179 | 0.715 | 2.5e-281 | |
| WB|WBGene00000123 | 1856 | ama-1 [Caenorhabditis elegans | 0.252 | 0.243 | 0.615 | 1.7e-270 | |
| UNIPROTKB|P16356 | 1856 | ama-1 "DNA-directed RNA polyme | 0.252 | 0.243 | 0.615 | 1.7e-270 |
| FB|FBgn0003277 RpII215 "RNA polymerase II 215kD subunit" [Drosophila melanogaster (taxid:7227)] | Back alignment and assigned GO terms |
|---|
Score = 1755 (622.8 bits), Expect = 0., Sum P(4) = 0.
Identities = 360/498 (72%), Positives = 389/498 (78%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVI 1012
V G D++SKQANENATLLFQCL+RSTLCTK V+E +RLS+EAFEWLVGEIE RFQQAQ
Sbjct: 1015 VTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQAQAN 1074
Query: 1013 A--CVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGG 1070
VG + P HF + G + ++ A
Sbjct: 1075 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKP---KAPSL 1131
Query: 1071 REGLIDTAVKTAETV-NVL-----VFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEM 1124
L A + AE NVL L +VTANTAIYYDPDPQ TVI EDQEFVNVYYEM
Sbjct: 1132 TVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEM 1191
Query: 1125 PDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRI 1184
PDFDPTRISPWLLRIELDRKRMTDKKLTME I+EKIN GFG+DLNCIFNDDNA+KLVLRI
Sbjct: 1192 PDFDPTRISPWLLRIELDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRI 1251
Query: 1185 RIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKR 1244
RIMN++++K QDE++AVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKR
Sbjct: 1252 RIMNNEENKFQDEDEAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKR 1311
Query: 1245 IIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVE 1304
I+ITE+GEFKAI +WLLETDGTS+MKVLSERDVDP+RT SNDICEIFQVLGIEAVRKSVE
Sbjct: 1312 IVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVE 1371
Query: 1305 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 1364
KEMN VLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL
Sbjct: 1372 KEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 1431
Query: 1365 MDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATXXXXXXXXX 1424
MDAAAHAE DPMRGVSENIIMGQLP+MGTGCFDLLLDAEKC+ GIEIP
Sbjct: 1432 MDAAAHAETDPMRGVSENIIMGQLPKMGTGCFDLLLDAEKCRFGIEIPNTLGNSMLGGAA 1491
Query: 1425 XXXXX-XTPSSIPGPPAW 1441
TPS P W
Sbjct: 1492 MFIGGGSTPSMTPPMTPW 1509
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| UNIPROTKB|J9NW09 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] | Back alignment and assigned GO terms |
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| ZFIN|ZDB-GENE-041008-78 polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Danio rerio (taxid:7955)] | Back alignment and assigned GO terms |
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| UNIPROTKB|P24928 POLR2A "DNA-directed RNA polymerase II subunit RPB1" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
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| MGI|MGI:98086 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Mus musculus (taxid:10090)] | Back alignment and assigned GO terms |
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| UNIPROTKB|F1PGS0 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] | Back alignment and assigned GO terms |
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| RGD|1587326 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Rattus norvegicus (taxid:10116)] | Back alignment and assigned GO terms |
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| UNIPROTKB|G3MZY8 POLR2A "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] | Back alignment and assigned GO terms |
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| WB|WBGene00000123 ama-1 [Caenorhabditis elegans (taxid:6239)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|P16356 ama-1 "DNA-directed RNA polymerase II subunit RPB1" [Caenorhabditis elegans (taxid:6239)] | Back alignment and assigned GO terms |
|---|
Prediction of Enzyme Commission (EC) Number
EC Number Prediction by Annotation Transfer from SWISS-PROT Entries
Original result of BLAST against SWISS-PROT
No confident hit for EC number transfering in SWISSPROT detected by BLAST
EC Number Prediction by EFICAz Software
| Prediction Level | EC number | Confidence of Prediction |
| 3rd Layer | 2.7.7 | 0.766 |
| 4th Layer | 2.7.7.6 | 0.824 |
Prediction of Functionally Associated Proteins
Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database
| ID | Alignment Graph | Length |
Definition |
E-value |
| Query | 1791 | |||
| cd02584 | 410 | cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of | 1e-174 | |
| PRK08566 | 882 | PRK08566, PRK08566, DNA-directed RNA polymerase su | 2e-97 | |
| TIGR02390 | 867 | TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer | 3e-88 | |
| pfam04990 | 135 | pfam04990, RNA_pol_Rpb1_7, RNA polymerase Rpb1, do | 3e-67 | |
| cd02584 | 410 | cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of | 2e-65 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' | 1e-64 | |
| pfam04990 | 135 | pfam04990, RNA_pol_Rpb1_7, RNA polymerase Rpb1, do | 3e-57 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 6e-57 | |
| cd02584 | 410 | cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of | 8e-49 | |
| cd06528 | 363 | cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol | 2e-47 | |
| PRK04309 | 383 | PRK04309, PRK04309, DNA-directed RNA polymerase su | 6e-47 | |
| TIGR02389 | 367 | TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer | 2e-46 | |
| cd02584 | 410 | cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of | 3e-45 | |
| pfam05000 | 108 | pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, do | 5e-44 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do | 1e-42 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do | 3e-41 | |
| cd02736 | 300 | cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o | 2e-40 | |
| pfam04983 | 158 | pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do | 8e-38 | |
| PRK14898 | 858 | PRK14898, PRK14898, DNA-directed RNA polymerase su | 6e-36 | |
| PRK14897 | 509 | PRK14897, PRK14897, unknown domain/DNA-directed RN | 1e-35 | |
| cd00630 | 158 | cd00630, RNAP_largest_subunit_C, Largest subunit o | 3e-35 | |
| PRK08566 | 882 | PRK08566, PRK08566, DNA-directed RNA polymerase su | 5e-33 | |
| cd00630 | 158 | cd00630, RNAP_largest_subunit_C, Largest subunit o | 1e-29 | |
| TIGR02390 | 867 | TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer | 2e-29 | |
| cd02735 | 309 | cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of | 2e-28 | |
| pfam04992 | 187 | pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, do | 4e-28 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 3e-27 | |
| cd02736 | 300 | cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o | 2e-26 | |
| TIGR02389 | 367 | TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer | 3e-24 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' | 4e-24 | |
| PRK04309 | 383 | PRK04309, PRK04309, DNA-directed RNA polymerase su | 4e-24 | |
| pfam04992 | 187 | pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, do | 6e-24 | |
| cd06528 | 363 | cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol | 2e-23 | |
| PRK14898 | 858 | PRK14898, PRK14898, DNA-directed RNA polymerase su | 1e-21 | |
| cd02735 | 309 | cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of | 1e-20 | |
| cd00630 | 158 | cd00630, RNAP_largest_subunit_C, Largest subunit o | 3e-20 | |
| pfam05000 | 108 | pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, do | 2e-18 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 3e-18 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do | 4e-18 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do | 2e-17 | |
| PRK14897 | 509 | PRK14897, PRK14897, unknown domain/DNA-directed RN | 2e-17 | |
| cd02736 | 300 | cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o | 1e-15 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do | 4e-15 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' | 3e-14 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 2e-13 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do | 2e-13 | |
| TIGR02389 | 367 | TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer | 3e-13 | |
| PRK04309 | 383 | PRK04309, PRK04309, DNA-directed RNA polymerase su | 5e-13 | |
| PRK14898 | 858 | PRK14898, PRK14898, DNA-directed RNA polymerase su | 9e-13 | |
| pfam04983 | 158 | pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do | 1e-12 | |
| cd06528 | 363 | cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol | 5e-12 | |
| TIGR02386 | 1140 | TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, | 2e-11 | |
| pfam04997 | 330 | pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do | 5e-11 | |
| cd02735 | 309 | cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of | 1e-10 | |
| PRK14897 | 509 | PRK14897, PRK14897, unknown domain/DNA-directed RN | 4e-10 | |
| PRK08566 | 882 | PRK08566, PRK08566, DNA-directed RNA polymerase su | 6e-10 | |
| PRK08566 | 882 | PRK08566, PRK08566, DNA-directed RNA polymerase su | 1e-09 | |
| TIGR02390 | 867 | TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer | 1e-09 | |
| TIGR02390 | 867 | TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer | 3e-09 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' | 2e-08 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 3e-08 | |
| PRK14906 | 1460 | PRK14906, PRK14906, DNA-directed RNA polymerase su | 3e-08 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 3e-07 | |
| TIGR02388 | 1227 | TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase | 4e-07 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 2e-06 | |
| PRK00566 | 1156 | PRK00566, PRK00566, DNA-directed RNA polymerase su | 2e-06 | |
| pfam04992 | 187 | pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, do | 3e-06 | |
| PRK02597 | 1331 | PRK02597, rpoC2, DNA-directed RNA polymerase subun | 3e-06 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 4e-06 | |
| cd02737 | 381 | cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) | 9e-06 | |
| cd02584 | 410 | cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of | 3e-05 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' | 3e-05 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 3e-05 | |
| cd02655 | 204 | cd02655, RNAP_beta'_C, Largest subunit (beta') of | 3e-05 | |
| cd02655 | 204 | cd02655, RNAP_beta'_C, Largest subunit (beta') of | 3e-05 | |
| TIGR02386 | 1140 | TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, | 4e-05 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 4e-05 | |
| TIGR02386 | 1140 | TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, | 2e-04 | |
| TIGR02388 | 1227 | TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase | 2e-04 | |
| CHL00117 | 1364 | CHL00117, rpoC2, RNA polymerase beta'' subunit; Re | 2e-04 | |
| smart00663 | 295 | smart00663, RPOLA_N, RNA polymerase I subunit A N- | 3e-04 | |
| PRK00566 | 1156 | PRK00566, PRK00566, DNA-directed RNA polymerase su | 6e-04 | |
| PRK00566 | 1156 | PRK00566, PRK00566, DNA-directed RNA polymerase su | 6e-04 | |
| smart00663 | 295 | smart00663, RPOLA_N, RNA polymerase I subunit A N- | 6e-04 | |
| TIGR02388 | 1227 | TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase | 7e-04 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 0.001 | |
| PRK02597 | 1331 | PRK02597, rpoC2, DNA-directed RNA polymerase subun | 0.002 | |
| PRK02597 | 1331 | PRK02597, rpoC2, DNA-directed RNA polymerase subun | 0.002 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' | 0.004 |
| >gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
Score = 532 bits (1372), Expect = e-174
Identities = 203/310 (65%), Positives = 243/310 (78%), Gaps = 13/310 (4%)
Query: 1094 VTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPT--RISPWLLRIELDRKRMTDKKL 1151
VTA T IYYDPDPQNTVI ED+EFV Y+E PD D R+SPWLLRIELDRK+MTDKKL
Sbjct: 112 VTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKL 171
Query: 1152 TMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLR 1211
+ME I++KI F DDLN IF+DDNAEKLV+RIRI+N D+ K +D EDD+FL+
Sbjct: 172 SMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLK 224
Query: 1212 CIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKV 1271
IE+NMLSDMTL+GIE I + ++KK++ I E+GEFK +W+LETDG +L +V
Sbjct: 225 KIESNMLSDMTLKGIEGI---RKVFIREENKKKVDI-ETGEFKKREEWVLETDGVNLREV 280
Query: 1272 LSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMT 1331
LS VDP RT SNDI EIF+VLGIEA RK++ KE+ V+ F G YVNYRHLALLCDVMT
Sbjct: 281 LSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMT 340
Query: 1332 AKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRM 1391
+GHLMAITRHGINRQDTG LMRCSFEETVD+L++AAA E D ++GVSENI++GQL +
Sbjct: 341 QRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPI 400
Query: 1392 GTGCFDLLLD 1401
GTGCFDLLLD
Sbjct: 401 GTGCFDLLLD 410
|
RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410 |
| >gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >gnl|CDD|218366 pfam04990, RNA_pol_Rpb1_7, RNA polymerase Rpb1, domain 7 | Back alignment and domain information |
|---|
| >gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|218366 pfam04990, RNA_pol_Rpb1_7, RNA polymerase Rpb1, domain 7 | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
| >gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
| >gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4 | Back alignment and domain information |
|---|
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3 | Back alignment and domain information |
|---|
| >gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|218368 pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, domain 6 | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
| >gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|218368 pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, domain 6 | Back alignment and domain information |
|---|
| >gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
| >gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4 | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
| >gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3 | Back alignment and domain information |
|---|
| >gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
| >gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
| >gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1 | Back alignment and domain information |
|---|
| >gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|218368 pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, domain 6 | Back alignment and domain information |
|---|
| >gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
| >gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
| >gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus | Back alignment and domain information |
|---|
| >gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus | Back alignment and domain information |
|---|
| >gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1791 | |||
| KOG0260|consensus | 1605 | 100.0 | ||
| KOG0261|consensus | 1386 | 100.0 | ||
| PRK14977 | 1321 | bifunctional DNA-directed RNA polymerase A'/A'' su | 100.0 | |
| KOG0262|consensus | 1640 | 100.0 | ||
| KOG0260|consensus | 1605 | 100.0 | ||
| PRK08566 | 882 | DNA-directed RNA polymerase subunit A'; Validated | 100.0 | |
| TIGR02390 | 868 | RNA_pol_rpoA1 DNA-directed RNA polymerase subunit | 100.0 | |
| KOG0261|consensus | 1386 | 100.0 | ||
| TIGR02386 | 1140 | rpoC_TIGR DNA-directed RNA polymerase, beta' subun | 100.0 | |
| PRK00566 | 1156 | DNA-directed RNA polymerase subunit beta'; Provisi | 100.0 | |
| PRK14977 | 1321 | bifunctional DNA-directed RNA polymerase A'/A'' su | 100.0 | |
| PRK09603 | 2890 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| PRK14906 | 1460 | DNA-directed RNA polymerase subunit beta'/alpha do | 100.0 | |
| PRK14844 | 2836 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| cd02584 | 410 | RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti | 100.0 | |
| cd02584 | 410 | RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti | 100.0 | |
| TIGR02389 | 367 | RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit | 100.0 | |
| cd06528 | 363 | RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R | 100.0 | |
| KOG0262|consensus | 1640 | 100.0 | ||
| PRK02597 | 1331 | rpoC2 DNA-directed RNA polymerase subunit beta'; P | 100.0 | |
| PRK14897 | 509 | unknown domain/DNA-directed RNA polymerase subunit | 100.0 | |
| TIGR02388 | 1227 | rpoC2_cyan DNA-directed RNA polymerase, beta'' sub | 100.0 | |
| PRK04309 | 383 | DNA-directed RNA polymerase subunit A''; Validated | 100.0 | |
| COG0086 | 808 | RpoC DNA-directed RNA polymerase, beta' subunit/16 | 100.0 | |
| cd02737 | 381 | RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher | 100.0 | |
| cd02736 | 300 | RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot | 100.0 | |
| cd02735 | 309 | RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic | 100.0 | |
| TIGR02386 | 1140 | rpoC_TIGR DNA-directed RNA polymerase, beta' subun | 100.0 | |
| PRK00566 | 1156 | DNA-directed RNA polymerase subunit beta'; Provisi | 100.0 | |
| PRK14898 | 858 | DNA-directed RNA polymerase subunit A''; Provision | 100.0 | |
| PF04998 | 277 | RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int | 100.0 | |
| TIGR02389 | 367 | RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit | 100.0 | |
| PF04990 | 135 | RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; Int | 100.0 | |
| PRK14906 | 1460 | DNA-directed RNA polymerase subunit beta'/alpha do | 100.0 | |
| TIGR02390 | 868 | RNA_pol_rpoA1 DNA-directed RNA polymerase subunit | 100.0 | |
| cd02737 | 381 | RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher | 100.0 | |
| cd06528 | 363 | RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R | 100.0 | |
| PRK08566 | 882 | DNA-directed RNA polymerase subunit A'; Validated | 100.0 | |
| PRK14897 | 509 | unknown domain/DNA-directed RNA polymerase subunit | 100.0 | |
| PRK14844 | 2836 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| CHL00117 | 1364 | rpoC2 RNA polymerase beta'' subunit; Reviewed | 100.0 | |
| PRK04309 | 383 | DNA-directed RNA polymerase subunit A''; Validated | 100.0 | |
| PF04998 | 277 | RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int | 100.0 | |
| PRK02597 | 1331 | rpoC2 DNA-directed RNA polymerase subunit beta'; P | 100.0 | |
| cd02736 | 300 | RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot | 100.0 | |
| PRK09603 | 2890 | bifunctional DNA-directed RNA polymerase subunit b | 99.98 | |
| TIGR02388 | 1227 | rpoC2_cyan DNA-directed RNA polymerase, beta'' sub | 99.98 | |
| cd02735 | 309 | RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic | 99.97 | |
| CHL00117 | 1364 | rpoC2 RNA polymerase beta'' subunit; Reviewed | 99.97 | |
| PRK14898 | 858 | DNA-directed RNA polymerase subunit A''; Provision | 99.95 | |
| cd00630 | 158 | RNAP_largest_subunit_C Largest subunit of RNA poly | 99.92 | |
| cd00630 | 158 | RNAP_largest_subunit_C Largest subunit of RNA poly | 99.92 | |
| PF04983 | 158 | RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; Int | 99.9 | |
| PF05000 | 108 | RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; Int | 99.89 | |
| PF04992 | 187 | RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; Int | 99.89 | |
| COG0086 | 808 | RpoC DNA-directed RNA polymerase, beta' subunit/16 | 99.86 | |
| cd02655 | 204 | RNAP_beta'_C Largest subunit (beta') of Bacterial | 99.82 | |
| cd02655 | 204 | RNAP_beta'_C Largest subunit (beta') of Bacterial | 99.8 | |
| PF04990 | 135 | RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; Int | 99.78 | |
| PF05000 | 108 | RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; Int | 99.15 | |
| PF04992 | 187 | RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; Int | 98.69 | |
| PF04997 | 337 | RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; Int | 97.82 | |
| TIGR02387 | 619 | rpoC1_cyan DNA-directed RNA polymerase, gamma subu | 92.04 | |
| PRK02625 | 627 | rpoC1 DNA-directed RNA polymerase subunit gamma; P | 91.69 | |
| CHL00018 | 663 | rpoC1 RNA polymerase beta' subunit | 89.54 |
| >KOG0260|consensus | Back alignment and domain information |
|---|
Probab=100.00 E-value=2.2e-188 Score=1714.42 Aligned_cols=894 Identities=62% Similarity=0.965 Sum_probs=826.8
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCC-CCceeCCCCcccHhhhhhhc
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMP-QPCILKPKPLWTGKQVFSLI 110 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP-~PaIlKP~~LWTGKQIfS~i 110 (1791)
++++|++|||+||+|||+|+| +.+|++++++|||+||++.|++..| +|||+||+||||||||||++
T Consensus 495 EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~~p~~d~~~Pa~pai~Kp~PlWTGkQifsli 574 (1605)
T KOG0260|consen 495 ELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMYVPDWDGPPPAKPAILKPKPLWTGKQIFSLI 574 (1605)
T ss_pred HHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhhccccCCCCCCCcccCCCCcccchhhheeee
Confidence 689999999999999999999 2369999999999999999999999 99999999999999999999
Q ss_pred CCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHH
Q psy3015 111 IPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTV 190 (1791)
Q Consensus 111 LP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL 190 (1791)
+|+++|+.+.+++|++++. .|++|+|++|+|.+|+++.|++||+++|++.|+|+|++|.+.||+.|+.|++.+|+|
T Consensus 575 iP~~in~~r~~s~h~d~~~----~~~~p~dt~~lie~g~l~~g~l~Kkt~G~s~g~lvh~i~~e~Gp~~~~~f~~~iQ~l 650 (1605)
T KOG0260|consen 575 IPGGINYIRDHSTHPDSED----ELISPGDTRVLIEGGELLIGVLCKKTVGSSAGGLVHVIFLEKGPKIARGFFDSIQTL 650 (1605)
T ss_pred cCCCcceecccccCcCCCc----ccccCCCceEEEeCCceEEEEeeccccccccCceEEEeehhhCHHHHHHHHHHHHHH
Confidence 9999999999999998654 388999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHH
Q psy3015 191 VNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKA 270 (1791)
Q Consensus 191 ~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270 (1791)
+|.||+.+|||+||+|.+++.+++++|++.|.+|+
T Consensus 651 in~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak--------------------------------------------- 685 (1605)
T KOG0260|consen 651 INSWLLREGFSIGIGDTIADAATMCVIQNTIKEAK--------------------------------------------- 685 (1605)
T ss_pred HHHHHHhcCccccccccccCHHHHHHHHHHHHHHH---------------------------------------------
Confidence 99999999999999999999999999999999988
Q ss_pred HHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhcc
Q psy3015 271 KEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVG 350 (1791)
Q Consensus 271 ~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvG 350 (1791)
++|.+++++++++.|++.||+|+.++||++||.+||+|||++|.++++++.+.||+++|+.+|||||++||+|+++|||
T Consensus 686 -~dv~~vi~~a~~~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~sl~esNn~k~Mv~aGSKGs~inisQ~saCVG 764 (1605)
T KOG0260|consen 686 -RDVLAVIREAQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVVAGSKGSFINISQVSACVG 764 (1605)
T ss_pred -HHHHHHHHHHhhccccCCcchhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcccHHHHHhhcCCCcceehhhhhhhhc
Confidence 5677788889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhc
Q psy3015 351 QQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAME 430 (1791)
Q Consensus 351 QQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LE 430 (1791)
||+|||+||||||.+||||||.++||+|++||||+||||+||+|+|||||||||||||||||||||+||||||||||+||
T Consensus 765 qQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~kame 844 (1605)
T KOG0260|consen 765 QQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAME 844 (1605)
T ss_pred cccccccccccCCCcccccccccCCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCccccchhhhhhhhcCCccccc
Q psy3015 431 SVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRRVVNSKPLLIG 510 (1791)
Q Consensus 431 Dl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 (1791)
|++|+||||||||.|++|||.|||||+|++.+|.|+.+++..++..|+++|+++..+...+..
T Consensus 845 Dimv~yDgTVRNs~gqviQf~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~----------------- 907 (1605)
T KOG0260|consen 845 DIMVAYDGTVRNSLGQVIQFKYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLS----------------- 907 (1605)
T ss_pred HHHhhcCcceecccceeEEEEeccCccccceeeccccccccchHHHHHhhhhhhhhcCcccch-----------------
Confidence 999999999999999999999999999999999999888888777776666653222110000
Q ss_pred cccchhhHHHHHHHHHHhccccchhHHHHHHHHHHhhhhhhhhhhcCCCCCccccccccchhhHHHHhhhhhhcccCCCh
Q psy3015 511 CWKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 590 (1791)
Q Consensus 511 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mt~~~~~~~~~~~gi~~~~~~~~~~~~~~e~~~~i~~a~~~~~~~~~ 590 (1791)
T Consensus 908 -------------------------------------------------------------------------------- 907 (1605)
T KOG0260|consen 908 -------------------------------------------------------------------------------- 907 (1605)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhhHHHHHHHHHHHHHhhcccccccccccceeeeecCCCcccccccccccceeecChhhhhcccccCCchhhHhhhhccH
Q psy3015 591 RGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNE 670 (1791)
Q Consensus 591 ~~ri~~~~~k~ie~V~~~yd~~vr~~vg~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~~~~~l~~~~~~ 670 (1791)
.+
T Consensus 908 ------------------------------------------------------------------------------~~ 909 (1605)
T KOG0260|consen 908 ------------------------------------------------------------------------------SE 909 (1605)
T ss_pred ------------------------------------------------------------------------------hh
Confidence 00
Q ss_pred HHHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccCChHHHHHHHHHHHHHHHHHHHHHhhccCCCcceeecc
Q psy3015 671 DVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPC 750 (1791)
Q Consensus 671 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~~~~~e~~kL~~~~~~Lr~i~~~~~~~~~l~~ 750 (1791)
+.+++ +..+..+++.++.||++|+.|+..++.++..++.++.+|+
T Consensus 910 ~~~~e-----------------------------------~~~~~~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~ 954 (1605)
T KOG0260|consen 910 EVVNE-----------------------------------ISELLKLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPE 954 (1605)
T ss_pred hHhhh-----------------------------------hhhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCcccccch
Confidence 11111 1222345567788999999999999999999999999999
Q ss_pred hhHHHHHHHhhhhccCCcccccccceEEEeccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccC
Q psy3015 751 NLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQ 830 (1791)
Q Consensus 751 N~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~ 830 (1791)
|++|+|||+++ +|.+..|..+.- +
T Consensus 955 n~~r~I~Na~~---------------~f~~~~r~~t~l-------------------------~---------------- 978 (1605)
T KOG0260|consen 955 NLQRIIWNALK---------------KFSIDERKPTDL-------------------------I---------------- 978 (1605)
T ss_pred hHHHHHHHHHh---------------hccccccccccc-------------------------c----------------
Confidence 99999999998 777877765540 0
Q ss_pred CCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccccCCccccccccccCCCCccccC
Q psy3015 831 DTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFG 910 (1791)
Q Consensus 831 ~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k~~~~~~~~~~~~~~~~~~~~~ 910 (1791)
-.+-+.||++ +. +++
T Consensus 979 ------------------------~~~v~~g~~~----------------l~---e~l---------------------- 993 (1605)
T KOG0260|consen 979 ------------------------PFKVVKGVKE----------------LA---EKL---------------------- 993 (1605)
T ss_pred ------------------------hhhhhhhhhh----------------hh---hee----------------------
Confidence 0233445555 32 555
Q ss_pred CCCCCCCCCCCCCccccCccccccccCCCCcCCCCCCCCcccccCCcchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccC
Q psy3015 911 SAATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRL 990 (1791)
Q Consensus 911 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rl 990 (1791)
+++.|+|.+|+ ||+ ||+|++|++|++|+|+++|||
T Consensus 994 ----------------------------------------~iv~g~~~~sr-aqr----l~~~lLrs~l~~krv~~e~rl 1028 (1605)
T KOG0260|consen 994 ----------------------------------------VIVRGEDYISR-AQR----LFNILLRSTLATKRVLEEYRL 1028 (1605)
T ss_pred ----------------------------------------EEeeCchhHHH-HHH----HHHHHHHhhHHHHHHHHHhcc
Confidence 68899999999 777 999999999999999999999
Q ss_pred CHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCc
Q psy3015 991 SSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRG 1048 (1791)
Q Consensus 991 n~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrG 1048 (1791)
|++||+|++|+|+.+|++++++| |||+ || |+.|||++|+|| |+++
T Consensus 1029 s~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvpr--lkei----------- 1095 (1605)
T KOG0260|consen 1029 SSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPR--LKEI----------- 1095 (1605)
T ss_pred cHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcc--hhhh-----------
Confidence 99999999999999999999999 9998 77 999999999999 9999
Q ss_pred ceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceeeeec
Q psy3015 1049 FVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYY 1122 (1791)
Q Consensus 1049 FV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Y 1122 (1791)
+|..++.+||+..+|+ ...+.|+.|.+ .||+ +|.++.....|+|||++.+|++++|.+||+.+|
T Consensus 1096 --~Nv~k~~ktpsLtV~l--------~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~ 1165 (1605)
T KOG0260|consen 1096 --INVAKNAKTPSLTVYL--------TGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYY 1165 (1605)
T ss_pred --hhhhccCCCceEEEEe--------cchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhh
Confidence 8999999999999999 56678888888 6776 789999999999999999999999999999999
Q ss_pred cCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHHHH
Q psy3015 1123 EMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVD 1202 (1791)
Q Consensus 1123 g~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~ 1202 (1791)
+.++.|..+++||++|+++|+.+|.+++++|++|.++|+..|+.|++++++++|++++++|+|+.+.+
T Consensus 1166 e~pd~D~~~ispwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~------------ 1233 (1605)
T KOG0260|consen 1166 EMPDEDVGRISPWLLRLELDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEE------------ 1233 (1605)
T ss_pred cCcccchhhcChHHHHhhhhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCcc------------
Confidence 99999999999999999999999999999999999999999999999999999999999999987653
Q ss_pred hhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcccc
Q psy3015 1203 KMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRT 1282 (1791)
Q Consensus 1203 ~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt 1282 (1791)
+++.|+++++.+++.+++++|++.|.||+|. ....|.|+...||+|+|||++|..+++.+++||.||
T Consensus 1234 --e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~-----------~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt 1300 (1605)
T KOG0260|consen 1234 --EDDVFLKCIEANMLGDMTLRGIPDIFKVYMS-----------PTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPART 1300 (1605)
T ss_pred --chhHHHHHHHHhhhhhcccCCccccceEEEe-----------ecCCCceeecceeEEecCchhHHhhhccCCCCcccc
Confidence 4678999999999999999999999999997 345788998899999999999999999999999999
Q ss_pred cchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhhhHH
Q psy3015 1283 FSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1362 (1791)
Q Consensus 1283 ~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeTv~ 1362 (1791)
+|||++||+++|||||+|.++++|+..|+.|+|.||||||++|+||+||++|++++|+|||++++..++|+|||||+|++
T Consensus 1301 ~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg~nr~~tgaLmrcSfEetv~ 1380 (1605)
T KOG0260|consen 1301 TSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMAITRHGINRQDTGALMRCSFEETVD 1380 (1605)
T ss_pred cccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceeeeeccccchhhccccccccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccccccccccc
Q psy3015 1363 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIP 1412 (1791)
Q Consensus 1363 iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~~~~~~~~ 1412 (1791)
+|++||++++.|.++||+||||+||+++.|||+||++++.++++..+...
T Consensus 1381 il~~aa~~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld~e~l~~~~~~~ 1430 (1605)
T KOG0260|consen 1381 ILMDAAAHAEKDPCRGVSENIMLGQLAPMGTGCFDLMLDAEKLKKGIEIP 1430 (1605)
T ss_pred HHHHHHhhhccCCCccceeeeeecccccCCCcceeeeccHHhhhccCccC
Confidence 99999999999999999999999999999999999999999998877553
|
|
| >KOG0261|consensus | Back alignment and domain information |
|---|
| >PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >KOG0262|consensus | Back alignment and domain information |
|---|
| >KOG0260|consensus | Back alignment and domain information |
|---|
| >PRK08566 DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >KOG0261|consensus | Back alignment and domain information |
|---|
| >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
| >PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional | Back alignment and domain information |
|---|
| >PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
| >cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
| >TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
| >cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
| >KOG0262|consensus | Back alignment and domain information |
|---|
| >PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
| >TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
| >PRK04309 DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
| >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain | Back alignment and domain information |
|---|
| >cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
| >cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
| >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
| >PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >PRK14898 DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
| >PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
| >PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional | Back alignment and domain information |
|---|
| >TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain | Back alignment and domain information |
|---|
| >cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
| >PRK08566 DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
| >PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
| >PRK04309 DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
| >PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
| >PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
| >cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
| >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
| >PRK14898 DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
| >cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit | Back alignment and domain information |
|---|
| >PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional | Back alignment and domain information |
|---|
| >CHL00018 rpoC1 RNA polymerase beta' subunit | Back alignment and domain information |
|---|
Homologous Structure Templates
Structure Templates Detected by BLAST
Original result of BLAST against Protein Data Bank
| ID | Alignment Graph | Length |
Definition |
E-value | |
| Query | 1791 | ||||
| 3h0g_A | 1752 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 1e-112 | ||
| 3h0g_A | 1752 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 3e-99 | ||
| 3h0g_A | 1752 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 2e-19 | ||
| 3j0k_A | 1455 | Orientation Of Rna Polymerase Ii Within The Human V | 1e-105 | ||
| 3j0k_A | 1455 | Orientation Of Rna Polymerase Ii Within The Human V | 1e-85 | ||
| 3j0k_A | 1455 | Orientation Of Rna Polymerase Ii Within The Human V | 2e-18 | ||
| 1i3q_A | 1733 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 1e-105 | ||
| 1i3q_A | 1733 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 1e-85 | ||
| 1i3q_A | 1733 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 2e-18 | ||
| 4a3c_A | 1732 | Rna Polymerase Ii Initial Transcribing Complex With | 1e-105 | ||
| 4a3c_A | 1732 | Rna Polymerase Ii Initial Transcribing Complex With | 1e-85 | ||
| 4a3c_A | 1732 | Rna Polymerase Ii Initial Transcribing Complex With | 3e-18 | ||
| 2waq_A | 880 | The Complete Structure Of The Archaeal 13-Subunit D | 4e-52 | ||
| 2waq_A | 880 | The Complete Structure Of The Archaeal 13-Subunit D | 1e-19 | ||
| 2pmz_A | 880 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 5e-52 | ||
| 2pmz_A | 880 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 9e-20 | ||
| 2waq_C | 395 | The Complete Structure Of The Archaeal 13-Subunit D | 1e-26 | ||
| 2y0s_C | 395 | Crystal Structure Of Sulfolobus Shibatae Rna Polyme | 2e-26 | ||
| 2pmz_C | 392 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 4e-26 | ||
| 3hkz_C | 395 | The X-Ray Crystal Structure Of Rna Polymerase From | 4e-26 | ||
| 2gho_D | 1233 | Recombinant Thermus Aquaticus Rna Polymerase For St | 1e-08 | ||
| 1l9u_D | 1524 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 1e-08 | ||
| 1i6v_D | 1264 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 5e-08 | ||
| 4gzy_D | 1534 | Crystal Structures Of Bacterial Rna Polymerase Paus | 3e-07 | ||
| 1iw7_D | 1524 | Crystal Structure Of The Rna Polymerase Holoenzyme | 3e-07 | ||
| 1hqm_D | 1265 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 4e-06 | ||
| 3iyd_D | 1413 | Three-Dimensional Em Structure Of An Intact Activat | 9e-05 | ||
| 3iyd_D | 1413 | Three-Dimensional Em Structure Of An Intact Activat | 6e-04 | ||
| 3lu0_D | 1407 | Molecular Model Of Escherichia Coli Core Rna Polyme | 9e-05 | ||
| 3lu0_D | 1407 | Molecular Model Of Escherichia Coli Core Rna Polyme | 6e-04 |
| >pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 | Back alignment and structure |
|
| >pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 | Back alignment and structure |
| >pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 | Back alignment and structure |
| >pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 | Back alignment and structure |
| >pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 | Back alignment and structure |
| >pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 | Back alignment and structure |
| >pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 | Back alignment and structure |
| >pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 | Back alignment and structure |
| >pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 | Back alignment and structure |
| >pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 | Back alignment and structure |
| >pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 | Back alignment and structure |
| >pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 | Back alignment and structure |
| >pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 | Back alignment and structure |
| >pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 | Back alignment and structure |
| >pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 | Back alignment and structure |
| >pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 | Back alignment and structure |
| >pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 395 | Back alignment and structure |
| >pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P21 Space Group Length = 395 | Back alignment and structure |
| >pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 392 | Back alignment and structure |
| >pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea Length = 395 | Back alignment and structure |
| >pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233 | Back alignment and structure |
| >pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524 | Back alignment and structure |
| >pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264 | Back alignment and structure |
| >pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused Elongation Complexes Length = 1534 | Back alignment and structure |
| >pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524 | Back alignment and structure |
| >pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1265 | Back alignment and structure |
| >pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413 | Back alignment and structure |
| >pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413 | Back alignment and structure |
| >pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407 | Back alignment and structure |
| >pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 | Back alignment and structure |
|---|
Score = 523 bits (1349), Expect = e-164
Identities = 133/399 (33%), Positives = 197/399 (49%), Gaps = 54/399 (13%)
Query: 71 NQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTR--THSTHPDDE 128
+E+ IL + + +P IL P+ +TGKQV S +P + N S+ P
Sbjct: 517 TKEEAQQILG-VADVKIDLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLC 575
Query: 129 DSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSS-GSLLHICFLELGHEVCGRFYGNI 187
+ P D+ VV+++G LL G+ KK++G S+LH E E N+
Sbjct: 576 KN----EDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNL 631
Query: 188 QTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHS 247
V ++ L+G ++ + D EI I +AK +V +IQK N +LEP PG
Sbjct: 632 FRVFIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPG-- 689
Query: 248 IGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILN 307
TL ++ EN + L+
Sbjct: 690 --------------------------------------------RTLEESLENYILDTLD 705
Query: 308 DARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRT 367
R G A K L +N M G++GS +NI+Q+ A +GQQ+V G+RI G+ RT
Sbjct: 706 KLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRT 765
Query: 368 LPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK 427
LPHF D PE+RGF+ +S+ GL P+E FFHA GGREGL+DTAV+T+++GY+QRRLI
Sbjct: 766 LPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLIN 825
Query: 428 AMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQR 466
A+ + YD TVR+ G++IQ+ YG+DG+ H +
Sbjct: 826 ALSDLRAEYDGTVRSLYGEVIQVAYGDDGVFPMYSAHGK 864
|
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 | Back alignment and structure |
|---|
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 | Back alignment and structure |
|---|
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 | Back alignment and structure |
|---|
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395 | Back alignment and structure |
|---|
| >4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395 | Back alignment and structure |
|---|
| >4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395 | Back alignment and structure |
|---|
| >4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} Length = 436 | Back alignment and structure |
|---|
| >1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265 | Back alignment and structure |
|---|
| >1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265 | Back alignment and structure |
|---|
| >1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265 | Back alignment and structure |
|---|
| >2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 | Back alignment and structure |
|---|
| >2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 | Back alignment and structure |
|---|
| >2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 | Back alignment and structure |
|---|
| >3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407 | Back alignment and structure |
|---|
| >3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407 | Back alignment and structure |
|---|
| >3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1791 | |||
| 3h0g_A | 1752 | DNA-directed RNA polymerase II subunit RPB1; trans | 100.0 | |
| 1twf_A | 1733 | B220, DNA-directed RNA polymerase II largest subun | 100.0 | |
| 3h0g_A | 1752 | DNA-directed RNA polymerase II subunit RPB1; trans | 100.0 | |
| 1twf_A | 1733 | B220, DNA-directed RNA polymerase II largest subun | 100.0 | |
| 4ayb_A | 880 | DNA-directed RNA polymerase; transferase, multi-su | 100.0 | |
| 1hqm_D | 1265 | DNA-directed RNA polymerase; transferase, transcri | 100.0 | |
| 2a6h_D | 1524 | DNA-directed RNA polymerase beta' chain; RNA polym | 100.0 | |
| 3lu0_D | 1407 | DNA-directed RNA polymerase subunit beta'; E. coli | 100.0 | |
| 2a6h_D | 1524 | DNA-directed RNA polymerase beta' chain; RNA polym | 100.0 | |
| 4ayb_C | 395 | DNA-directed RNA polymerase; transferase, multi-su | 100.0 | |
| 1hqm_D | 1265 | DNA-directed RNA polymerase; transferase, transcri | 100.0 | |
| 3lu0_D | 1407 | DNA-directed RNA polymerase subunit beta'; E. coli | 100.0 | |
| 4ayb_A | 880 | DNA-directed RNA polymerase; transferase, multi-su | 100.0 | |
| 4ayb_C | 395 | DNA-directed RNA polymerase; transferase, multi-su | 99.95 | |
| 3qqc_A | 436 | DNA-directed RNA polymerase subunit B, DNA-direct | 98.91 | |
| 3qqc_A | 436 | DNA-directed RNA polymerase subunit B, DNA-direct | 88.08 |
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
Probab=100.00 E-value=1.6e-167 Score=1687.99 Aligned_cols=903 Identities=50% Similarity=0.824 Sum_probs=795.6
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
.||++++|+++|++++|+|++ .+.|+++++++||+||+..|++.+|+|||+||++|||||||||++|
T Consensus 509 ~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~~~~~~~~~pai~kp~~~wtGkqifs~il 588 (1752)
T 3h0g_A 509 EITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDWDGILPPPVILKPKVLWTGKQILSLII 588 (1752)
T ss_dssp HTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSSSCCSSCCCCSBCSSSCEEETTHHHHTTS
T ss_pred HHhcCccceecCCCCCceeeecchhhhheeeeccccccCCHHHHHHHHHhhcccCCccCccceecCcCCCchhhHHhhhC
Confidence 689999999999999999998 3469999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHH
Q psy3015 112 PGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVV 191 (1791)
Q Consensus 112 P~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~ 191 (1791)
|+++||..... ...+.+++|++|+|+||||++|++||++||++.+||||.||++||+++|+.|||++|+|+
T Consensus 589 p~~~~~~~~~~---------~~~~~~~~d~~v~i~~gell~g~l~K~~lg~~~~~li~~i~~~~G~~~~~~~ld~~~~l~ 659 (1752)
T 3h0g_A 589 PKGINLIRDDD---------KQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQRVV 659 (1752)
T ss_dssp CSSBCEECCCS---------SCCSSCTTTCSEEECBSCEEEECCSHHHHSSCTTCHHHHSSSSSCTTTHHHHHHHHHHHH
T ss_pred cCCCCceeccc---------cccCcCCCcCeEEEEcCeEEecccchHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHH
Confidence 99999965321 112567889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHH
Q psy3015 192 NNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAK 271 (1791)
Q Consensus 192 ~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (1791)
++||+++||||||+|+++++++.+++.++|++|+
T Consensus 660 ~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~---------------------------------------------- 693 (1752)
T 3h0g_A 660 NYWLLHNGFSIGIGDTIADADTMKEVTRTVKEAR---------------------------------------------- 693 (1752)
T ss_dssp HHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTT----------------------------------------------
T ss_pred HHHHHhcCceechhhcccCHHHHHHHHHHHHHHH----------------------------------------------
Confidence 9999999999999999999999888888888776
Q ss_pred HHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccC
Q psy3015 272 EDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 351 (1791)
Q Consensus 272 ~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQ 351 (1791)
++|.+++++++.|.|+..||++++++||++|+++||++|+++++.+++++++.|++++|+.||||||.+||+||+|||||
T Consensus 694 ~~v~~~~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gq 773 (1752)
T 3h0g_A 694 RQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQ 773 (1752)
T ss_dssp HHHHHHHTTTTTTCCCCCSSCCTTHHHHHHHHHHHHHHHHHHHHHHHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCC
T ss_pred HHHHHHHHHHHcCCCccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhhccccCHHHHHHHHhccCC
Confidence 46667788888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcc
Q psy3015 352 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMES 431 (1791)
Q Consensus 352 Q~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LED 431 (1791)
|+++|+|||+||++||||||.++|++|+++|||+|||++||+|+|||||||||||||||||||||+||||||||||+|||
T Consensus 774 q~~~GkrIp~g~~~rtLP~f~k~d~~~~a~GfV~~sF~~GL~p~EfFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leD 853 (1752)
T 3h0g_A 774 QIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMED 853 (1752)
T ss_dssp CCSTTSSSCCCSTTSSSTTSCSSCCSTTTSSCCSSCTTTCCCHHHHHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTT
T ss_pred CccCCccCCCCCCCccCCCCCCCCCCcccCcchhhcccCCCCHHHHHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCccccchhhhhhhhcCCcccccc
Q psy3015 432 VMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRRVVNSKPLLIGC 511 (1791)
Q Consensus 432 l~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 (1791)
|+|+|||||||++|+||||+|||||+||+.+|.|+++++.+++..|+++|+++..+.. .+.
T Consensus 854 v~V~YDgTVRns~g~ivQF~YGeDGlD~~~~e~q~~~~~~~s~~~f~~~~~~~~~~~~-~~~------------------ 914 (1752)
T 3h0g_A 854 VMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDR-SLS------------------ 914 (1752)
T ss_dssp CEEETTTEEECTTSCEEESSSSSSCBCGGGEEEEECTTTSCCHHHHTTTSCCCTTTTC-CGG------------------
T ss_pred eEEeeCCeeEcCCCcEEEEecCCCCcChHHhhccccccccCCHHHHHHHhcccccccc-ccc------------------
Confidence 9999999999999999999999999999999999999999999999888887543321 000
Q ss_pred ccchhhHHHHHHHHHHhccccchhHHHHHHHHHHhhhhhhhhhhcCCCCCccccccccchhhHHHHhhhhhhcccCCChh
Q psy3015 512 WKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR 591 (1791)
Q Consensus 512 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mt~~~~~~~~~~~gi~~~~~~~~~~~~~~e~~~~i~~a~~~~~~~~~~ 591 (1791)
.+
T Consensus 915 ------------------------------------------------------------~~------------------ 916 (1752)
T 3h0g_A 915 ------------------------------------------------------------LY------------------ 916 (1752)
T ss_dssp ------------------------------------------------------------GT------------------
T ss_pred ------------------------------------------------------------HH------------------
Confidence 00
Q ss_pred hhHHHHHHHHHHHHHhhcccccccccccceeeeecCCCcccccccccccceeecChhhhhcccccCCchhhHhhhhccHH
Q psy3015 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNED 671 (1791)
Q Consensus 592 ~ri~~~~~k~ie~V~~~yd~~vr~~vg~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 671 (1791)
+ +
T Consensus 917 ----------------------------~--------------~------------------------------------ 918 (1752)
T 3h0g_A 917 ----------------------------M--------------E------------------------------------ 918 (1752)
T ss_dssp ----------------------------S--------------C------------------------------------
T ss_pred ----------------------------H--------------H------------------------------------
Confidence 0 0
Q ss_pred HHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccCChHHHHHHHHHHHHHHHHHHHHHh-hccCCCcceeecc
Q psy3015 672 VLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALRE-IFSSGESNVVLPC 750 (1791)
Q Consensus 672 ~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~~~~~e~~kL~~~~~~Lr~-i~~~~~~~~~l~~ 750 (1791)
..+..+.+++..+++||++|.+++..||+ ++..++.++.+|+
T Consensus 919 -------------------------------------~~l~~~~~~~~~l~~E~~~l~~dr~~lr~~i~~~~~~~~~lP~ 961 (1752)
T 3h0g_A 919 -------------------------------------NSIENDSSVQDLLDEEYTQLVADRELLCKFIFPKGDARWPLPV 961 (1752)
T ss_dssp -------------------------------------SCCTTSCSSTHHHHHHHHHHHHHHTTSSSSSSSCSCCEEEEES
T ss_pred -------------------------------------HHhccCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccCCc
Confidence 00001112234566788999999998987 6777778889999
Q ss_pred hhHHHHHHHhhhhccCCcccccccceEEEeccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccC
Q psy3015 751 NLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQ 830 (1791)
Q Consensus 751 N~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~ 830 (1791)
|+.|+||++++ +|.+..|..
T Consensus 962 N~~R~i~~~~~---------------~f~~~~~~~--------------------------------------------- 981 (1752)
T 3h0g_A 962 NVQRIIQNALQ---------------IFHLEAKKP--------------------------------------------- 981 (1752)
T ss_dssp CHHHHTTTTTT---------------TSCCCTTSC---------------------------------------------
T ss_pred cHHHHHHHHHH---------------hcCCCcCcc---------------------------------------------
Confidence 99999998766 333322211
Q ss_pred CCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccccCCccccccccccCCCCccccC
Q psy3015 831 DTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFG 910 (1791)
Q Consensus 831 ~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k~~~~~~~~~~~~~~~~~~~~~ 910 (1791)
|.|.-..+ +.+|+| ++ +++
T Consensus 982 --s~l~p~~~------------------~~~v~~----------------~~---~~l---------------------- 1000 (1752)
T 3h0g_A 982 --TDLLPSDI------------------INGLNE----------------LI---AKL---------------------- 1000 (1752)
T ss_dssp --CCCCHHHH------------------HHHHHH----------------HH---TTC----------------------
T ss_pred --CCCCHHHH------------------HHHHHH----------------HH---Hhh----------------------
Confidence 11111111 113333 33 444
Q ss_pred CCCCCCCCCCCCCccccCccccccccCCCCcCCCCCCCCcccccCCcchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccC
Q psy3015 911 SAATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRL 990 (1791)
Q Consensus 911 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rl 990 (1791)
++++|.|.|+++|++||++||++++|+.|++|+++++++|
T Consensus 1001 ----------------------------------------~~~~g~d~l~~~~~~na~~l~~~~lr~~l~~k~~~~~~~l 1040 (1752)
T 3h0g_A 1001 ----------------------------------------TIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRL 1040 (1752)
T ss_dssp ----------------------------------------CCSCCCSTTTTHHHHTSSHHHHHHHTTSSSHHHHHHSSCC
T ss_pred ----------------------------------------hcccCCcchhhhhhhchHHHHHHHHHhhhhhhhhhhhcCc
Confidence 4667899999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCc
Q psy3015 991 SSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRG 1048 (1791)
Q Consensus 991 n~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrG 1048 (1791)
|+++|+|+++++..+|..+++.| |||+ || |++++||+|+|| |+|+
T Consensus 1041 ~~~~~~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPR--LkEI----------- 1107 (1752)
T 3h0g_A 1041 NKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPR--LKEI----------- 1107 (1752)
T ss_dssp CHHHHHHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGG--HHHH-----------
T ss_pred CHHHHHHHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhHHhhhhccccccccccCccc--HHHH-----------
Confidence 99999999999999999999999 8887 88 789999999999 9999
Q ss_pred ceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceeeeec
Q psy3015 1049 FVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYY 1122 (1791)
Q Consensus 1049 FV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Y 1122 (1791)
+|..++.+||++++|+ .+...++.|.+ .+++ +|.++++.++|.|||++.+|++.+|.++|+.||
T Consensus 1108 --Inask~ikTP~mtv~L--------~~~~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d~~~v~~~~ 1177 (1752)
T 3h0g_A 1108 --LNVAKNIKTPSLTIYL--------MPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFF 1177 (1752)
T ss_dssp --HTTCSCCSCCCCEECC--------CSSSCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSSCSHHHHHH
T ss_pred --HhhhcCCCCCeEEEEe--------cCccccCHHHHHHHHHhhccEEHHHheeEEEEEEecCccceEEeecHHHHHHHh
Confidence 8999999999999999 45555566766 4554 677899999999999999999999999999999
Q ss_pred cCCCCC----CCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchh
Q psy3015 1123 EMPDFD----PTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEE 1198 (1791)
Q Consensus 1123 g~dg~D----~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~e 1198 (1791)
..++.| ....++|+++++||+.+|.++++++++|.++|.+.++.++.+++++++++++++++|+..+.+.... ++
T Consensus 1178 ~~~~~~~~~~~~~~~~~~~rl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~-~~ 1256 (1752)
T 3h0g_A 1178 AIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAE-DD 1256 (1752)
T ss_dssp HTTCSSTTCSSCSCCCCEEEEECCTTSSTTTTCCHHHHTTSGGGSSTTSCCEECCCTTCSSCEEEECCCCCSCCCCC-SS
T ss_pred ccchhhhhcccccccceeEEEEecHHHHHHcCCCHHHHHHHHHhhccCCeeEeecCCCccceeEEEEeccccccccc-cc
Confidence 876655 4567899999999999999999999999999999998899998988888888888887543211100 00
Q ss_pred HHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCC
Q psy3015 1199 DAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVD 1278 (1791)
Q Consensus 1199 e~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVD 1278 (1791)
+ ...+++.+|+.++..+|.+++|+||++|++++++ +.++.++..++.|....+|+|.|||+||.++|..++||
T Consensus 1257 ~--~~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv~i~-----~~~~~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD 1329 (1752)
T 3h0g_A 1257 D--NMIEEDVFLKTIEGHMLESISLRGVPNITRVYMM-----EHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVD 1329 (1752)
T ss_dssp C--CCSCSCHHHHHHHHHHTTCCCSSCCTTCCCCCEE-----EEEEEEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCC
T ss_pred c--ccccHHHHHHHHHHhhccceEEecCCCccEEEEe-----cccceeecCCCcccccceEEEEecccCHHHHhCcCCCc
Confidence 0 1123456788888778999999999999999987 33455567777787778999999999999999999999
Q ss_pred cccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchh
Q psy3015 1279 PVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFE 1358 (1791)
Q Consensus 1279 p~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFE 1358 (1791)
++||+||||+||+++|||||||++|++|++.|+.++|++||+|||+||||+||++|++++||||||++++.|+|+|||||
T Consensus 1330 ~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~s~l~~aSFE 1409 (1752)
T 3h0g_A 1330 ATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFE 1409 (1752)
T ss_dssp TTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCSCCCSHHHHHHHHS
T ss_pred cccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccCCeEEeechhhhccCCCCHHHHhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccccc
Q psy3015 1359 ETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK 1406 (1791)
Q Consensus 1359 eTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~~ 1406 (1791)
+|+++|++||++|+.|+|+||+|||||||++++|||+||+++++.+++
T Consensus 1410 ~T~~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GTG~fdll~~~~~l~ 1457 (1752)
T 3h0g_A 1410 ETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDMLM 1457 (1752)
T ss_dssp CCTHHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBTTSCEECCCHHHHH
T ss_pred HHHHHHHHHHHhcCcccccChhHHhhcCCCcCCccceEEEEeCHHHhc
Confidence 999999999999999999999999999999999999999999999887
|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... | Back alignment and structure |
|---|
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A | Back alignment and structure |
|---|
| >1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D | Back alignment and structure |
|---|
| >2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D | Back alignment and structure |
|---|
| >3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* | Back alignment and structure |
|---|
| >2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D | Back alignment and structure |
|---|
| >4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C | Back alignment and structure |
|---|
| >1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D | Back alignment and structure |
|---|
| >3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* | Back alignment and structure |
|---|
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A | Back alignment and structure |
|---|
| >4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C | Back alignment and structure |
|---|
| >3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} | Back alignment and structure |
|---|
| >3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} | Back alignment and structure |
|---|
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
E-value |
| 1791 | ||||
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 1e-111 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 4e-77 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 7e-45 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 1e-27 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 2e-24 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 1e-19 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 8e-19 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 6e-10 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 3e-05 | |
| d1smyd_ | 1504 | e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t | 5e-45 | |
| d1smyd_ | 1504 | e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t | 7e-32 | |
| d1smyd_ | 1504 | e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t | 7e-30 | |
| d1smyd_ | 1504 | e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t | 7e-19 | |
| d1smyd_ | 1504 | e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t | 1e-10 | |
| d1smyd_ | 1504 | e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t | 4e-07 |
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
class: Multi-domain proteins (alpha and beta) fold: beta and beta-prime subunits of DNA dependent RNA-polymerase superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase family: RNA-polymerase beta-prime domain: RBP1 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Score = 385 bits (990), Expect = e-111
Identities = 172/461 (37%), Positives = 262/461 (56%), Gaps = 20/461 (4%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQV- 1011
+ G++++ + A +A LF CL+RS L T+ V + YRL+ +AF+W++ IE +F ++ V
Sbjct: 999 LRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVH 1058
Query: 1012 ----IACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067
+ + Q++ E +A +
Sbjct: 1059 PGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVY 1118
Query: 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDF 1127
+ K + L VT + IYYDPDP++TVIPED+E + +++ + D
Sbjct: 1119 LEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDE 1178
Query: 1128 DPTR----ISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLR 1183
+ + SPWLLR+ELDR M DK LTM + E+I F +DL I+++DN EKL++R
Sbjct: 1179 EAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIR 1238
Query: 1184 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKK 1243
R++ DA + E+D L+ IE ML ++TL+G+E I +V M
Sbjct: 1239 CRVVR------PKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM-----KYD 1287
Query: 1244 RIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSV 1303
R + + +GE+ +W+LETDG +L +V++ +DP R ++N +I +VLGIEA R ++
Sbjct: 1288 RKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAAL 1347
Query: 1304 EKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDV 1363
KE+ V+ G YVNYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++
Sbjct: 1348 YKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEI 1407
Query: 1364 LMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEK 1404
L +A A AE D RGVSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1408 LFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEES 1448
|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 | Back information, alignment and structure |
|---|
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1791 | |||
| d1twfa_ | 1449 | RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta | 100.0 | |
| d1smyd_ | 1504 | RNA-polymerase beta-prime {Thermus thermophilus [T | 100.0 | |
| d1twfa_ | 1449 | RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta | 100.0 | |
| d1smyd_ | 1504 | RNA-polymerase beta-prime {Thermus thermophilus [T | 100.0 |
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} | Back information, alignment and structure |
|---|
class: Multi-domain proteins (alpha and beta) fold: beta and beta-prime subunits of DNA dependent RNA-polymerase superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase family: RNA-polymerase beta-prime domain: RBP1 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Probab=100.00 E-value=1.6e-129 Score=1336.12 Aligned_cols=903 Identities=46% Similarity=0.761 Sum_probs=756.0
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
.+|++++|+++|++++|++++ .+.|+++++++|++||+..+++.+|+|||+||+++||||||||++|
T Consensus 502 ~Lm~~~~nilsp~~G~pi~~~~QD~~lg~y~LT~~~~f~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~tgkqi~s~~l 581 (1449)
T d1twfa_ 502 QLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAI 581 (1449)
T ss_dssp HHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCCSCCCCCSBCSSSCEEEHHHHHHHHS
T ss_pred HHhhhhcccccccCCceeeeeccchhhhhhhhhcccccCCHHHHHHHHHhcccccccccCCeEEeeeeccccceEEEEEc
Confidence 489999999999999999998 3458999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHH
Q psy3015 112 PGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVV 191 (1791)
Q Consensus 112 P~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~ 191 (1791)
|.++++.+... ...+.++.|+.|+|+||+|++|++||+++|++.+||+|.+|++||+++|..||+.+|+|+
T Consensus 582 ~~~~~~~~~~~---------~~~~~~~~~~~~~i~~g~l~~g~l~k~~~g~~~~~li~~i~~~~G~~~~~~~l~~~~~l~ 652 (1449)
T d1twfa_ 582 PNGIHLQRFDE---------GTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVV 652 (1449)
T ss_dssp CTTCCEEECCT---------TCCTTCTTCCSEEEETTEEEESCCCHHHHSSCTTSHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred cCCceeeeccC---------CccccccCCceEEEECCeeeeccchhhhcccccccccccccccccHHHHHHHHHHHHHHH
Confidence 99888754321 124556788999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHH
Q psy3015 192 NNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAK 271 (1791)
Q Consensus 192 ~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (1791)
++||+++|||||++|+++++.+.+++.+.+.+++
T Consensus 653 ~~~l~~~Gfs~gi~D~~~~~~~~~~~~~~~~~~~---------------------------------------------- 686 (1449)
T d1twfa_ 653 NFWLLHNGFSTGIGDTIADGPTMREITETIAEAK---------------------------------------------- 686 (1449)
T ss_dssp HHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHH----------------------------------------------
T ss_pred HHHHHhcchheeeccccccchhhHHHHHHHHHHh----------------------------------------------
Confidence 9999999999999999999998888888777766
Q ss_pred HHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccC
Q psy3015 272 EDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 351 (1791)
Q Consensus 272 ~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQ 351 (1791)
+++.++.++++.+.+...++.++++++|++++++|+++++.+++.+.+.+.++|++++|+.||||||.+|++||+||+||
T Consensus 687 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~v~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGakGs~~n~~Qi~g~~Gq 766 (1449)
T d1twfa_ 687 KKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQ 766 (1449)
T ss_dssp HHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEE
T ss_pred hhHHHHHHHHHHhhhccccCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccchHhheeccccCCccchHHHHhhhhh
Confidence 34455666777888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcc
Q psy3015 352 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMES 431 (1791)
Q Consensus 352 Q~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LED 431 (1791)
|+++|+|||.++.+|+||||.++|.+|+++|||.|||++||+|+|||||||||||||||||||||+||||||||||+|||
T Consensus 767 q~~~g~ri~~~~~~r~lp~f~~~~~~~~~~GfI~~sf~~GL~p~Eyf~h~~~gReGLiDTAvkTa~sGYl~RrLvk~led 846 (1449)
T d1twfa_ 767 QSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALED 846 (1449)
T ss_dssp CCBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred hcccCccccccccccccccCCCCCCCccccCcccchhhhhhcchheeeeeccchhhhhhhcccccccHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCccccchhhhhhhhcCCcccccc
Q psy3015 432 VMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRRVVNSKPLLIGC 511 (1791)
Q Consensus 432 l~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 (1791)
|+|+||+||||++|+||||.|||||+||+.+|.+.++.+..++..+..++.++..+......
T Consensus 847 v~v~yD~tvr~~~g~IiQf~YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------ 908 (1449)
T d1twfa_ 847 IMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLD------------------ 908 (1449)
T ss_dssp CEECTTSCEECTTCCEEESSGGGTTBCGGGEEEEECGGGSSCHHHHHHHHCCCTTCTTTSCC------------------
T ss_pred eEEEecCccCcCCceEEEEEEcCccccceEEEEeecceeccchHHhhhhhhhcccccccccC------------------
Confidence 99999999999999999999999999999999988887777766665555443211100000
Q ss_pred ccchhhHHHHHHHHHHhccccchhHHHHHHHHHHhhhhhhhhhhcCCCCCccccccccchhhHHHHhhhhhhcccCCChh
Q psy3015 512 WKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR 591 (1791)
Q Consensus 512 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mt~~~~~~~~~~~gi~~~~~~~~~~~~~~e~~~~i~~a~~~~~~~~~~ 591 (1791)
T Consensus 909 -------------------------------------------------------------------------------- 908 (1449)
T d1twfa_ 909 -------------------------------------------------------------------------------- 908 (1449)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhHHHHHHHHHHHHHhhcccccccccccceeeeecCCCcccccccccccceeecChhhhhcccccCCchhhHhhhhccHH
Q psy3015 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNED 671 (1791)
Q Consensus 592 ~ri~~~~~k~ie~V~~~yd~~vr~~vg~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 671 (1791)
...++ .
T Consensus 909 ----------------------------------------~~~~~----------------------------------~ 914 (1449)
T d1twfa_ 909 ----------------------------------------PSLLE----------------------------------S 914 (1449)
T ss_dssp ----------------------------------------TTTBT----------------------------------T
T ss_pred ----------------------------------------hhHhh----------------------------------h
Confidence 00000 0
Q ss_pred HHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccCChHHHHHHHHHHHHHHHHHHHHHhhccCCCcceeecch
Q psy3015 672 VLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPCN 751 (1791)
Q Consensus 672 ~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~~~~~e~~kL~~~~~~Lr~i~~~~~~~~~l~~N 751 (1791)
..++ ..+......+++++.++.+.+..+|.++.........|+|
T Consensus 915 -~~ei-----------------------------------~~~~~~~~i~~~~~~~l~~~r~~l~~~~~~~~~~~~~p~~ 958 (1449)
T d1twfa_ 915 -GSEI-----------------------------------LGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVN 958 (1449)
T ss_dssp -HHHH-----------------------------------TTCHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCEEEEESC
T ss_pred -hHHH-----------------------------------hhhHHHHHHHHHHHHHHHHHHHHHHHHhcCccccccCcch
Confidence 0000 0011122234556778888888899998888888999999
Q ss_pred hHHHHHHHhhhhccCCcccccccceEEEeccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccCC
Q psy3015 752 LMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQD 831 (1791)
Q Consensus 752 ~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~~ 831 (1791)
+.++++++... +.... .........++.
T Consensus 959 ~~~~~~~~~~~--~~~~~----------~~~~~~~~~~~~---------------------------------------- 986 (1449)
T d1twfa_ 959 IRRIIQNAQQT--FHIDH----------TKPSDLTIKDIV---------------------------------------- 986 (1449)
T ss_dssp HHHHHHHHHHH--TTCCT----------TSCBCCCHHHHH----------------------------------------
T ss_pred HHHHHHhhhhh--ccccc----------CccccccHHHHH----------------------------------------
Confidence 99998876651 11000 000000010000
Q ss_pred CcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccccCCccccccccccCCCCccccCC
Q psy3015 832 TGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFGS 911 (1791)
Q Consensus 832 ~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k~~~~~~~~~~~~~~~~~~~~~~ 911 (1791)
.++.+ +. +.+
T Consensus 987 ----------------------------~~~~~----------------l~---~~~----------------------- 996 (1449)
T d1twfa_ 987 ----------------------------LGVKD----------------LQ---ENL----------------------- 996 (1449)
T ss_dssp ----------------------------HHHHH----------------HH---TTC-----------------------
T ss_pred ----------------------------HHHHH----------------HH---hhh-----------------------
Confidence 00000 11 111
Q ss_pred CCCCCCCCCCCCccccCccccccccCCCCcCCCCCCCCcccccCCcchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccCC
Q psy3015 912 AATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLS 991 (1791)
Q Consensus 912 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rln 991 (1791)
.+..+.+.++.++..+++.+|.+++++.|+++.++.+++++
T Consensus 997 ---------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~ 1037 (1449)
T d1twfa_ 997 ---------------------------------------LVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLT 1037 (1449)
T ss_dssp ---------------------------------------CSCCCCSHHHHHHHHHTTHHHHHHHHHHSCHHHHHHTSCCC
T ss_pred ---------------------------------------heecccchhhhhhcccccceeeeeeccccchhhhhhhcccC
Confidence 23345677889999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCcc
Q psy3015 992 SEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRGF 1049 (1791)
Q Consensus 992 ~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrGF 1049 (1791)
.+.+.|++..+..+|..+++.| +||. || +.+++|++|+|| |.|+
T Consensus 1038 ~~~~~~~~~~~~~ky~~slv~pGEaVGiiAAQSIGEP~TQmTLnTFH~AG~~~~nvT~GiPR--l~EI------------ 1103 (1449)
T d1twfa_ 1038 KQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPR--LKEI------------ 1103 (1449)
T ss_dssp HHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHH--HHHH------------
T ss_pred HHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhhccchhhhhhhhhhhcceeeecccccchh--hhhh------------
Confidence 9999999999999999999999 8887 87 778899999999 9999
Q ss_pred eeeccccCCCcceEEEeecCCCCccchhhhccchhHHHHH------HHHHHhcceEEEECCCCCCcccccCcceeeeecc
Q psy3015 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLV------FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYE 1123 (1791)
Q Consensus 1050 V~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtGYIqR------RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg 1123 (1791)
.++.++.+||+.+++.. +......+...+-+ +|.++.+...|.||++++++++.++.+++++++.
T Consensus 1104 -l~ask~iktp~~~v~l~--------~~~~~~~~~~k~~~~~i~~~~l~~vv~~~~v~~~~~~~~~~i~~~~~~i~~~~~ 1174 (1449)
T d1twfa_ 1104 -LNVAKNMKTPSLTVYLE--------PGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFS 1174 (1449)
T ss_dssp -TTTCSSCSSCEEEEEBC--------SSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSC
T ss_pred -eeeecccCCcceeEEec--------cccchhHHHHHhhhheeeeeeccceeeeeEEEEcCCCceEEEEEecceeeEEEE
Confidence 78889999999999983 22222333332222 5778888899999999999999999999998877
Q ss_pred CCCCC----CCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhH
Q psy3015 1124 MPDFD----PTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEED 1199 (1791)
Q Consensus 1124 ~dg~D----~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee 1199 (1791)
..+.. .....+|++++++++..+.++++++.++.+++...++.+..+.+++++.++..++.++........
T Consensus 1175 ~~~~~~~~~~~~~~~~ilrl~l~~~~~~~k~i~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~----- 1249 (1449)
T d1twfa_ 1175 LLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDA----- 1249 (1449)
T ss_dssp C----------CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC------------
T ss_pred eccchheeeecccCCceEEEEEchhhcccCCCCHHHHHHHHHHhcCCCeEEEecCCCcceEEEecccCCcccccc-----
Confidence 54432 344568999999999999999999999999999988888888888888888888887654322110
Q ss_pred HHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCc
Q psy3015 1200 AVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDP 1279 (1791)
Q Consensus 1200 ~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp 1279 (1791)
.....+...++.+...++.+++|+|+++|.++.+. ...+.+....+.|....+|+|+|+|+||.+++..+.|||
T Consensus 1250 -~~~~~~~~~l~~i~~~~l~~~~v~Gi~~I~rv~i~-----~~~~~~~~~~~~~~~~~~~vl~teG~nl~~~l~~~~iD~ 1323 (1449)
T d1twfa_ 1250 -ETEAEEDHMLKKIENTMLENITLRGVENIERVVMM-----KYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDP 1323 (1449)
T ss_dssp ----CCTTHHHHHHHHHHHHHCEEESCTTCCCEEEE-----EEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCT
T ss_pred -ccccchHHHHHHHHhhccCCcEEeCCCCeEEEEEe-----cccceeeCCCCcCccCCcEEEEcCcCCHHHHhccCCccc
Confidence 11223445566666667788999999999999876 334566777778877789999999999999999999999
Q ss_pred ccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhh
Q psy3015 1280 VRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 1359 (1791)
Q Consensus 1280 ~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEe 1359 (1791)
.+++||||++|+++|||||||++|++|++.||..+|++||+|||+||||+||++|.+++|||+|+++.+.|||++||||+
T Consensus 1324 ~~~~sNdI~dil~~lGIEAar~~ii~EI~~V~~~~Gi~Id~rHi~LIad~MT~~G~~~~i~R~gi~~~~~S~l~~aSFEe 1403 (1449)
T d1twfa_ 1324 TRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEE 1403 (1449)
T ss_dssp TTCBCSCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSC
T ss_pred ccCccCcHHHHHHHHhHHHHHHHHHHHHHHHHHhcCcEECHHHHHHHHHHHCcCCeEeeccHHHhccCCcCHHHHhhchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhcccccc
Q psy3015 1360 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKC 1405 (1791)
Q Consensus 1360 Tv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~ 1405 (1791)
|.++|.+||++|+.|+|+|++|||++|+++|+|||+||++++++++
T Consensus 1404 T~~vL~~AAi~g~~D~L~G~senIi~G~~ip~GTG~fdll~d~~~l 1449 (1449)
T d1twfa_ 1404 TVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESL 1449 (1449)
T ss_dssp SHHHHHHHHHHTCEECCCSHHHHHHTTCCCSSGGGSSEEEECSCCC
T ss_pred HHHHHHHHHhcCCcccCCCcHHHeecCCCCCCcccccEEEechhhC
Confidence 9999999999999999999999999999999999999999998753
|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|