Citrus Sinensis ID: 002296
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 | 940 | 2.2.26 [Sep-21-2011] | |||||||
| Q9P7X8 | 1174 | Probable DNA-directed RNA | yes | no | 0.871 | 0.697 | 0.432 | 0.0 | |
| Q75DS1 | 1196 | DNA-directed RNA polymera | yes | no | 0.891 | 0.700 | 0.448 | 0.0 | |
| O74633 | 1234 | DNA-directed RNA polymera | N/A | no | 0.888 | 0.676 | 0.430 | 0.0 | |
| P22138 | 1203 | DNA-directed RNA polymera | yes | no | 0.891 | 0.696 | 0.436 | 0.0 | |
| Q54BM1 | 1130 | DNA-directed RNA polymera | yes | no | 0.928 | 0.772 | 0.400 | 0.0 | |
| P70700 | 1135 | DNA-directed RNA polymera | yes | no | 0.908 | 0.752 | 0.407 | 0.0 | |
| Q9H9Y6 | 1135 | DNA-directed RNA polymera | yes | no | 0.915 | 0.758 | 0.405 | 0.0 | |
| Q5REE8 | 1136 | DNA-directed RNA polymera | yes | no | 0.915 | 0.757 | 0.406 | 0.0 | |
| O54888 | 1135 | DNA-directed RNA polymera | yes | no | 0.892 | 0.739 | 0.380 | 1e-175 | |
| P28365 | 1166 | DNA-directed RNA polymera | N/A | no | 0.915 | 0.738 | 0.377 | 1e-172 |
| >sp|Q9P7X8|RPA2_SCHPO Probable DNA-directed RNA polymerase I subunit RPA2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpa2 PE=3 SV=2 | Back alignment and function desciption |
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Score = 734 bits (1896), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 393/908 (43%), Positives = 558/908 (61%), Gaps = 89/908 (9%)
Query: 38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLK 97
R+ +Y +L+ ++F + G P E G P+M+++ RCHL+G +L++ K
Sbjct: 106 ARERLTTYKSRLV--LKFSWSVNGGPRQSEMREVGMIPIMVRSNRCHLEGLSPAELIAHK 163
Query: 98 EEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQS 157
EE+ EMGGYFI+NG+E++ R +ILPK+N+P +++R SF +R Y+ + IRCVR DQS
Sbjct: 164 EESEEMGGYFIVNGIEKLIRMLILPKRNHPTAIIRPSFANRGTSYSQYGLSIRCVRPDQS 223
Query: 158 SVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEK 217
S+T L+YL NG F + EYL+P ++LKAL++T+D EIF +
Sbjct: 224 SLTNTLHYLNNGVTMFRFHWRKNEYLIPSMMILKALLETSDKEIFEGIV----------G 273
Query: 218 GAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277
+G+ +++RV+++L + L ++ + LQ++G F+ V+ + + V +++
Sbjct: 274 KDLGNTFLTDRVELMLRAYKSYGLYSQTETLQYLGSKFRVVLGVAEDLTDVEVGRFLLQK 333
Query: 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLE 337
+ VHL + DKF LL+FM++KL++LV +DNPDS Q+QEILL G L LKEK+E
Sbjct: 334 VVLVHLREAKDKFRLLLFMIRKLYALVAGECCADNPDSPQHQEILLGGFLYGQILKEKIE 393
Query: 338 DWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGL 397
DWL + I ++ + DF + + +V K + IGT ++ L TG L + TGL
Sbjct: 394 DWLNSIRAQINLDVRRSAPGVDFSDRKYLTRVFSK-INNDIGTKLQYFLSTGNLVSNTGL 452
Query: 398 DLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDG 457
DLQQ GYTV AE+LNF RF+S FR VHRGA FA L+TT+VRKLLPE+WGF+CPVHTPDG
Sbjct: 453 DLQQATGYTVVAEKLNFYRFLSHFRMVHRGAFFAELKTTTVRKLLPEAWGFMCPVHTPDG 512
Query: 458 EPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517
PCGLLNH+ C + ++ V IPSL + PP+V+
Sbjct: 513 SPCGLLNHLARKCEIVTHPSD--------------------VSQIPSLLLSLGVDPPSVV 552
Query: 518 S-------VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAA-----------SVIPDDLEVG 559
V LDG++VG + V LR +K+ A + +P DLE+G
Sbjct: 553 GHESGWGCVQLDGKIVGWCTYKLAKHVADVLRLMKIEYAVKLRNGTATEPAKVPLDLEIG 612
Query: 560 YVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDG 619
YVP S G YPGLYLF++P + VRPV++IS + ++++GPFEQV+M+I C
Sbjct: 613 YVPPSHNGQYPGLYLFSNPARMVRPVKHIS-----TGELDMLGPFEQVYMDIAC------ 661
Query: 620 GRRNAFP-------ATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQ 672
FP +TH E PT +LS+VAN+TP+SD NQSPRNMYQCQM KQTMG
Sbjct: 662 -----FPKEIVPKVSTHVEYSPTNVLSIVANMTPFSDFNQSPRNMYQCQMGKQTMGTPGT 716
Query: 673 ALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNK 732
AL++R D KLY LQT QTP+VR + YG+D YP GTNA+VAV++YTGYDMEDAMILNK
Sbjct: 717 ALRYRTDNKLYRLQTGQTPVVRPKLHNTYGLDHYPNGTNAVVAVISYTGYDMEDAMILNK 776
Query: 733 SSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRR------NKDAKSLHSVIDSDGLPY 786
S+ +RG +G +Y+ E+ DLS K RG+ + + + +D+DGLP+
Sbjct: 777 SAHERGFGYGTVYKGESFDLS---QKRRRGEPVVHHFGFAPGSTPRREWLQKLDADGLPF 833
Query: 787 VGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAV---DMKNSKNLPQKANIRFR 843
+G + G+P + YD++T + G+E FVD V + D+ +S+ Q+ +++ R
Sbjct: 834 IGIKLEDGDPIVAYYDESTGQNFIETYHGTEPGFVDEVRLLGNDVGDSEC--QQIHVKLR 891
Query: 844 HTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLE 903
TR+PIIGDKFSSRHGQKG+CSQ WP +DMPF+ +GM+PD+IINPHAFPSRMTI M +E
Sbjct: 892 ITRSPIIGDKFSSRHGQKGICSQKWPTVDMPFT-ESGMQPDIIINPHAFPSRMTIGMFIE 950
Query: 904 SVAAKVVA 911
S+A K A
Sbjct: 951 SLAGKAGA 958
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DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft. Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812) EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6 |
| >sp|Q75DS1|RPA2_ASHGO DNA-directed RNA polymerase I subunit RPA2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPA2 PE=3 SV=2 | Back alignment and function description |
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| >sp|O74633|RPA2_NEUCR DNA-directed RNA polymerase I subunit RPA2 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=acr-2 PE=1 SV=2 | Back alignment and function description |
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| >sp|P22138|RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPA135 PE=1 SV=1 | Back alignment and function description |
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| >sp|Q54BM1|RPA2_DICDI DNA-directed RNA polymerase I subunit rpa2 OS=Dictyostelium discoideum GN=polr1b PE=3 SV=1 | Back alignment and function description |
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| >sp|P70700|RPA2_MOUSE DNA-directed RNA polymerase I subunit RPA2 OS=Mus musculus GN=Polr1b PE=2 SV=2 | Back alignment and function description |
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| >sp|Q9H9Y6|RPA2_HUMAN DNA-directed RNA polymerase I subunit RPA2 OS=Homo sapiens GN=POLR1B PE=1 SV=2 | Back alignment and function description |
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| >sp|Q5REE8|RPA2_PONAB DNA-directed RNA polymerase I subunit RPA2 OS=Pongo abelii GN=POLR1B PE=2 SV=1 | Back alignment and function description |
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| >sp|O54888|RPA2_RAT DNA-directed RNA polymerase I subunit RPA2 OS=Rattus norvegicus GN=Polr1b PE=1 SV=1 | Back alignment and function description |
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| >sp|P28365|RPA2_EUPOC DNA-directed RNA polymerase I subunit RPA2 OS=Euplotes octocarinatus GN=RPA2 PE=3 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 | 940 | ||||||
| 255578257 | 1159 | DNA-directed RNA polymerase I subunit, p | 0.955 | 0.774 | 0.758 | 0.0 | |
| 359487166 | 1142 | PREDICTED: DNA-directed RNA polymerase I | 0.954 | 0.785 | 0.766 | 0.0 | |
| 296087844 | 1113 | unnamed protein product [Vitis vinifera] | 0.922 | 0.778 | 0.791 | 0.0 | |
| 449458081 | 1173 | PREDICTED: DNA-directed RNA polymerase I | 0.958 | 0.768 | 0.722 | 0.0 | |
| 356548837 | 1175 | PREDICTED: DNA-directed RNA polymerase I | 0.955 | 0.764 | 0.721 | 0.0 | |
| 356563684 | 1175 | PREDICTED: DNA-directed RNA polymerase I | 0.955 | 0.764 | 0.722 | 0.0 | |
| 297851416 | 1188 | hypothetical protein ARALYDRAFT_313639 [ | 0.952 | 0.753 | 0.685 | 0.0 | |
| 224053240 | 1109 | predicted protein [Populus trichocarpa] | 0.938 | 0.795 | 0.725 | 0.0 | |
| 79356046 | 1178 | nuclear RNA polymerase A2 [Arabidopsis t | 0.951 | 0.758 | 0.683 | 0.0 | |
| 12324162 | 1114 | DNA-directed RNA polymerase subunit, put | 0.930 | 0.785 | 0.702 | 0.0 |
| >gi|255578257|ref|XP_002529996.1| DNA-directed RNA polymerase I subunit, putative [Ricinus communis] gi|223530519|gb|EEF32401.1| DNA-directed RNA polymerase I subunit, putative [Ricinus communis] | Back alignment and taxonomy information |
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Score = 1489 bits (3854), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 702/925 (75%), Positives = 803/925 (86%), Gaps = 27/925 (2%)
Query: 7 ADFEPLRELVRHHIESFDYMLDEGLSEMFDH-----------------CRQAKISYTGKL 49
D+ L+EL RHHI+SFDYM++ GL M D+ CRQAKISYTGK
Sbjct: 16 GDYSALQELTRHHIDSFDYMIERGLEIMLDNIKPESSRTKHKRLLPFECRQAKISYTGKF 75
Query: 50 MADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFIL 109
ADV F+Y G V+RE++NFGQ P+MLK+R CHL G DSQ+LVS EE+AEMGGYFIL
Sbjct: 76 EADVCFEY--HGKAVIREKYNFGQLPIMLKSRLCHLYGVDSQQLVSFNEESAEMGGYFIL 133
Query: 110 NGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRK------DQSSVTLKL 163
NGLERV R +I+PK+NYPMS VR SFRDRREGYTDKAVVIRCVR+ DQSSV++KL
Sbjct: 134 NGLERVVRLLIMPKRNYPMSTVRGSFRDRREGYTDKAVVIRCVREYQSSLTDQSSVSVKL 193
Query: 164 YYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSP 223
YYL +GS RLGFW+QG+EYLLP GIVLKAL +T D EI+ LTCCYDEKY+K KGAVGS
Sbjct: 194 YYLRSGSARLGFWIQGREYLLPAGIVLKALAETTDREIYEKLTCCYDEKYEKAKGAVGSQ 253
Query: 224 LVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHL 283
LV ER KIIL EV+DLSL T+ +CL+HIGEHFQPV+DGL+ E++ VA V++DYIFVHL
Sbjct: 254 LVGERAKIILDEVRDLSLFTQSECLRHIGEHFQPVMDGLEKETFSNVAHAVLKDYIFVHL 313
Query: 284 NDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKG 343
N+ +DKFNLLIFMLQKLFSLVD TSV DNPDSLQNQE+LLPGHL+TIYLKEKLE+WLRK
Sbjct: 314 NNYDDKFNLLIFMLQKLFSLVDQTSVVDNPDSLQNQEVLLPGHLVTIYLKEKLEEWLRKA 373
Query: 344 KKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRA 403
KK++Q+EI N F+F ++ ++KKV++KNPS I ++E MLKTGRL TQTGLDLQQRA
Sbjct: 374 KKVLQEEIAKN-NNFNFLSVLDVKKVIDKNPSTTISLAVENMLKTGRLVTQTGLDLQQRA 432
Query: 404 GYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLL 463
GYTVQAERLNFLRF+SFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLL
Sbjct: 433 GYTVQAERLNFLRFLSFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLL 492
Query: 464 NHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDG 523
NHMT +CR+ SY+DS+G ++DF +R SIL VL +GM SLPKLV++GPP VLSVLLDG
Sbjct: 493 NHMTRSCRITSYFDSQGAVKDFFDIRKSILGVLTSLGMTSSLPKLVQAGPPQVLSVLLDG 552
Query: 524 RVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVR 583
RVVG IPSS++EKVV HLRRLKV+A+SVIPDDLEVGYVPLS+GGA+PGLYLFTSP +F+R
Sbjct: 553 RVVGSIPSSQVEKVVVHLRRLKVAASSVIPDDLEVGYVPLSMGGAFPGLYLFTSPSRFIR 612
Query: 584 PVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVAN 643
PV+NIS+P+ E +NIELIGPFEQVFMEIRCPDGG+GGR +AFPATHEEIHPT MLSVVAN
Sbjct: 613 PVKNISIPAGEGENIELIGPFEQVFMEIRCPDGGNGGRSDAFPATHEEIHPTDMLSVVAN 672
Query: 644 LTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGI 703
LTP+SDHNQSPRNMYQCQMAKQTM FS+Q+L+FRADQKLYHLQTPQTPIVRT++YTKY +
Sbjct: 673 LTPWSDHNQSPRNMYQCQMAKQTMAFSLQSLRFRADQKLYHLQTPQTPIVRTSSYTKYCV 732
Query: 704 DEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQ 763
DEYPTGTNAIVAVLAYTGYDMEDAMILNKSSV+RGMCHGQIYQTETIDLS++G++ DR Q
Sbjct: 733 DEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVERGMCHGQIYQTETIDLSEEGSRSDRAQ 792
Query: 764 KLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDY 823
++FRR+ KSLHSVIDSDGLPYVGQMIHP EPYCSIY++ TN+ RTN+RKGS+ V VDY
Sbjct: 793 RMFRRSNIDKSLHSVIDSDGLPYVGQMIHPNEPYCSIYNEITNTTRTNNRKGSDPVIVDY 852
Query: 824 VAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883
VA+D KN K+L QK NIRFRH RNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP
Sbjct: 853 VAIDTKNKKHL-QKVNIRFRHPRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 911
Query: 884 DLIINPHAFPSRMTIAMLLESVAAK 908
DLIINPHAFPSRMTIAMLLES+AAK
Sbjct: 912 DLIINPHAFPSRMTIAMLLESLAAK 936
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Source: Ricinus communis Species: Ricinus communis Genus: Ricinus Family: Euphorbiaceae Order: Malpighiales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|359487166|ref|XP_002263835.2| PREDICTED: DNA-directed RNA polymerase I subunit RPA2 [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|296087844|emb|CBI35100.3| unnamed protein product [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|449458081|ref|XP_004146776.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|356548837|ref|XP_003542805.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|356563684|ref|XP_003550091.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|297851416|ref|XP_002893589.1| hypothetical protein ARALYDRAFT_313639 [Arabidopsis lyrata subsp. lyrata] gi|297339431|gb|EFH69848.1| hypothetical protein ARALYDRAFT_313639 [Arabidopsis lyrata subsp. lyrata] | Back alignment and taxonomy information |
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| >gi|224053240|ref|XP_002297732.1| predicted protein [Populus trichocarpa] gi|222844990|gb|EEE82537.1| predicted protein [Populus trichocarpa] | Back alignment and taxonomy information |
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| >gi|79356046|ref|NP_564341.2| nuclear RNA polymerase A2 [Arabidopsis thaliana] gi|332193031|gb|AEE31152.1| nuclear RNA polymerase A2 [Arabidopsis thaliana] | Back alignment and taxonomy information |
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| >gi|12324162|gb|AAG52049.1|AC022455_3 DNA-directed RNA polymerase subunit, putative; 8546-1198 [Arabidopsis thaliana] | 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 | 940 | ||||||
| TAIR|locus:2019272 | 1178 | NRPA2 "nuclear RNA polymerase | 0.919 | 0.733 | 0.721 | 0.0 | |
| ASPGD|ASPL0000012082 | 1231 | AN3933 [Emericella nidulans (t | 0.561 | 0.428 | 0.415 | 4.8e-209 | |
| RGD|620822 | 1135 | Polr1b "polymerase (RNA) I pol | 0.472 | 0.391 | 0.404 | 2e-161 | |
| UNIPROTKB|O54888 | 1135 | Polr1b "DNA-directed RNA polym | 0.472 | 0.391 | 0.404 | 2e-161 | |
| POMBASE|SPBP23A10.07 | 1174 | rpa2 "DNA-directed RNA polymer | 0.7 | 0.560 | 0.451 | 3e-157 | |
| DICTYBASE|DDB_G0293560 | 1130 | rpa2 "RNA polymerase I, second | 0.710 | 0.591 | 0.447 | 4.6e-150 | |
| UNIPROTKB|E2REX8 | 1135 | POLR1B "DNA-directed RNA polym | 0.540 | 0.447 | 0.391 | 7.5e-101 | |
| UNIPROTKB|F5GZX4 | 1173 | POLR1B "DNA-directed RNA polym | 0.541 | 0.433 | 0.399 | 2.5e-100 | |
| UNIPROTKB|Q9H9Y6 | 1135 | POLR1B "DNA-directed RNA polym | 0.541 | 0.448 | 0.399 | 2.5e-100 | |
| UNIPROTKB|A6QLS0 | 1135 | POLR1B "DNA-directed RNA polym | 0.538 | 0.445 | 0.397 | 3.2e-100 |
| TAIR|locus:2019272 NRPA2 "nuclear RNA polymerase A2" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 3364 (1189.2 bits), Expect = 0., Sum P(2) = 0.
Identities = 628/871 (72%), Positives = 747/871 (85%)
Query: 38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLK 97
CRQAKISYTG MADV F+Y D VVR++F+FGQFP+ML ++ C L+GAD +KL+ K
Sbjct: 90 CRQAKISYTGTFMADVCFKYNDG--VVVRDKFDFGQFPIMLMSKLCSLKGADCRKLLKCK 147
Query: 98 EEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQS 157
E +EMGGYFILNG+ERVFR VI PK+N+P SM+R+SFRDR+EGY+ KAVV RCVR DQS
Sbjct: 148 ESTSEMGGYFILNGIERVFRCVIAPKRNHPTSMIRNSFRDRKEGYSSKAVVTRCVRDDQS 207
Query: 158 SVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEK 217
SVT+KLYYL NGS R+GFW+ G+EYLLPVG+VLKAL ++ D EI+ L CCY E Y +
Sbjct: 208 SVTVKLYYLRNGSARVGFWIVGREYLLPVGLVLKALTNSCDEEIYESLNCCYSEHYGRGD 267
Query: 218 GAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277
GA+G+ LV ER KIIL EV+DL L TR QC +H+G+HFQPV+DG++ ES VAE V+RD
Sbjct: 268 GAIGTQLVRERAKIILDEVRDLGLFTREQCRKHLGQHFQPVLDGVKKESLSIVAEAVLRD 327
Query: 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLE 337
Y+FVHL++++DKFNLLIF++QKL+SLVD TS+ DNPDSLQNQEIL+PGH+ITIYLKEKLE
Sbjct: 328 YLFVHLDNDHDKFNLLIFIIQKLYSLVDQTSLPDNPDSLQNQEILVPGHVITIYLKEKLE 387
Query: 338 DWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGL 397
+WLRK K L++DE++N KF F +LA++KK++ KNP + IGTSIET+LKTG L TQ+GL
Sbjct: 388 EWLRKCKSLLKDELDNTNSKFSFESLADVKKLINKNPPRSIGTSIETLLKTGALKTQSGL 447
Query: 398 DLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDG 457
DLQQRAGYTVQAERLNFLRF+SFFRAVHRGASFAGLRTT+VRKLLPESWGFLCPVHTPDG
Sbjct: 448 DLQQRAGYTVQAERLNFLRFLSFFRAVHRGASFAGLRTTTVRKLLPESWGFLCPVHTPDG 507
Query: 458 EPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517
PCGLLNHMT T R+ S +DS+GNIRDF K+R S++ VL G GM+PSLPKLV++GPP V+
Sbjct: 508 TPCGLLNHMTRTSRITSQFDSKGNIRDFLKIRKSVVDVLTGAGMVPSLPKLVRAGPPKVI 567
Query: 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTS 577
VLLDG+VVG + S+ + KVV+++RRLKV A SVIP+DLEVGYVP S+GG+YPGLYL +
Sbjct: 568 HVLLDGQVVGTLSSNLVTKVVSYIRRLKVEAPSVIPEDLEVGYVPTSMGGSYPGLYLASC 627
Query: 578 PPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGM 637
P +F+RPV+NIS+PS+ NIELIGPFEQVFMEI CPDGG+GGR N+ ATHEEIHPTGM
Sbjct: 628 PARFIRPVKNISIPSD---NIELIGPFEQVFMEISCPDGGNGGRNNSSLATHEEIHPTGM 684
Query: 638 LSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNT 697
+SVVANLTP+SDHNQSPRNMYQCQMAKQTM +S QAL+FRADQK+YHLQTPQ+P+VRT T
Sbjct: 685 ISVVANLTPWSDHNQSPRNMYQCQMAKQTMAYSTQALQFRADQKIYHLQTPQSPVVRTKT 744
Query: 698 YTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN 757
YT Y IDE PTGTNAIVAVLA+TG+DMEDAMILNKSSV+RGMCHGQIYQTE IDLSD +
Sbjct: 745 YTTYSIDENPTGTNAIVAVLAHTGFDMEDAMILNKSSVERGMCHGQIYQTENIDLSDQNS 804
Query: 758 KVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSE 817
+ D G K FRR+ + K+ H ID+DGLP VGQ ++P EPYCSIYD+ TN R RKG++
Sbjct: 805 RFDSGSKSFRRSTN-KAEHFRIDADGLPSVGQKLYPDEPYCSIYDEVTNKTRHMKRKGTD 863
Query: 818 SVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSG 877
V VD+V+VDMK+ K+ PQ+ANIRFRH RNPIIGDKFSSRHGQKGVCSQLWPDIDMPF+G
Sbjct: 864 PVIVDFVSVDMKSKKH-PQRANIRFRHARNPIIGDKFSSRHGQKGVCSQLWPDIDMPFNG 922
Query: 878 VTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908
VTGMRPDLIINPHAFPSRMTIAMLLES+AAK
Sbjct: 923 VTGMRPDLIINPHAFPSRMTIAMLLESIAAK 953
|
|
| ASPGD|ASPL0000012082 AN3933 [Emericella nidulans (taxid:162425)] | Back alignment and assigned GO terms |
|---|
| RGD|620822 Polr1b "polymerase (RNA) I polypeptide B" [Rattus norvegicus (taxid:10116)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|O54888 Polr1b "DNA-directed RNA polymerase I subunit RPA2" [Rattus norvegicus (taxid:10116)] | Back alignment and assigned GO terms |
|---|
| POMBASE|SPBP23A10.07 rpa2 "DNA-directed RNA polymerase I complex subunit Rpa2" [Schizosaccharomyces pombe (taxid:4896)] | Back alignment and assigned GO terms |
|---|
| DICTYBASE|DDB_G0293560 rpa2 "RNA polymerase I, second largest subunit" [Dictyostelium discoideum (taxid:44689)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|E2REX8 POLR1B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|F5GZX4 POLR1B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|Q9H9Y6 POLR1B "DNA-directed RNA polymerase I subunit RPA2" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|A6QLS0 POLR1B "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] | 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 Ezypred Server
Original result from Ezypred Server
Fail to connect to Ezypred Server
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
Functionally Associated Proteins Detected by STRING
Original result from the STRING server
 |
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 | fgenesh1_pm.C_scaffold_1002419 | annotation not avaliable (1188 aa) | |||||||||
(Arabidopsis lyrata) | |||||||||||
 | fgenesh2_kg.5__2208__AT3G57660.1 | • | • | • | • | • | 0.962 | ||||
 | fgenesh2_kg.5__2151__AT3G57150.1 | • | • | • | 0.849 | ||||||
 | fgenesh2_kg.8__1958__AT5G60040.1 | • | • | • | • | • | 0.831 | ||||
 | scaffold_101731.1 | • | 0.756 | ||||||||
 | fgenesh1_pm.C_scaffold_7002163 | • | • | 0.733 | |||||||
 | fgenesh2_kg.3__2374__AT3G21540.1 | • | 0.720 | ||||||||
 | fgenesh2_kg.6__3261__AT4G04940.1 | • | 0.708 | ||||||||
 | Al_scaffold_0007_3549 | • | • | • | • | 0.699 | |||||
 | fgenesh1_pm.C_scaffold_6001142 | • | 0.695 | ||||||||
 | scaffold_200152.1 | • | 0.685 |
Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
| ID | Alignment Graph | Length |
Definition |
E-value |
| Query | 940 | |||
| COG0085 | 1060 | COG0085, RpoB, DNA-directed RNA polymerase, beta s | 1e-134 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 1e-117 | |
| pfam00562 | 373 | pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do | 1e-101 | |
| PRK08565 | 1103 | PRK08565, PRK08565, DNA-directed RNA polymerase su | 6e-93 | |
| TIGR03670 | 599 | TIGR03670, rpoB_arch, DNA-directed RNA polymerase | 2e-65 | |
| PRK07225 | 605 | PRK07225, PRK07225, DNA-directed RNA polymerase su | 4e-63 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 8e-50 | |
| pfam04563 | 394 | pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub | 1e-29 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 1e-26 | |
| PRK09606 | 494 | PRK09606, PRK09606, DNA-directed RNA polymerase su | 2e-22 | |
| pfam04565 | 68 | pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do | 4e-22 | |
| pfam06883 | 58 | pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 | 1e-15 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 1e-14 | |
| pfam04561 | 185 | pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do | 8e-11 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 1e-09 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 2e-08 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 7e-08 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 7e-08 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 3e-07 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 7e-06 |
| >gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
Score = 429 bits (1105), Expect = e-134
Identities = 215/1001 (21%), Positives = 335/1001 (33%), Gaps = 212/1001 (21%)
Query: 3 RKKSADFEPLRELVRHHIESFDYMLDEGLSEMFD-------------------------- 36
K +F L LV ++S++ EGL E+F
Sbjct: 15 FGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESYNGNTELEYGSYRLGEPPK 74
Query: 37 ----HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQK 92
CR ++Y+ L + + G + + G P+M +
Sbjct: 75 FYPEECRLRGLTYSAPLYVKLRLVVNETGEEIKEQEVYMGDIPLMTR------------- 121
Query: 93 LVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCV 152
GGYFI+NG ERV S A VI
Sbjct: 122 -----------GGYFIINGTERVIVSQEHRSPGVIF---VEKKDKTGSKVLYVARVIPY- 166
Query: 153 RKDQSSVTL--KLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYD 210
R K + + +PV I+L+AL D EI D
Sbjct: 167 RGSWLEFEFDPKDNLYVRIDRK---------RKIPVTILLRALGLETDEEIIEAF--GGD 215
Query: 211 EKYKKEKGAVGSPLVSERVKIILAEVQDLSLT--TRLQCLQHIGEHFQPVIDGLQSESYY 268
E + E + +L ++ T L+ IG V E Y
Sbjct: 216 ELTD--------LVPPEGEEALLEIYEEAKGEKITARNALELIGSRVFVVKRYDAKEGRY 267
Query: 269 AVAETVIRDYIFVHLNDNNDKFNL--------LIFMLQKLFSLVDHTSVSDNPDSLQNQE 320
A+ V+ + HL + ++++L +I M++ L L D+ D L N+
Sbjct: 268 KRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRR 327
Query: 321 ILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKN------- 373
+ L G L+ + L R ++K+ +EK
Sbjct: 328 LRLVGELLENLFRVGLSRMER-----------------------DVKERLEKADKRDTLV 364
Query: 374 PSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGL 433
P I L TG R+ + ++ N L +S R +
Sbjct: 365 PQDLINAKPIHALITGFFG---------RSQLSQFMDQTNPLSELSHKRRLSALGLSRER 415
Query: 434 RTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSIL 493
VR + P +G +CP+ TP+G GL+ + R+ N F + T
Sbjct: 416 AGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARI--------NEYGFLE--TPYR 465
Query: 494 RVLIGV-GMIPSLPKLVKSGPPAVLSVLLDGRVVGVI--PSSEIEKVVAHLRRLKVSAAS 550
+VL G + ++ V + G+ G + P +E++V RR S
Sbjct: 466 KVLDGSLVVDE-----IEYLSADEEDVYVIGQANGTLDEPGELVEELV-ECRRGGSGEVS 519
Query: 551 VIPDD------------LEVGYVPLSLGGAYPGL-YLFTSPPKFVRPVRNISLPSEESQN 597
V + + VG + L S + +
Sbjct: 520 VADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPLVGTG 579
Query: 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNM 657
+E + + I G TH EI P +L + A+L PY +HNQSP N+
Sbjct: 580 MEYLDAEDSGAAVI-AKRPGVV--------THVEISPIVILGIEASLIPYPEHNQSPYNL 630
Query: 658 YQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVL 717
Y+ + Q G + + L R D L P V T E G NA+VA +
Sbjct: 631 YKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFM 682
Query: 718 AYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRR--NKDAKSL 775
+ GY+ EDA+I+++ SV+R + + + D G + R N ++L
Sbjct: 683 PWNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKL----GPEEIRDIPNVSEEAL 738
Query: 776 HSVIDSDGLPYVGQMIHPGEPYCSIYDKTT------------------NSWRTNSRK--G 815
+D DG+ +G + G+ K T R S +
Sbjct: 739 -RNLDEDGIIRIGAEVKGGDILVG---KVTPKGETELTPEERLLRIFGEKVRDTSLRVPH 794
Query: 816 SESVFVDYVAVDMKNSKNLP---QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDID 872
E VD V V P + + R P IGDK + RHG KGV S++ P D
Sbjct: 795 GEEGIVDDVQV-FTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQED 853
Query: 873 MPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYM 913
MPF G PD+I+NP PSRM I +LE+ K A +
Sbjct: 854 MPFL-EDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALL 893
|
Length = 1060 |
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6 | Back alignment and domain information |
|---|
| >gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B | Back alignment and domain information |
|---|
| >gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3 | Back alignment and domain information |
|---|
| >gnl|CDD|219216 pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 specific domain | Back alignment and domain information |
|---|
| >gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2 | Back alignment and domain information |
|---|
| >gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit | 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|214397 CHL00207, rpoB, RNA polymerase beta subunit; 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|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit | Back alignment and domain information |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 940 | |||
| KOG0216 | 1111 | consensus RNA polymerase I, second largest subunit | 100.0 | |
| PRK08565 | 1103 | DNA-directed RNA polymerase subunit B; Provisional | 100.0 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 100.0 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 100.0 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 100.0 | |
| cd00653 | 866 | RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po | 100.0 | |
| TIGR02013 | 1065 | rpoB DNA-directed RNA polymerase, beta subunit. Th | 100.0 | |
| PRK00405 | 1112 | rpoB DNA-directed RNA polymerase subunit beta; Rev | 100.0 | |
| CHL00001 | 1070 | rpoB RNA polymerase beta subunit | 100.0 | |
| CHL00207 | 1077 | rpoB RNA polymerase beta subunit; Provisional | 100.0 | |
| PRK09603 | 2890 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| PRK14844 | 2836 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| PRK07225 | 605 | DNA-directed RNA polymerase subunit B'; Validated | 100.0 | |
| TIGR03670 | 599 | rpoB_arch DNA-directed RNA polymerase subunit B. T | 100.0 | |
| PRK09606 | 494 | DNA-directed RNA polymerase subunit B''; Validated | 100.0 | |
| PF00562 | 386 | RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int | 100.0 | |
| PF04563 | 203 | RNA_pol_Rpb2_1: RNA polymerase beta subunit; Inter | 100.0 | |
| PF04565 | 68 | RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; Int | 99.94 | |
| PF04561 | 190 | RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; Int | 99.85 | |
| PF04566 | 63 | RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; Int | 99.48 | |
| PF06883 | 58 | RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do | 99.09 | |
| PF04567 | 48 | RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int | 98.39 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 97.59 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 97.29 | |
| PHA03394 | 865 | lef-8 DNA-directed RNA polymerase subunit beta-lik | 95.84 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 94.78 |
| >KOG0216 consensus RNA polymerase I, second largest subunit [Transcription] | Back alignment and domain information |
|---|
Probab=100.00 E-value=7.8e-231 Score=1937.08 Aligned_cols=895 Identities=52% Similarity=0.864 Sum_probs=840.5
Q ss_pred CCCCcCCccCchhhHHHHHHHHHHHHHHHHHHHH--------------------------------------------HH
Q 002296 2 ARKKSADFEPLRELVRHHIESFDYMLDEGLSEMF--------------------------------------------DH 37 (940)
Q Consensus 2 ~~~~~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii--------------------------------------------~e 37 (940)
|+.+-+.++.++.++++|++|||...+.||.... .|
T Consensus 5 ~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~~~~~g~kis~~ve~i~iakP~l~~~~~ss~~r~lyPaE 84 (1111)
T KOG0216|consen 5 PPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKVPLKAGDKISMKVESIQIAKPMLSDKVHSSDTRKLYPAE 84 (1111)
T ss_pred CcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhcccccCCceeEEEEEEEecCCCCCccccccccccccchh
Confidence 5666777889999999999999999998887664 89
Q ss_pred HHHcCCeeeeEEEEEEEEEEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEE
Q 002296 38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFR 117 (940)
Q Consensus 38 cR~r~~TYsa~l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr 117 (940)
||+|++||+|.+.|+|.|.+| ++.+......+|.+||||+|++|||.|++++||++++|++.|+||||||||+|||||
T Consensus 85 cRqR~~TY~Gkl~v~v~wsVN--g~~~~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkEe~~EmGGYFIvNGIEKvIR 162 (1111)
T KOG0216|consen 85 CRQRGLTYKGKLVVRVSWSVN--GGHVVIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKEESSEMGGYFIVNGIEKVIR 162 (1111)
T ss_pred HhhccceecceEEEEEEEEEC--CeeeeeeeeecCccceEEeccccccCCCChHHHhhccCchhhcCcEEEEcChHHhhh
Confidence 999999999999999999999 888888899999999999999999999999999999999999999999999999999
Q ss_pred EEEeccCCccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCC
Q 002296 118 SVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTN 197 (940)
Q Consensus 118 ~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~s 197 (940)
++|+++||+|+++.|++|++||..||+|++++|||++|+++.+++|||+.||.+.++|.++|.+|.+|++++||||...|
T Consensus 163 mLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSsvtn~LHYLnnGtv~~~F~~rK~eylvPv~lILKAL~~ts 242 (1111)
T KOG0216|consen 163 MLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSSVTNVLHYLNNGTVMFRFSHRKREYLVPVVLILKALTNTT 242 (1111)
T ss_pred hheeccCCCceEEechhhhhcCCCccccceEEEEeccccccceeEEEEecCCcEEEEEEEeeeeehhhHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHh
Q 002296 198 DLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277 (940)
Q Consensus 198 D~eI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~ 277 (940)
|+|||+.++ +++..++|+.++++.||+++++++++||++|++|||++||+++...+.+++.++|+++|++
T Consensus 243 DeEIf~~lv----------~g~~gdqfl~~rv~~mLr~v~ee~l~trtqcl~yLGs~FRaVl~~v~~~~D~evg~fILr~ 312 (1111)
T KOG0216|consen 243 DEEIFEGLV----------GGDEGDQFLTSRVELMLREVQEENLFTRTQCLQYLGSRFRAVLDFVPEQPDLEVGRFILRE 312 (1111)
T ss_pred HHHHHHHHh----------CCccCceeHHHHHHHHHHHHhhcccccHHHHHHHHhhhhhhhhcCCCCCchHHHHHHHHHh
Confidence 999999997 5777889999999999999999999999999999999999877755568999999999999
Q ss_pred HhccCCCCCcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Q 002296 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357 (940)
Q Consensus 278 ~ll~Hl~~~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~ 357 (940)
+++.||+++.+||.+|++|+|||++++.|+|.+||+|+.+|||++++|+|++.+|+|++++|+..++.++++.+.+.+.+
T Consensus 313 ~VlvHLd~~~DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~LkEriEe~l~~~~~~vr~~l~~~~~~ 392 (1111)
T KOG0216|consen 313 YVLVHLDSDEDKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILKERIEEWLRFISAQVRRDLYKLGFK 392 (1111)
T ss_pred heEEEecccHHHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999886667
Q ss_pred ccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccccCCccccccccc
Q 002296 358 FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS 437 (940)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~ 437 (940)
.++.+..++++++.+.+ ..|+++|++||||||++++++++++|++|+|++|||+||+|||||||.||||++|++||+|+
T Consensus 393 ~~~~~~~~i~~~~~r~~-~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRavhRGa~f~~mrTTt 471 (1111)
T KOG0216|consen 393 EDFLDISAIRKVFMRTN-GNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRAVHRGAFFAEMRTTT 471 (1111)
T ss_pred chhHhHHHHHHHHhhcc-ccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHHHhcccchhheeehh
Confidence 77777778888888776 49999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecCCccccCCCCcce
Q 002296 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517 (940)
Q Consensus 438 vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~ 517 (940)
+|||.|++|||+||||||||+||||+||||..|+|++..++.+ .+.++|.++||.|... .... .+..|
T Consensus 472 vRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s----------~ip~~L~~~Gm~p~~~-~~~~-G~~l~ 539 (1111)
T KOG0216|consen 472 VRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVS----------FIPSILFELGMVPSSH-LVEA-GEPLY 539 (1111)
T ss_pred hHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchh----------hhhHHHHhcCCCchhc-cccC-CCcee
Confidence 9999999999999999999999999999999999999877653 3889999999998732 2222 23479
Q ss_pred EEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCCCCCc
Q 002296 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN 597 (940)
Q Consensus 518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~~~~~ 597 (940)
+|++||+++||++.+.+..+++.||++|...+..||.++||+||+.+.+++||++||+|++||++|||.+++.+ .
T Consensus 540 ~VlldGk~vG~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~nl~~~-----~ 614 (1111)
T KOG0216|consen 540 PVLLDGKVVGWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKNLSLD-----S 614 (1111)
T ss_pred EEEECCEEEEeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhccccC-----c
Confidence 99999999999999999999999999999877789999999999999999999999999999999999999887 8
Q ss_pred eeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhcccccccccccceeEEEe
Q 002296 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFR 677 (940)
Q Consensus 598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~~~n~~~R 677 (940)
+||||++||++++||+.++++.+.. +||.|++|+.+||++|+||||+||||||||||||||+||+||+|.++|..|
T Consensus 615 ~e~iG~fEQvym~i~~~~~e~~~~v----~th~E~~pt~~ls~~anliP~sD~NQSPRNmYQCQMgKQtmg~p~~a~~~r 690 (1111)
T KOG0216|consen 615 VEWIGPFEQVYMNIAIDPKEIFPDV----TTHVELHPTGILSIVANLIPFSDHNQSPRNMYQCQMGKQTMGTPGHALRTR 690 (1111)
T ss_pred hhhcccHHHhhhhhccchhhcCCCc----ceeEEecccchHhHhhcCccccccCCCchhHHHhhhhhhhcCCccccchhc
Confidence 9999999999999999999998876 899999999999999999999999999999999999999999999999999
Q ss_pred ccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEEEEEeeccCC
Q 002296 678 ADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN 757 (940)
Q Consensus 678 ~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~ 757 (940)
+|+|+|+|++||.|+|++..|+.+++|++|.|+||+|||+|||||||||||||||+|+||||+++++||++.++|.++..
T Consensus 691 adnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~~ 770 (1111)
T KOG0216|consen 691 ADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKRS 770 (1111)
T ss_pred ccCceEEecCCCCceeecccccccccccCCCCcceEEEEEeecccChhhhhhhchhhhhccccceeEEeeeeechhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999876553
Q ss_pred CcCccceeecc-CCCChhhhcccCCCCCcccCcEecCCCcEEEEeecCCCcEEEeeccCCCcEEEEEEEEEecCCCCCce
Q 002296 758 KVDRGQKLFRR-NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQ 836 (940)
Q Consensus 758 ~~~~~~~~~~~-~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~ 836 (940)
+ ...|.. |..++ .++||+||+|.+|+++..||++++.++...++++..+|++.|+|+||.|++..++.|+..+
T Consensus 771 r----~~~F~~~p~~~~--~~~ld~dgLP~~G~kl~~~dp~~~y~d~~t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k 844 (1111)
T KOG0216|consen 771 R----SKHFGRSPGEPE--LKKLDADGLPSIGQKLEYGDPYYAYFDEETGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEK 844 (1111)
T ss_pred c----eeeeeeCCCCcc--ccccCCCCCCCCcccccCCCcEEEEEcccCCceEEEEecCCCCeeeEEEEEccccCCCccc
Confidence 2 445664 33333 7899999999999999999999999999999999999999999999999999998877668
Q ss_pred EEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhH
Q 002296 837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENL 916 (940)
Q Consensus 837 ~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~ 916 (940)
.+.|++|.+|+|.||||||||||||||||+.||.+||||| ++|++||||||||||||||||||++|+||||+||+||++
T Consensus 845 ~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFt-esGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~ 923 (1111)
T KOG0216|consen 845 CATITLRIPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFT-ESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNA 923 (1111)
T ss_pred eEEEEEEecCCCcccchhhhhccccccccccCCCCCCCcc-ccCcCcceeeCCCCCcccccHHHHHHHHhchhhcccccc
Confidence 8999999999999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred HHHH-hhhhhhhHHHHHHhhhc
Q 002296 917 WMQH-HLQIQSRKLMEILGLMN 937 (940)
Q Consensus 917 ~~~~-~~~~~~~~~~~~~~~~~ 937 (940)
+|-- |.++.-..|++|||+|-
T Consensus 924 ~Datpf~~~E~~t~~dyfg~~L 945 (1111)
T KOG0216|consen 924 QDATPFIFSEENTAIDYFGEML 945 (1111)
T ss_pred ccCCceeecCcccHHHHHHHHH
Confidence 8332 22233334999999984
|
|
| >PRK08565 DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
| >KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit | Back alignment and domain information |
|---|
| >PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed | Back alignment and domain information |
|---|
| >CHL00001 rpoB RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >CHL00207 rpoB RNA polymerase beta subunit; Provisional | Back alignment and domain information |
|---|
| >PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >PRK07225 DNA-directed RNA polymerase subunit B'; Validated | Back alignment and domain information |
|---|
| >TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B | Back alignment and domain information |
|---|
| >PRK09606 DNA-directed RNA polymerase subunit B''; Validated | Back alignment and domain information |
|---|
| >PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
| >PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2 | Back alignment and domain information |
|---|
| >PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional | Back alignment and domain information |
|---|
| >KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] | 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 | 940 | ||||
| 2waq_B | 1131 | The Complete Structure Of The Archaeal 13-Subunit D | 2e-61 | ||
| 2pmz_B | 1124 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 4e-61 | ||
| 3h0g_B | 1210 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 5e-46 | ||
| 1i3q_B | 1224 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 7e-45 | ||
| 1iw7_C | 1119 | Crystal Structure Of The Rna Polymerase Holoenzyme | 8e-11 | ||
| 1i6v_C | 1118 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 5e-10 | ||
| 1hqm_C | 1119 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 5e-10 | ||
| 1l9u_C | 1118 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 5e-10 | ||
| 1ynj_C | 1119 | Taq Rna Polymerase-Sorangicin Complex Length = 1119 | 5e-10 | ||
| 3iyd_C | 1342 | Three-Dimensional Em Structure Of An Intact Activat | 7e-08 | ||
| 3lu0_C | 1342 | Molecular Model Of Escherichia Coli Core Rna Polyme | 7e-08 |
| >pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131 | Back alignment and structure |
|
| >pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 | Back alignment and structure |
| >pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 | Back alignment and structure |
| >pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 | Back alignment and structure |
| >pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1119 | Back alignment and structure |
| >pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 | Back alignment and structure |
| >pdb|1HQM|C Chain C, 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 = 1119 | Back alignment and structure |
| >pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 | Back alignment and structure |
| >pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex Length = 1119 | Back alignment and structure |
| >pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1342 | Back alignment and structure |
| >pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Length = 1131 | Back alignment and structure |
|---|
Score = 715 bits (1847), Expect = 0.0
Identities = 222/988 (22%), Positives = 378/988 (38%), Gaps = 161/988 (16%)
Query: 12 LRELVRHHIESFDYMLDEGLSEMFD----------------------------------- 36
+ LVR H++S++ + L E+ D
Sbjct: 23 SKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRESDRGERE 82
Query: 37 ----HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQK 92
R ++Y L + ++ E G P+MLK+ + K
Sbjct: 83 ISPMEARLRNLTYAAPLWLTMI--PVENNIEAEPEEVYIGDLPIMLKSAIDPISQYTLDK 140
Query: 93 LVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCV 152
L+ + E+ + GGYFI+NG ERV + N V T A +I
Sbjct: 141 LIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNR----VLVDTGKTGSNITHTAKIISST 196
Query: 153 RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEK 212
+ VT++ L +G+ + F +P I+++AL D +I + D +
Sbjct: 197 AGYRVPVTIE--RLKDGTFHVSF--PAVPGKIPFVILMRALGILTDRDIVYAV--SLDPE 250
Query: 213 YKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAE 272
+ E + + Q S+ L IG G + E+ A+
Sbjct: 251 IQNE--------------LFPSLEQASSIANVDDALDFIGSRVAI---GQKRENRIEKAQ 293
Query: 273 TVIRDYIFVHL----NDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLI 328
+I Y HL +D K L + + K+ L D+ D N+ + L G L
Sbjct: 294 QIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLF 353
Query: 329 TIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKT 388
+ + +++ ++ K L + + + I L T
Sbjct: 354 ASLFRVAFKAFVKDLTYQLEKSKVRGRK----LALKALVR------PDIVTERIRHALAT 403
Query: 389 GRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGF 448
G + R G + +R N+L +S R V + R L WG
Sbjct: 404 GNW-------VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQ-PNFEARDLHGTQWGR 455
Query: 449 LCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIP----- 503
+CP TP+G GL+ ++ ++A + + + L +G++P
Sbjct: 456 MCPFETPEGPNSGLVKNLALMAQIAVGINE-----------KIVEKTLYEMGVVPVEEVI 504
Query: 504 ---SLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGY 560
+ ++ V+L+GR+VG + E++ +R + I D++ VG+
Sbjct: 505 RRVTEGGEDQNEYLKWSKVILNGRLVGYY--RDGEELAKKIRERRRKG--EISDEVNVGH 560
Query: 561 VPLSLGGAYPGLYLFTSPPKFVRPVRNIS-------------LPSEE--------SQNIE 599
+ +++ + RP+ +S L S IE
Sbjct: 561 IVTDFINE---VHVNCDSGRVRRPLIIVSNGNPLVTREDIEKLDSGSITFDDLVRQGKIE 617
Query: 600 LIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQ 659
+ E+ + TH EI +L + A++ PY +HNQSPRN YQ
Sbjct: 618 YLDAEEEENAYVALEP-----SDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQ 672
Query: 660 CQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAY 719
MAKQ +G + R D + + L PQ P+V+T G P G NAI+AV+++
Sbjct: 673 SAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732
Query: 720 TGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN-KVDRGQKLFRRNKDAKS--LH 776
TGY+MED++I+N+SSV+RGM ++ + + + D+ + K +
Sbjct: 733 TGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYY 792
Query: 777 SVIDSDGLPYVGQMIHPGEPYCSIYDKTTN-----------SWRTNSR--KGSESVFVDY 823
+++ +G+ + G+ + R S + E VD
Sbjct: 793 RLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDL 852
Query: 824 VAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883
V + + + +R R R P IGDKF+SRHGQKGV L P +DMP++ V G+ P
Sbjct: 853 VLIT--ETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYT-VKGVVP 909
Query: 884 DLIINPHAFPSRMTIAMLLESVAAKVVA 911
D+I+NPHA PSRMT+ ++E +A K A
Sbjct: 910 DVILNPHALPSRMTLGQIMEGIAGKYAA 937
|
| >1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Length = 1224 | Back alignment and structure |
|---|
| >3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210 | Back alignment and structure |
|---|
| >3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210 | 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 |
|---|
| >2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 | Back alignment and structure |
|---|
| >3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 940 | |||
| 3h0g_B | 1210 | DNA-directed RNA polymerase II subunit RPB2; trans | 100.0 | |
| 1twf_B | 1224 | DNA-directed RNA polymerase II 140 kDa polypeptid; | 100.0 | |
| 4ayb_B | 1131 | DNA-directed RNA polymerase; transferase, multi-su | 100.0 | |
| 2a6h_C | 1119 | DNA-directed RNA polymerase beta chain; RNA polyme | 100.0 | |
| 3lu0_C | 1342 | DNA-directed RNA polymerase subunit beta; E. coli | 100.0 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 99.88 | |
| 3lti_A | 296 | DNA-directed RNA polymerase subunit beta; BBM2, nu | 98.8 | |
| 3tbi_B | 228 | DNA-directed RNA polymerase subunit beta; transcri | 98.61 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 90.89 |
| >3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
Probab=100.00 E-value=9.5e-216 Score=1985.67 Aligned_cols=848 Identities=27% Similarity=0.389 Sum_probs=738.9
Q ss_pred ccCchhhHHHHHHHHHHHHHHHHHHHH---------------------------------------------------HH
Q 002296 9 FEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------------------DH 37 (940)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~ii---------------------------------------------------~e 37 (940)
++..++||+|||||||+|+++||++|+ +|
T Consensus 24 ff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~~e~d~~~~~l~P~E 103 (1210)
T 3h0g_B 24 FFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQE 103 (1210)
T ss_dssp HHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCCBCTTSCBCCCCTTT
T ss_pred HhcccchHHHHHHHHHHHHHHhHHHHHhccCcEEecCccCcccccccCCceEEEEEEEEEEcCCceecCCCcccccCHHH
Confidence 345789999999999999999999876 79
Q ss_pred HHHcCCeeeeEEEEEEEEEEecCC----------C-----ceEeeEEeecccceeecCCCccCCCCChHHHHhccccccc
Q 002296 38 CRQAKISYTGKLMADVEFQYLDAG----------S-----PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAE 102 (940)
Q Consensus 38 cR~r~~TYsa~l~v~i~~~~~~~~----------~-----~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D 102 (940)
||+|++||+|||+|+|++.++... . .....++.||+|||||||++|||++++++||++.||||+|
T Consensus 104 cRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~s~~eL~~~gEcp~D 183 (1210)
T 3h0g_B 104 ARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYD 183 (1210)
T ss_dssp TTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSCCHHHHHHTTCCTTC
T ss_pred HHhcCCccceeEEEEEEEEEcCccccccccccccccccccccccceEEEecCCEEeCCCcccCCCCCHHHHHhcCCCCCC
Confidence 999999999999999999876211 0 1123579999999999999999999999999999999999
Q ss_pred CCcEEEEcCceeEEEEEEeccCCccEEEEeccccCCCCcceeeEEEEEeeecCCCce--EEEEEEEe------CCeEEEE
Q 002296 103 MGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSV--TLKLYYLL------NGSVRLG 174 (940)
Q Consensus 103 ~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~--~~~l~y~~------~g~~~l~ 174 (940)
+||||||||+||||++|+..++|+|+++. +++..|+.+++.+||+++++++. +++++|.. ++.+.++
T Consensus 184 ~GGYFIING~EKVII~qerla~N~~iv~~-----~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~~~~~~i~~~ 258 (1210)
T 3h0g_B 184 QGGYFIINGSEKVIIAQERSAANIVQVFK-----KAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRAT 258 (1210)
T ss_dssp CCCCBCGGGSCBCCCBCBCCCCSCCCCCC-----CCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTTSCSCCCCCC
T ss_pred CCCEEEEeCEEEEEEechhhccceEEEEe-----ecCCCCceEEEEEEEEecCCccceeEEEEEEEeccccCCCceEEEE
Confidence 99999999999999999888899998753 35667888999999999876533 33444433 5677777
Q ss_pred EEeecccccccHhhHHHhccCCCHHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhcc
Q 002296 175 FWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEH 254 (940)
Q Consensus 175 ~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~ 254 (940)
|.+.+. +||+++||||||.+||+||++.|+. +..+..+.+.+..+++++. .++|+++||+|||++
T Consensus 259 ~~~~~~--~IPi~ivlkALg~~sD~EI~~~I~~-----------~~~d~~~~~~l~~slee~~--~i~tq~~aL~yIG~r 323 (1210)
T 3h0g_B 259 LPYIRS--DIPIVIVFRALGVVPDRDILEHICY-----------DPNDFQMLEMMKPCIEEAF--VIQDKDIALDYIGKR 323 (1210)
T ss_dssp CTTSCS--CCCSHHHHTTTTCCSTTHHHHHHCC-----------SSCCHHHHHTHHHHHHTTS--SCCSSHHHHHTTCCC
T ss_pred Eecccc--CCcHHHHHHHcCCCCHHHHHHHHhC-----------CCCcHHHHHHHHHHHHHhh--hcCCHHHHHHHHHHh
Confidence 777654 6999999999999999999999972 2234555666666666543 489999999999999
Q ss_pred ccccccCCCCccHHHHHHHHHHhHhccCCCCC----cchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHH
Q 002296 255 FQPVIDGLQSESYYAVAETVIRDYIFVHLNDN----NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITI 330 (940)
Q Consensus 255 fr~~~~~~~~~~~~~~~~~~L~~~ll~Hl~~~----~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~ 330 (940)
|+.. ..++.+++++|+++|+++|||||+.. .+||.||++|+|||++++.|++.+||+|||+||||+|+|+||+.
T Consensus 324 ~~~~--~~~~~~~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~ 401 (1210)
T 3h0g_B 324 GSTT--GVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLAS 401 (1210)
T ss_dssp SSSC--CCCHHHHHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHH
T ss_pred cccc--CCCchhHHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHHH
Confidence 9853 23566788999999999999999954 48999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEcc
Q 002296 331 YLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAE 410 (940)
Q Consensus 331 lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvle 410 (940)
+||+.|+++++++++.+++.+.+ ++.+++. .+++ ++.||++|++|||||||+++.+ +++|++||||||+
T Consensus 402 lfr~~~~~~~~~i~~~l~k~~~~-~~~~~~~------~~i~---~~~It~~l~~~laTGNW~~~kk-~~~~~sGvsqvl~ 470 (1210)
T 3h0g_B 402 LFRMLFRKMTRDVYKYMQKCVET-NREFNLT------LAVK---SNIITNGLRYSLATGNWGDQKR-SMVNRVGVSQVLN 470 (1210)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-CCSCCCT------TSSC---STTTSHHHHHHHSSSCSSTTSS-CCSCCCCSCCBCC
T ss_pred HHHHHHHHHHHHHHHHHHHHhhc-CCccCHH------Hhcc---hhhhHHHHHHHhhcCCcccccc-cccCcCCEEEEcc
Confidence 99999999999999999998876 4444431 2332 4589999999999999998765 4689999999999
Q ss_pred ccchHHHhhhhcccccCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhH
Q 002296 411 RLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRT 490 (940)
Q Consensus 411 Rln~~~~lSh~Rrv~rg~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~ 490 (940)
|+||+|+|||||||+ +++++++|+++||+||||||||+||+|||||++||||||||++|+||++.+.+
T Consensus 471 R~n~~s~lShlRrv~-~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~----------- 538 (1210)
T 3h0g_B 471 RYTFASTLSHLRRTN-TPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSA----------- 538 (1210)
T ss_dssp CSSHHHHHHHTTBBC-CSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSS-----------
T ss_pred cCCHHHHHHHHHhcc-CchhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcH-----------
Confidence 999999999999997 67889999999999999999999999999999999999999999999987766
Q ss_pred HHHHHHHhCCCeecCCccccCCCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCC
Q 002296 491 SILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYP 570 (940)
Q Consensus 491 ~i~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~ 570 (940)
.|.++|.++||+++. +......++.++|||||+|+|++ .+|..|++.||.|||+| .|+.+++|++ +...+
T Consensus 539 pI~~~l~~~gme~le-~~~~~~~~~~tkVfvNG~wVGvh--~dp~~Lv~~lR~lRR~g--~Is~eVSIvr-----dir~r 608 (1210)
T 3h0g_B 539 PIIEFLEEWGLETLE-DYNPSASPNATKVFVNGVWLGVH--RDPAHLTETLRSLRRRL--DISAEVSIVR-----DIREK 608 (1210)
T ss_dssp HHHHHHHSSSCCCCS-CCCSSSSSSSCCCCSTTCCCCCC--SCHHHHHHHHHHHHTTT--SSCTTCCCCC-----CTTTC
T ss_pred HHHHHHHHhCCcchh-hcCcccCCCceEEEECCEEEEEe--CCHHHHHHHHHHHhhcC--CCCCceEEEe-----cCCCC
Confidence 599999999999873 34444556789999999999995 67999999999999998 6888888753 34578
Q ss_pred ceEEecCCCceeceEEeccCC-------CC-------------------------------CCCceeeecccceeeeeee
Q 002296 571 GLYLFTSPPKFVRPVRNISLP-------SE-------------------------------ESQNIELIGPFEQVFMEIR 612 (940)
Q Consensus 571 ~i~i~~d~gR~~RPv~~~~~~-------~~-------------------------------~~~~iE~i~~~Eq~~~~Ia 612 (940)
+++||||+||+||||++|+++ +. ..|.|||||++||++++||
T Consensus 609 E~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l~k~hi~~L~~~~~~~~~~~~~~~~w~~Lv~~GvIEylDaeEEet~mIa 688 (1210)
T 3h0g_B 609 ELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIA 688 (1210)
T ss_dssp CCCCCCSSCCBCCEEEECCCSSCSSSSCCCSSCHHHHHHHHHHHTCCCSCTTCCCSSTTTTTTTSEEECCTTTGGGCCEE
T ss_pred eEEEecCCCcccceEEEEccCCcccccccccccHHHHHHHhcccccccccccccCCHHHHHhCCCEEEecHhhhhceeEE
Confidence 999999999999999998764 11 2478999999999999999
Q ss_pred cCCCCCCC----------------C--------CCCccceecccCCCccccceeecccCCCCCCCccchhhccccccccc
Q 002296 613 CPDGGDGG----------------R--------RNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMG 668 (940)
Q Consensus 613 ~~~~~~~~----------------~--------~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig 668 (940)
++++|+.. . .....||||||||++|||+|||+||||||||||||||||||+|||||
T Consensus 689 mtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~~~~~~~~THcEIhPsmILGIcASiIPFpdHNQSPRNtYQ~aMgKQamG 768 (1210)
T 3h0g_B 689 MSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMG 768 (1210)
T ss_dssp SCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCSCCSCCSCSEECSCGGGSSCSSSTTSSSSTTSCSHHHHHHHHHHTTCCS
T ss_pred ecHHHhhhhhhhhccccccccccchhhccccCCCcccccccccccchhhhhheeecccCccccccchhhhhhhhhccccc
Confidence 99988732 0 01245899999999999999999999999999999999999999999
Q ss_pred ccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEE
Q 002296 669 FSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTE 748 (940)
Q Consensus 669 ~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~ 748 (940)
++++|+..|+||++|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+||||||+++|++|
T Consensus 769 ~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~~~~~elp~G~NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~y 848 (1210)
T 3h0g_B 769 VYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTY 848 (1210)
T ss_dssp CCCTTTTTSCCSSEEEESSCBCCSSBCTTSTTTTCTTSCSCCEECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEEE
T ss_pred ccccccccccCccccEeecCcCccccchhHHHhCCCcccCccceEEEEeccCCCChhhheeeehhheecCceEEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeccCCCcCccceeeccCCCC------hhhhcccCCCCCcccCcEecCCCcEEEEeecCC--------------CcE
Q 002296 749 TIDLSDDGNKVDRGQKLFRRNKDA------KSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSW 808 (940)
Q Consensus 749 ~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~--------------~~~ 808 (940)
.++.... .....+.|..|+.. ...+++||+||||+||++|++|||||||.+|+. .++
T Consensus 849 ~~~~~~~---~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gDiligK~~p~~~~~~~~~~~~~~~~~rd 925 (1210)
T 3h0g_B 849 TDQEKKI---GMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRD 925 (1210)
T ss_dssp EECCCCC---SSSCCCCCCCCCTTSCCSCCSCCGGGCCTTSSCCTTCCCCTTCCCCCCCCCC-----------CCCCCCC
T ss_pred EEEeeec---CCCceeEEcCCCcchhcccchhhHhhcCCCCCcCCCCEecCCCEEEEEecCCCCCchhhcccccccccce
Confidence 8864221 11235567777543 235799999999999999999999999987642 234
Q ss_pred EEeeccCCCcEEEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeC
Q 002296 809 RTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIIN 888 (940)
Q Consensus 809 ~~~~~~~~e~g~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~N 888 (940)
.+++++++|+|+||+|.++.+++| .+.|+|++|+.|.|++|||||||||||||||+|||+|||||+ +||++||||||
T Consensus 926 ~s~~~~~~e~g~Vd~V~~~~~~~g--~~~vkv~~~~~R~~~~GDK~a~RhGqKGvi~~i~~~edmPf~-~~G~~pDii~N 1002 (1210)
T 3h0g_B 926 VSTPLRSTESGIVDQVMVTTNQEG--LKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFS-AQGIVPDIIIN 1002 (1210)
T ss_dssp CCCCCCTTCCCCCCEEEEEECSSS--SEEEEEEECCCBCCCTTCEEECTTCCCEEEEEEECTTTSCCB-TTTBCCSEECC
T ss_pred eeEEecCCCCeEEEEEEEEEecCC--CeEEEEEEEEecCCCchhhhhcccCCCceeeEEeccccCCcC-CCCCCCeEEEC
Confidence 588999999999999999988764 588999999999999999999999999999999999999999 99999999999
Q ss_pred CCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 889 PHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 889 Ph~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
|||||||||||||+|+++||+|++.|.+.
T Consensus 1003 P~~~PSRMtigq~~E~~~g~~~~~~g~~~ 1031 (1210)
T 3h0g_B 1003 PHAIPSRMTVAHLVECQLSKVSALSGFEG 1031 (1210)
T ss_dssp GGGSTTSCCHHHHHHHHHHHHSSSSCCCC
T ss_pred CCcCCCCccchhhhHhHHHHHHHhcCCce
Confidence 99999999999999999999999999753
|
| >1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... | Back alignment and structure |
|---|
| >4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B | Back alignment and structure |
|---|
| >2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... | Back alignment and structure |
|---|
| >3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* | Back alignment and structure |
|---|
| >3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} | Back alignment and structure |
|---|
| >3lti_A DNA-directed RNA polymerase subunit beta; BBM2, nucleotidyltransferase, transcription, transferase; HET: MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A | Back alignment and structure |
|---|
| >3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli} | Back alignment and structure |
|---|
| >3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} | 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 |
| 940 | ||||
| d1twfb_ | 1207 | e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c | 1e-118 | |
| d1smyc_ | 1119 | e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop | 4e-75 |
| >d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1207 | 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 domain: RBP2 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Score = 387 bits (995), Expect = e-118
Identities = 231/1030 (22%), Positives = 378/1030 (36%), Gaps = 169/1030 (16%)
Query: 15 LVRHHIESFDYMLDEGLSEMFD-------------------------------------- 36
LV ++SF+ +D L ++
Sbjct: 26 LVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMV 85
Query: 37 -------------HCRQAKISYTGKLMADVEFQYLDA-----------------GSPVVR 66
R ++Y+ L DV+ + +A
Sbjct: 86 NESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSES 145
Query: 67 ERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126
+ G+ P+ML+++ C+L A L LKE +MGGYFI+NG E+V + N
Sbjct: 146 GKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNI 205
Query: 127 PMSMVRSSFRDRREGYTDKAVVIRCVRKDQS----SVTLKLYYLLNGSVR-LGFWLQGKE 181
F+ IR + S ++ +KLY S R + L +
Sbjct: 206 VQV-----FKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIK 260
Query: 182 YLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSL 241
+P+ I+ +AL D EI H CYD + + +
Sbjct: 261 QDIPIVIIFRALGIIPDGEILEH--ICYDVNDWQML-----------EMLKPCVEDGFVI 307
Query: 242 TTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHL----NDNNDKFNLLIFML 297
R L IG + G++ E A+ +++ H+ + K L +M+
Sbjct: 308 QDRETALDFIGRRGTAL--GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMI 365
Query: 298 QKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357
+L D+ D + + L G L+ K + + D +
Sbjct: 366 NRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTK-------DIFRYMQRT 418
Query: 358 FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRF 417
+ + N+K + +K I + ++ L TG Q + RAG + R +
Sbjct: 419 VEEAHDFNMKLAI---NAKTITSGLKYALATGNWGEQKK-AMSSRAGVSQVLNRYTYSST 474
Query: 418 ISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYD 477
+S R + G + R+L WG +CP TP+G+ CGL+ +++ + S
Sbjct: 475 LSHLRRTNTPIGRDG-KLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCI-SVGT 532
Query: 478 SRGNIRDFSKMR----------------TSILRVLIGVGMIPSLPKLVKSGPPAVLSVLL 521
I F T + + G+ + +L+++ +
Sbjct: 533 DPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDI 592
Query: 522 DGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPP-- 579
+ V + E E + ++ DD +G+ L + + + T
Sbjct: 593 NPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDI 652
Query: 580 --KFVRPVRNISLPSEESQNIELIGPFEQVFMEIRC-------------------PDGGD 618
F +E I E+ + I P
Sbjct: 653 EGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRI 712
Query: 619 GGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRA 678
+A TH EIHP+ +L V A++ P+ DHNQSPRN YQ M KQ MG + R
Sbjct: 713 RVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRM 772
Query: 679 DQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738
D L PQ P+ T E P G NAIVA+ Y+GY+ ED+MI+N+SS+DRG
Sbjct: 773 DTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRG 832
Query: 739 MCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSV---IDSDGLPYVGQMIHPGE 795
+ +++ G + + +R + H +D DGL G + +
Sbjct: 833 LFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGED 892
Query: 796 PYCSIYDKTT------------NSWRTNSR--KGSESVFVDYVAVDMKNSKNLPQKANIR 841
+ +S R S + +E+ VD V + +++ + +R
Sbjct: 893 VIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVL--VTTNQDGLKFVKVR 950
Query: 842 FRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAML 901
R T+ P IGDKF+SRHGQKG + DMPF+ G+ PDLIINPHA PSRMT+A L
Sbjct: 951 VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA-EGIVPDLIINPHAIPSRMTVAHL 1009
Query: 902 LESVAAKVVA 911
+E + +KV A
Sbjct: 1010 IECLLSKVAA 1019
|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 | 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 | 940 | |||
| d1twfb_ | 1207 | RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta | 100.0 | |
| d1smyc_ | 1119 | RNA-polymerase beta {Thermus thermophilus [TaxId: | 100.0 | |
| d1smyc_ | 1119 | RNA-polymerase beta {Thermus thermophilus [TaxId: | 96.77 |
| >d1twfb_ e.29.1.1 (B:) RBP2 {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 domain: RBP2 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Probab=100.00 E-value=5.7e-186 Score=1768.03 Aligned_cols=849 Identities=27% Similarity=0.404 Sum_probs=700.5
Q ss_pred cCchhhHHHHHHHHHHHHHHHHHHHH---------------------------------------------------HHH
Q 002296 10 EPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------------------DHC 38 (940)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi~~gl~~ii---------------------------------------------------~ec 38 (940)
...++||+|||||||+||++||++|+ +||
T Consensus 21 f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i~kP~~~e~~g~~~~l~P~Ec 100 (1207)
T d1twfb_ 21 FREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEA 100 (1207)
T ss_dssp HHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEEEEEECCSSSCCEECCHHHH
T ss_pred hCCCCccHHHHHHHHHHHHHCHHHHHHhcCCeEeeccccccccccCCCceEEEEEEEEEEcCCeEEcCCCcccccCHHHH
Confidence 34689999999999999999999997 799
Q ss_pred HHcCCeeeeEEEEEEEEEEecC-----------------CCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccc
Q 002296 39 RQAKISYTGKLMADVEFQYLDA-----------------GSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAA 101 (940)
Q Consensus 39 R~r~~TYsa~l~v~i~~~~~~~-----------------~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~ 101 (940)
|+|++||+|+|+|+|++.+... ......++|+||+|||||+|++|||++++++++++.||||+
T Consensus 101 R~r~lTYs~~l~v~i~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv~S~~C~L~~~~~~~l~~~gEc~~ 180 (1207)
T d1twfb_ 101 RLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPF 180 (1207)
T ss_dssp HHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTTSGGGTCCHHHHHHTTCCTT
T ss_pred HhcCCccceEEEEEEEEEEEecccccccccceeecccccccceeeeeEEEEECCEEeCCCcccCCCcCHHHHHHcCCCCC
Confidence 9999999999999998754210 11223567999999999999999999999999999999999
Q ss_pred cCCcEEEEcCceeEEEEEEeccCCccEEEEeccccCCCCcceeeEEEEEeeecCCCc--eEEEEEEEe-CCe--EEEEEE
Q 002296 102 EMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSS--VTLKLYYLL-NGS--VRLGFW 176 (940)
Q Consensus 102 D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s--~~~~l~y~~-~g~--~~l~~~ 176 (940)
|+||||||||+||||++|+...+|+++++.+ ++..++.+++.+||+.+++.. .|+.+.+.. ++. ..+++.
T Consensus 181 D~GGYFIING~EKVIi~Q~r~~~n~~~v~~~-----~~~~~~~~~~~irS~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 255 (1207)
T d1twfb_ 181 DMGGYFIINGSEKVLIAQERSAGNIVQVFKK-----AAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKAT 255 (1207)
T ss_dssp CCCCSEEETTEEEEECEEEEECSSCCEEEEC-----CTTSSEEEEEEEECCCSSSCCCCCEEEEEEESCSSCSSCCEEEE
T ss_pred CCCcEEEECCEEEEEEEEEecCCCeEEEEEc-----CCCCceEEEEEEEEEeCCCCceeEEEEEEEEEcCCccceEEEEE
Confidence 9999999999999999999999999987654 456778899999999876543 445544332 221 234555
Q ss_pred eecccccccHhhHHHhccCCCHHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhcccc
Q 002296 177 LQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQ 256 (940)
Q Consensus 177 ~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr 256 (940)
+.+...+||+++||||||..||+||++.++. +..+..+.+.+...++. ...+.|+++|+.|||++++
T Consensus 256 ~~~~~~~IPl~illrALG~~sD~eI~~~i~~-----------~~~~~~~~~~l~~~~~~--~~~~~t~e~al~yig~~~~ 322 (1207)
T d1twfb_ 256 LPYIKQDIPIVIIFRALGIIPDGEILEHICY-----------DVNDWQMLEMLKPCVED--GFVIQDRETALDFIGRRGT 322 (1207)
T ss_dssp CTTCSSCEEHHHHHHHTTCCSHHHHHHHHCC-----------CTTCHHHHHHHHHHHHH--TTTCCSHHHHHHHHHHTTS
T ss_pred eehhcccchHHHHHHHhCCcchhhhhhhccc-----------CchhhHHHHHHHHHHhh--ccchhhHHHHHHHHHhhcc
Confidence 5555558999999999999999999999972 11222222333222222 2468899999999999876
Q ss_pred ccccCCCCccHHHHHHHHHHhHhccCCCC----CcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHH
Q 002296 257 PVIDGLQSESYYAVAETVIRDYIFVHLND----NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYL 332 (940)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~L~~~ll~Hl~~----~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf 332 (940)
.. ........+.++++|++.+|||++. +..|+.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+|
T Consensus 323 ~~--~~~~~~~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~~~f 400 (1207)
T d1twfb_ 323 AL--GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF 400 (1207)
T ss_dssp CT--TSCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHHHHH
T ss_pred cc--CCCccchHHHHHHHHHhhhccccccccchhhhHHHHHHHHHHHHHHhhhcccCCcchhhhccchhhhHHHHHHHHH
Confidence 43 2345567889999999999999984 34799999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEcccc
Q 002296 333 KEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERL 412 (940)
Q Consensus 333 ~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRl 412 (940)
|+.|+++++.+++.+.+...+ .+.++ +..+ .+++.||++|++||+||||.++.+ .++|++|+||+|+|+
T Consensus 401 r~~~~~~~~~i~~~~~~~~~~-~~~~~------~~~~---~~~~~it~~i~~~~~TGn~~~~~~-~~~~~~G~sq~l~r~ 469 (1207)
T d1twfb_ 401 KTLFKKLTKDIFRYMQRTVEE-AHDFN------MKLA---INAKTITSGLKYALATGNWGEQKK-AMSSRAGVSQVLNRY 469 (1207)
T ss_dssp HHHHHHHHHHHHHHHHSCCC---------------CC---CCTHHHHHHHHHHHHHCCCC----------CCCEEECCCS
T ss_pred HHHHHHHHHHHHhhhcccccc-ccccC------hhhh---hccCcHHHHHHHHHhcCccccccc-ccccccchhhhhhhc
Confidence 999999888877766533221 11111 1111 235689999999999999988765 568999999999999
Q ss_pred chHHHhhhhcccccCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHH
Q 002296 413 NFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSI 492 (940)
Q Consensus 413 n~~~~lSh~Rrv~rg~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i 492 (940)
||+++|||+||||+| +++++|+++||+||||||||+||+|||||++||||||||++|+|+.+.+.. .+
T Consensus 470 n~l~~lSh~Rrv~~~-~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~-----------~~ 537 (1207)
T d1twfb_ 470 TYSSTLSHLRRTNTP-IGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPM-----------PI 537 (1207)
T ss_dssp SHHHHHHHHTEEECC-C------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCH-----------HH
T ss_pred CHHHHHHhhhcccCC-cccccccchhhhcchhhccceeeeeCCCCCcccceeccceeeeeccccccc-----------ee
Confidence 999999999999985 779999999999999999999999999999999999999999999876654 47
Q ss_pred HHHHHhCCCeecCCccccCCCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCce
Q 002296 493 LRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGL 572 (940)
Q Consensus 493 ~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i 572 (940)
.++|..+|+.+.. ........+.++||+||.|+|++ .++..+++.+|.+|+.| .++.++++.+. ....++
T Consensus 538 ~~~l~~~g~~~~~-~~~~~~~~~~~~V~~nG~~~G~~--~~~~~l~~~lr~~R~~g--~i~~~~s~~~~-----~~~~~i 607 (1207)
T d1twfb_ 538 ITFLSEWGMEPLE-DYVPHQSPDATRVFVNGVWHGVH--RNPARLMETLRTLRRKG--DINPEVSMIRD-----IREKEL 607 (1207)
T ss_dssp HHHHHHTTCEEGG-GCCGGGCTTCEEEEETTEEEEEE--SCHHHHHHHHHHHHHHT--SSCTTCEEEEE-----TTTTEE
T ss_pred eEEeeccCcccce-eeeeccccccceeeeeeeEEEEE--cchheeehheeeeeecc--Cccceeeeeee-----ccccce
Confidence 7888999998763 23333345678999999999997 46789999999999998 56766666433 345789
Q ss_pred EEecCCCceeceEEeccCCCC----------------------------------------CCCceeeecccceeeeeee
Q 002296 573 YLFTSPPKFVRPVRNISLPSE----------------------------------------ESQNIELIGPFEQVFMEIR 612 (940)
Q Consensus 573 ~i~~d~gR~~RPv~~~~~~~~----------------------------------------~~~~iE~i~~~Eq~~~~Ia 612 (940)
+|+||+||++|||+.+.++.. ..|.|||||++||+++.||
T Consensus 608 ~i~td~Gr~~rPlfi~~nd~~~~~~~~~mqrq~v~~l~~~e~~~v~~~~e~~~~~~~~~~~~~g~ieyid~~E~~~~~Ia 687 (1207)
T d1twfb_ 608 KIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIA 687 (1207)
T ss_dssp EEECCSCCEEEEEEEEECCCTTSSCEESCCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTTCCEE
T ss_pred EEEecCccccCCceeecchhhhcccceeeeHhhHhhhhccccccccccccchhhccccccccCCceeeecchhcceEEEE
Confidence 999999999999987765421 1467999999999999999
Q ss_pred cCCCCCCCCC-------------------CCccceecccCCCccccceeecccCCCCCCCccchhhccccccccccccee
Q 002296 613 CPDGGDGGRR-------------------NAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQA 673 (940)
Q Consensus 613 ~~~~~~~~~~-------------------~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~~~n 673 (940)
+.++++.... ....+||+||+|+.|||++|++|||+||||||||+|||||+|||||++++|
T Consensus 688 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~th~Ei~p~~ilg~~as~iPf~~hNqSpRn~yq~qm~KQa~G~~~~~ 767 (1207)
T d1twfb_ 688 MQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTN 767 (1207)
T ss_dssp SSGGGGCC---------CCCTTSCCCCCCCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHHHGGGBCBCSCTT
T ss_pred ecccccccccccccccccccchhheeeecccccccccccccceEEeeecceEEecccccccceeecccCCcccCCccccc
Confidence 9998875311 013489999999999999999999999999999999999999999999999
Q ss_pred EEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEEEEEee
Q 002296 674 LKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLS 753 (940)
Q Consensus 674 ~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~ 753 (940)
+..|.|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+||||||+++|++|.+++.
T Consensus 768 ~~~r~D~~~~~l~~pQ~Plv~t~~~~~~~~~e~p~G~N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~ 847 (1207)
T d1twfb_ 768 YNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK 847 (1207)
T ss_dssp TTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCC
T ss_pred cceeccccceeEecCCCceeeccchhhhhhhcccchhceEEEEEeccCcccccccccchhhhhhcccceeeeEEEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988754
Q ss_pred ccCCCcCccceeeccCC------CChhhhcccCCCCCcccCcEecCCCcEEEEeecCCC--------------cEEEeec
Q 002296 754 DDGNKVDRGQKLFRRNK------DAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTN--------------SWRTNSR 813 (940)
Q Consensus 754 ~~~~~~~~~~~~~~~~~------~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~~--------------~~~~~~~ 813 (940)
.... ...+.|..|. .....+++||+||+|++|++|++||+|+||+.+... ++.++.+
T Consensus 848 ~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~~~~~~~~~~s~~~ 924 (1207)
T d1twfb_ 848 KYGM---SITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPL 924 (1207)
T ss_dssp CSCT---TCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC-------------CCBBCCEEC
T ss_pred cccc---cccccccccccccccccchhhhhcccccccccccccccCCceeeeeeeccCCchhhhhhccccccccceeEEc
Confidence 3221 2334444442 223457899999999999999999999999776532 2447788
Q ss_pred cCCCcEEEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCcc
Q 002296 814 KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFP 893 (940)
Q Consensus 814 ~~~e~g~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~P 893 (940)
+.+++|+||+|.++.+.+ +.+.++|++|+.|+|+||||||||||||||||+|||+|||||| +||++|||||||||||
T Consensus 925 ~~~~~g~V~~v~~~~~~~--~~~~~kv~i~~~R~p~iGDKfasRhGqKGv~s~i~p~eDMPf~-~dG~~pDiI~NP~g~P 1001 (1207)
T d1twfb_ 925 RSTENGIVDQVLVTTNQD--GLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFT-AEGIVPDLIINPHAIP 1001 (1207)
T ss_dssp CTTCCEEEEEEEEEECSS--SCEEEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTSCEE-TTSCCCSEEECGGGST
T ss_pred cCCCCeEEEEEEEeeccc--ccceeeEEEEEEeccchhhhhhhccCCcceeeeeechhhCCcC-CCCCCccEEECCCcCc
Confidence 889999999999998765 4689999999999999999999999999999999999999999 9999999999999999
Q ss_pred ccccHHHHHHHHHHHHHhhchhHH
Q 002296 894 SRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 894 SRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
||||||||+|+++|||||++|.++
T Consensus 1002 SRMtiGql~E~~~gk~~~~~g~~~ 1025 (1207)
T d1twfb_ 1002 SRMTVAHLIECLLSKVAALSGNEG 1025 (1207)
T ss_dssp TTTCHHHHHHHHHHHHHHHHCSCE
T ss_pred ccCcHHHHHHHHHHHHHHhcCCcc
Confidence 999999999999999999999987
|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|