Citrus Sinensis ID: 001179
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 | 1131 | 2.2.26 [Sep-21-2011] | |||||||
| Q9P7X8 | 1174 | Probable DNA-directed RNA | yes | no | 0.894 | 0.862 | 0.432 | 0.0 | |
| Q75DS1 | 1196 | DNA-directed RNA polymera | yes | no | 0.911 | 0.862 | 0.444 | 0.0 | |
| Q9H9Y6 | 1135 | DNA-directed RNA polymera | yes | no | 0.931 | 0.927 | 0.427 | 0.0 | |
| P70700 | 1135 | DNA-directed RNA polymera | yes | no | 0.924 | 0.921 | 0.427 | 0.0 | |
| Q54BM1 | 1130 | DNA-directed RNA polymera | yes | no | 0.939 | 0.940 | 0.418 | 0.0 | |
| Q5REE8 | 1136 | DNA-directed RNA polymera | yes | no | 0.931 | 0.926 | 0.427 | 0.0 | |
| O74633 | 1234 | DNA-directed RNA polymera | N/A | no | 0.910 | 0.834 | 0.429 | 0.0 | |
| P22138 | 1203 | DNA-directed RNA polymera | yes | no | 0.916 | 0.862 | 0.434 | 0.0 | |
| O54888 | 1135 | DNA-directed RNA polymera | yes | no | 0.911 | 0.908 | 0.406 | 0.0 | |
| P28365 | 1166 | DNA-directed RNA polymera | N/A | no | 0.945 | 0.916 | 0.395 | 0.0 |
| >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 = 916 bits (2368), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 495/1144 (43%), Positives = 697/1144 (60%), Gaps = 132/1144 (11%)
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 SVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLY 963
S+A K G+ HG D+TPF S E ++ D GE L G+NYHG E +Y
Sbjct: 951 SLAGKAGACHGLAQDSTPFIYS-----------EQQTAADYFGEQLVKAGYNYHGNEPMY 999
Query: 964 SGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEM 1023
SG+ G E+ +I+IG VYYQRLRHMVSDKFQVR+TG + +TRQP+KGRKR GGIRFGEM
Sbjct: 1000 SGITGQEMKADIYIGVVYYQRLRHMVSDKFQVRTTGPIHNLTRQPVKGRKRAGGIRFGEM 1059
Query: 1024 ERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARA 1083
ERD+++ HG ++L+ DRL CSDY + VC CGS+++ + + G+ A
Sbjct: 1060 ERDAVIGHGTSFLMQDRLMNCSDYAQSWVCRDCGSIISIM-------STISMNGVGSA-- 1110
Query: 1084 PKKVTCHAC-QTSKGMET---------------------VAMPYVFRYLAAELAAMNIKI 1121
+V C +C + + G+E +A+P VF YL AEL AMNIK+
Sbjct: 1111 -SEVRCRSCAKPALGLEDTSDIWQDGSGKKFVGGTNTTLIALPSVFNYLTAELTAMNIKM 1169
Query: 1122 TLQL 1125
L++
Sbjct: 1170 MLEV 1173
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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|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|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|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|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|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|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 | 1131 | ||||||
| 359487166 | 1142 | PREDICTED: DNA-directed RNA polymerase I | 0.989 | 0.979 | 0.781 | 0.0 | |
| 255578257 | 1159 | DNA-directed RNA polymerase I subunit, p | 0.989 | 0.965 | 0.773 | 0.0 | |
| 356548837 | 1175 | PREDICTED: DNA-directed RNA polymerase I | 0.988 | 0.951 | 0.745 | 0.0 | |
| 449458081 | 1173 | PREDICTED: DNA-directed RNA polymerase I | 0.992 | 0.957 | 0.735 | 0.0 | |
| 296087844 | 1113 | unnamed protein product [Vitis vinifera] | 0.943 | 0.958 | 0.783 | 0.0 | |
| 356563684 | 1175 | PREDICTED: DNA-directed RNA polymerase I | 0.990 | 0.953 | 0.745 | 0.0 | |
| 224053240 | 1109 | predicted protein [Populus trichocarpa] | 0.972 | 0.991 | 0.741 | 0.0 | |
| 297851416 | 1188 | hypothetical protein ARALYDRAFT_313639 [ | 0.985 | 0.938 | 0.698 | 0.0 | |
| 79356046 | 1178 | nuclear RNA polymerase A2 [Arabidopsis t | 0.981 | 0.942 | 0.698 | 0.0 | |
| 12324162 | 1114 | DNA-directed RNA polymerase subunit, put | 0.964 | 0.979 | 0.714 | 0.0 |
| >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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Score = 1887 bits (4889), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 892/1141 (78%), Positives = 1007/1141 (88%), Gaps = 22/1141 (1%)
Query: 8 DFEPLRELVRHHIESFDYMLDEGLSEMFD-----------------HCRQAKISYTGKLM 50
D+EPLREL +HHI+SFD++++ GL + CRQAKISY+GKL+
Sbjct: 7 DYEPLRELFQHHIDSFDHLVEFGLETLLMSVKPRSARTMRDALYPFECRQAKISYSGKLL 66
Query: 51 ADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILN 110
ADV FQY +RE+FN GQFP+MLK++ CHL+GAD QKLVS KEE++EMGGYFILN
Sbjct: 67 ADVCFQY--GNGVAIREKFNLGQFPIMLKSKLCHLRGADPQKLVSCKEESSEMGGYFILN 124
Query: 111 GLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGS 170
GLERV R +ILPK+NYPMSMVR+SFRDRREGYTDKAVVIRCVR+DQS+VT+KLYYL NGS
Sbjct: 125 GLERVVRLLILPKRNYPMSMVRNSFRDRREGYTDKAVVIRCVREDQSAVTVKLYYLRNGS 184
Query: 171 VRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVK 230
RLGFW+QG+EYLLPVG+VLKAL+DT D EI+ LTCCY EKY+ KGAVG+ LV ERVK
Sbjct: 185 ARLGFWIQGREYLLPVGVVLKALIDTTDHEIYESLTCCYSEKYEGGKGAVGTQLVGERVK 244
Query: 231 IILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKF 290
IIL EV+DLSL TR QCLQHIGEHFQ V+DGL++ESY VA+ V+R+YIFVHL++N DKF
Sbjct: 245 IILDEVRDLSLFTRHQCLQHIGEHFQLVMDGLENESYSIVADAVLREYIFVHLDNNYDKF 304
Query: 291 NLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDE 350
NLLIFM+QKLFSL+D TSV DNPD LQNQE+LLPGHLITIYLKEKL++WL K ++L+QDE
Sbjct: 305 NLLIFMVQKLFSLIDQTSVPDNPDVLQNQEVLLPGHLITIYLKEKLQEWLYKARRLLQDE 364
Query: 351 IENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAE 410
I N K F+F +LA++KKVM+KNPS+QI ++E MLKTGRL TQ+GLDLQQRAG TVQAE
Sbjct: 365 I-NKRKNFEFSSLAHVKKVMDKNPSRQISLAVENMLKTGRLVTQSGLDLQQRAGMTVQAE 423
Query: 411 RLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTC 470
RLNFLRF+S FRAVHRGASFAGLRTTSVRKLLPE+WGFLCPVHTPDGEPCGLLNHM STC
Sbjct: 424 RLNFLRFLSHFRAVHRGASFAGLRTTSVRKLLPEAWGFLCPVHTPDGEPCGLLNHMASTC 483
Query: 471 RVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIP 530
R+ SY+DSRGN RDF K+R SIL VLIG+GM P+LPKLV++GPP VLSV+LDGRVVG IP
Sbjct: 484 RITSYFDSRGNTRDFFKIRMSILSVLIGIGMTPALPKLVQAGPPEVLSVILDGRVVGSIP 543
Query: 531 SSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL 590
SSE+E V HLRRLKVSA SVIPDDLEVGY+PLS+GGAYPGLYLFTSP +FVRPVRNIS+
Sbjct: 544 SSEVETAVNHLRRLKVSAISVIPDDLEVGYIPLSMGGAYPGLYLFTSPSRFVRPVRNISI 603
Query: 591 PSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDH 650
PSEE +IELIGPFEQV+MEIRCPDG DGGRRN FPATHEEIHPTGMLSVVA+LTP+SDH
Sbjct: 604 PSEEGHDIELIGPFEQVYMEIRCPDGSDGGRRNIFPATHEEIHPTGMLSVVASLTPWSDH 663
Query: 651 NQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGT 710
NQSPRNMYQCQM KQTM FS QA+ RADQKLYHLQTPQTPIVRT+ Y KY +DE+PTGT
Sbjct: 664 NQSPRNMYQCQMGKQTMAFSSQAINCRADQKLYHLQTPQTPIVRTSAYVKYSMDEFPTGT 723
Query: 711 NAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNK 770
NAIVAVLAY+GYDMEDAMILNKSSVDRG+CHGQIYQTETIDLSD+ NK DRGQ++FRR+
Sbjct: 724 NAIVAVLAYSGYDMEDAMILNKSSVDRGLCHGQIYQTETIDLSDENNKSDRGQRMFRRSN 783
Query: 771 DAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKN 830
KS +S+IDSDGLPYVGQMI+P EPYCSIY++ T+S R KGSE V VDYVA+D KN
Sbjct: 784 VDKSANSLIDSDGLPYVGQMINPNEPYCSIYNEVTSSTRATKLKGSEPVIVDYVALDAKN 843
Query: 831 SKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPH 890
K+ PQK NIRFR RNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPH
Sbjct: 844 KKH-PQKVNIRFRRPRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPH 902
Query: 891 AFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLR 950
AFPSRMTIAMLLESVAAKGGSLHGKF+DATPF++S++K NG+ G+ ES SLVDELG ML
Sbjct: 903 AFPSRMTIAMLLESVAAKGGSLHGKFVDATPFSDSLRKANGEAGS-ESSSLVDELGSMLT 961
Query: 951 TCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIK 1010
+ GFNYHGVEVLYSG YGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGT+DQ+TRQPIK
Sbjct: 962 SYGFNYHGVEVLYSGFYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTVDQVTRQPIK 1021
Query: 1011 GRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKR 1070
GRKRGGGIRFGEMERDS+LAHGAAYLLHDRLHTCSD+H+ADVCSLCGS+LT + I PQKR
Sbjct: 1022 GRKRGGGIRFGEMERDSMLAHGAAYLLHDRLHTCSDHHIADVCSLCGSILTTSIIQPQKR 1081
Query: 1071 AIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGDGAT 1130
A+REIGGLPP RAPKKVTCHACQTSKGMETV+MPY+FR+LAAELAAMNIK+TLQL +GA
Sbjct: 1082 AVREIGGLPPGRAPKKVTCHACQTSKGMETVSMPYIFRFLAAELAAMNIKMTLQLSNGAG 1141
Query: 1131 A 1131
A
Sbjct: 1142 A 1142
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Source: Vitis vinifera Species: Vitis vinifera Genus: Vitis Family: Vitaceae Order: Vitales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >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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| >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|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|296087844|emb|CBI35100.3| unnamed protein product [Vitis vinifera] | 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|224053240|ref|XP_002297732.1| predicted protein [Populus trichocarpa] gi|222844990|gb|EEE82537.1| predicted protein [Populus trichocarpa] | Back alignment and taxonomy information |
|---|
| >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 |
|---|
| >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 | 1131 | ||||||
| TAIR|locus:2019272 | 1178 | NRPA2 "nuclear RNA polymerase | 0.954 | 0.916 | 0.719 | 0.0 | |
| ZFIN|ZDB-GENE-040426-1598 | 1132 | polr1b "polymerase (RNA) I pol | 0.462 | 0.462 | 0.494 | 3.5e-235 | |
| UNIPROTKB|E2REX8 | 1135 | POLR1B "DNA-directed RNA polym | 0.465 | 0.464 | 0.490 | 4e-234 | |
| UNIPROTKB|A6QLS0 | 1135 | POLR1B "DNA-directed RNA polym | 0.465 | 0.464 | 0.490 | 5.8e-233 | |
| UNIPROTKB|F5GZX4 | 1173 | POLR1B "DNA-directed RNA polym | 0.465 | 0.449 | 0.488 | 7.3e-233 | |
| UNIPROTKB|Q9H9Y6 | 1135 | POLR1B "DNA-directed RNA polym | 0.465 | 0.464 | 0.488 | 7.3e-233 | |
| ASPGD|ASPL0000012082 | 1231 | AN3933 [Emericella nidulans (t | 0.864 | 0.794 | 0.448 | 5.8e-231 | |
| UNIPROTKB|F5H643 | 924 | POLR1B "DNA-directed RNA polym | 0.465 | 0.570 | 0.488 | 6.1e-207 | |
| RGD|620822 | 1135 | Polr1b "polymerase (RNA) I pol | 0.372 | 0.370 | 0.508 | 2.7e-203 | |
| UNIPROTKB|O54888 | 1135 | Polr1b "DNA-directed RNA polym | 0.372 | 0.370 | 0.508 | 2.7e-203 |
| TAIR|locus:2019272 NRPA2 "nuclear RNA polymerase A2" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 4184 (1477.9 bits), Expect = 0., Sum P(2) = 0.
Identities = 786/1093 (71%), Positives = 932/1093 (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 VTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDE 937
VTGMRPDLIINPHAFPSRMTIAMLLES+AAKGGSLHGKF+DATPF ++VKKTNG+ +E
Sbjct: 923 VTGMRPDLIINPHAFPSRMTIAMLLESIAAKGGSLHGKFVDATPFRDAVKKTNGE---EE 979
Query: 938 SKS--LVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQV 995
SKS LVD+LG ML+ GFN++G E LYSG G EL CEIF+GPVYYQRLRHMVSDKFQV
Sbjct: 980 SKSSLLVDDLGSMLKEKGFNHYGTETLYSGYLGVELKCEIFMGPVYYQRLRHMVSDKFQV 1039
Query: 996 RSTGTMDQITRQPXXXXXXXXXXXFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSL 1055
RSTG +DQ+T QP FGEMERDSLLAHGA+YLLHDRLHT SD+H+ADVCSL
Sbjct: 1040 RSTGQVDQLTHQPIKGRKRGGGIRFGEMERDSLLAHGASYLLHDRLHTSSDHHIADVCSL 1099
Query: 1056 CGSVLTATFIH-PQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAEL 1114
CGS+LT++ ++ QK+ I+EIG LPP R PKKVTC++C+TSKGMETVAMPYVFRYLAAEL
Sbjct: 1100 CGSLLTSSVVNVQQKKLIQEIGKLPPGRTPKKVTCYSCKTSKGMETVAMPYVFRYLAAEL 1159
Query: 1115 AAMNIKITLQLGD 1127
A+MNIK+TLQL D
Sbjct: 1160 ASMNIKMTLQLSD 1172
|
|
| ZFIN|ZDB-GENE-040426-1598 polr1b "polymerase (RNA) I polypeptide B" [Danio rerio (taxid:7955)] | 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|A6QLS0 POLR1B "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] | 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 |
|---|
| ASPGD|ASPL0000012082 AN3933 [Emericella nidulans (taxid:162425)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|F5H643 POLR1B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] | 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 |
|---|
Prediction of Enzyme Commission (EC) Number
EC Number Prediction by Annotation Transfer from SWISS-PROT Entries
Original result of BLAST against SWISS-PROT
| ID | Name | Annotated EC number | Identity | Query coverage | Hit coverage | RBH(Q2H) | RBH(H2Q) |
| Q5REE8 | RPA2_PONAB | 2, ., 7, ., 7, ., 6 | 0.4277 | 0.9310 | 0.9269 | yes | no |
| P22138 | RPA2_YEAST | 2, ., 7, ., 7, ., 6 | 0.4345 | 0.9168 | 0.8620 | yes | no |
| O54888 | RPA2_RAT | 2, ., 7, ., 7, ., 6 | 0.4065 | 0.9115 | 0.9083 | yes | no |
| Q9H9Y6 | RPA2_HUMAN | 2, ., 7, ., 7, ., 6 | 0.4272 | 0.9310 | 0.9277 | yes | no |
| Q9P7X8 | RPA2_SCHPO | 2, ., 7, ., 7, ., 6 | 0.4326 | 0.8947 | 0.8620 | yes | no |
| P70700 | RPA2_MOUSE | 2, ., 7, ., 7, ., 6 | 0.4272 | 0.9248 | 0.9215 | yes | no |
| Q54BM1 | RPA2_DICDI | 2, ., 7, ., 7, ., 6 | 0.4186 | 0.9398 | 0.9407 | yes | no |
| Q75DS1 | RPA2_ASHGO | 2, ., 7, ., 7, ., 6 | 0.4443 | 0.9115 | 0.8620 | yes | no |
| P20028 | RPA2_DROME | 2, ., 7, ., 7, ., 6 | 0.3916 | 0.8992 | 0.9007 | yes | no |
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 | 0.921 |
| 4th Layer | 2.7.7.6 | 0.914 |
Prediction of Functionally Associated Proteins
Functionally Associated Proteins Detected by STRING
Original result from the STRING server
 |
 |
 |
 |
 |
 |
 |
 |
 |
|||
 | gw1.I.7000.1 | hypothetical protein (1109 aa) | |||||||||
(Populus trichocarpa) | |||||||||||
 | eugene3.00060510 | • | • | • | • | • | • | 0.911 | |||
 | gw1.X.1387.1 | • | • | 0.910 | |||||||
 | estExt_Genewise1_v1.C_LG_XIV2383 | • | • | 0.910 | |||||||
 | estExt_Genewise1_v1.C_LG_III0729 | • | • | 0.910 | |||||||
 | gw1.I.8101.1 | • | • | 0.910 | |||||||
 | fgenesh4_pm.C_LG_VIII000317 | • | • | 0.910 | |||||||
 | gw1.I.2477.1 | • | • | 0.908 | |||||||
 | eugene3.00400106 | • | • | 0.902 | |||||||
 | fgenesh4_pg.C_LG_XII000913 | • | • | 0.902 | |||||||
 | gw1.II.1445.1 | • | • | 0.901 |
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 | 1131 | |||
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 0.0 | |
| COG0085 | 1060 | COG0085, RpoB, DNA-directed RNA polymerase, beta s | 0.0 | |
| PRK08565 | 1103 | PRK08565, PRK08565, DNA-directed RNA polymerase su | 1e-157 | |
| pfam00562 | 373 | pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do | 1e-149 | |
| TIGR03670 | 599 | TIGR03670, rpoB_arch, DNA-directed RNA polymerase | 1e-129 | |
| PRK07225 | 605 | PRK07225, PRK07225, DNA-directed RNA polymerase su | 1e-128 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 9e-50 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 2e-35 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 3e-32 | |
| pfam04563 | 394 | pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub | 3e-30 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 1e-26 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 6e-25 | |
| PRK09606 | 494 | PRK09606, PRK09606, DNA-directed RNA polymerase su | 1e-22 | |
| pfam04565 | 68 | pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do | 4e-22 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 4e-21 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 7e-21 | |
| pfam04560 | 78 | pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, do | 3e-17 | |
| pfam06883 | 58 | pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 | 1e-15 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 2e-13 | |
| pfam04561 | 185 | pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do | 5e-11 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 1e-08 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 7e-08 |
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | Back alignment and domain information |
|---|
Score = 636 bits (1642), Expect = 0.0
Identities = 213/512 (41%), Positives = 275/512 (53%), Gaps = 56/512 (10%)
Query: 628 THEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQT 687
TH EI P+ +LSV A+L P+ +HNQSPRN+YQ M KQ +G ++R D KLY L
Sbjct: 396 THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLY 455
Query: 688 PQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747
PQ P+V T E P G NAIVAV++Y+GY+ EDA+I+NKSSVDRG Y+
Sbjct: 456 PQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKK 515
Query: 748 ETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNS 807
I+L N + + N + +D DG+ G + PG+ +
Sbjct: 516 YEIELRKTKNGPEEITRGDIPNVS-EEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
Query: 808 WRTNSR--------------KGSESVFVDYVAV-DMKNSKNLPQKANIRFRHTRNPIIGD 852
T G E VD V + + + + + R R P IGD
Sbjct: 575 ESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGD 634
Query: 853 KFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSL 912
KF+SRHGQKGV S++ P DMPF+ G+ PD+I+NPH FPSRMTI LLES+ K G+L
Sbjct: 635 KFASRHGQKGVISKILPQEDMPFT-EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAL 693
Query: 913 HGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELT 972
GKF DATPF D ++ +++ E+L G NY+G EVLY G G L
Sbjct: 694 LGKFGDATPF-------------DGAE--EEDISELLGEAGLNYYGKEVLYDGRTGEPLE 738
Query: 973 CEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHG 1032
IF+GPVYYQRL+HMV DK RSTG +TRQP+KGR RGGG RFGEMERD+L+AHG
Sbjct: 739 APIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHG 798
Query: 1033 AAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHAC 1092
AAYLL +RL SD VA VC CG +L+A C C
Sbjct: 799 AAYLLQERLTIKSDDVVARVCVKCGIILSANL------------------------CRLC 834
Query: 1093 QTSKGMETVAMPYVFRYLAAELAAMNIKITLQ 1124
+ + V +PY F+ L EL +MNI L+
Sbjct: 835 KKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation. Length = 866 |
| >gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional | 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|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|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|233685 TIGR02013, rpoB, DNA-directed 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|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed | 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|214330 CHL00001, rpoB, 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|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7 | 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|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; 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|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 |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1131 | |||
| KOG0216 | 1111 | consensus RNA polymerase I, second largest subunit | 100.0 | |
| PRK08565 | 1103 | DNA-directed RNA polymerase subunit B; Provisional | 100.0 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 100.0 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 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 | |
| PF00562 | 386 | RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int | 100.0 | |
| PRK09606 | 494 | DNA-directed RNA polymerase subunit B''; Validated | 100.0 | |
| PF04563 | 203 | RNA_pol_Rpb2_1: RNA polymerase beta subunit; Inter | 100.0 | |
| PF04560 | 81 | RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; Int | 99.96 | |
| PF04565 | 68 | RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; Int | 99.93 | |
| 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 | 99.42 | |
| PF06883 | 58 | RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do | 99.04 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 98.84 | |
| PF04567 | 48 | RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int | 98.43 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 97.79 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 97.7 | |
| PHA03394 | 865 | lef-8 DNA-directed RNA polymerase subunit beta-lik | 94.23 |
| >KOG0216 consensus RNA polymerase I, second largest subunit [Transcription] | Back alignment and domain information |
|---|
Probab=100.00 E-value=4.2e-285 Score=2421.88 Aligned_cols=1062 Identities=54% Similarity=0.924 Sum_probs=998.7
Q ss_pred CCCCcCccccchhhHHHHHHHHHHHHHHhHHHHH--------------------------------------------HH
Q 001179 2 ARKKSADFEPLRELVRHHIESFDYMLDEGLSEMF--------------------------------------------DH 37 (1131)
Q Consensus 2 ~~~~~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii--------------------------------------------~e 37 (1131)
|+++..+++.++.++++|++|||...+.||...- .|
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 4566677889999999999999999998876654 99
Q ss_pred HHHcCCeeeEEEEEEEEEEEecCCCceEEEEEeecccceeeccCcccCCCCChHHHHhhccccccCCcEEEEcCceeEEE
Q 001179 38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFR 117 (1131)
Q Consensus 38 cR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~D~GGYFIING~EKVIr 117 (1131)
||+|.+||++.+.|+|.|.+| ++.+......+|.+||||+|++|||.+++++||++++|++.|+||||||||+|||||
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 999999999999999999998 777778889999999999999999999999999999999999999999999999999
Q ss_pred EEEeccCCceEEEEeccccCCCcceeeEEEEEeeeecCCCceEEEEEEEeCCeEEEEEEEecccccccHhhHHHhccCCC
Q 001179 118 SVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTN 197 (1131)
Q Consensus 118 ~qi~~~~N~~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~~~~l~~~~~g~~~l~~~~~k~~~~IPi~ilLkALg~~s 197 (1131)
++|+++||+|++++|++|++|+++|++|+++||||++|+++.+++|||+.||.+.++|.++|.++.+|++++||||-..|
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 HHHHHHhhccccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcccccccCCCCccHHHHHHHHHHh
Q 001179 198 DLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277 (1131)
Q Consensus 198 D~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~r~~~~~~~~~~~~e~g~~~L~~ 277 (1131)
|+|||+.|+ +++..++|+.++++.||+++.+.+++||++||.|||++||+++..-+++++.|+|+++|++
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 5777899999999999999999999999999999999999776655559999999999999
Q ss_pred hhcccCCCchhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Q 001179 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357 (1131)
Q Consensus 278 ~ll~Hl~~~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~l~~~~~~~~~~ 357 (1131)
++++||+++.+||.+|++|++||++++.|++.+||+|+..|||++++|+|++..|+|+++++++.++.++++.+.+.+.+
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 99999999999999999999999999999999999999999999999999999999999999999999999999876667
Q ss_pred cccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhccccccCCccccccccc
Q 001179 358 FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS 437 (1131)
Q Consensus 358 ~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~ 437 (1131)
.++.+..++.+++.+++ ..|+++|++||||||++++++++++|++|++++|||+||+|||||||.||||++|++|++|+
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 77777888888998877 49999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhHHHHHHHhcCceecCcccccCCCCCce
Q 001179 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517 (1131)
Q Consensus 438 ~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~ 517 (1131)
+|||.|++||||||||||||+||||+||||..|+|++..++.+ .|.++|.++||.|... .... ....|
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 9999999999999999999999999999999999999888763 5889999999998642 2222 23479
Q ss_pred EEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCeEEEEcCCCcceeeEEEecCCCCCCcc
Q 001179 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN 597 (1131)
Q Consensus 518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~td~GRl~RPv~~~~~~~~~~g~ 597 (1131)
+|++||+++||++.+.+..+++.||++|......||.++||.||+.+.+++||++||+|++||++|||.++..+ .
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 eeeecccceeeeeeecCCCCCCCCCCCCceeEEeecCCCcccceeccccCCCCCCCccccccccccccccccccceEEEe
Q 001179 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFR 677 (1131)
Q Consensus 598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~~n~~~R 677 (1131)
+||||++||+++.||+.++++.+.. +||.|++|+.+||++|+||||+|||||||||||||||||+||+|.++++.|
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 cccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEEEEEEecccCC
Q 001179 678 ADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN 757 (1131)
Q Consensus 678 ~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~~~~~~ 757 (1131)
.|+|+|+|++||.|+|++..|+.+++|++|.|+||+|||+|||||||||||||||+|+||||+++++||++.+++.+...
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 Ccccccccccc-CCCChhhhcccCCCCCcccCcEEcCCCCeeEEeecCCCcEEeeecCCCcceEEEEEEEeccCCCCCCe
Q 001179 758 KVDRGQKLFRR-NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQ 836 (1131)
Q Consensus 758 ~~~~~~~~f~~-~~~~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~~~~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~ 836 (1131)
+ +..|.. |...+ ..+||+||||.+|+++..||++++.++..+++.+..+|++.|+|+||.|++..++.++..+
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 334553 33333 6899999999999999999999999999999999999999999999999999998876558
Q ss_pred EEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCCCCccchhHhHHHHHhhhccccCce
Q 001179 837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKF 916 (1131)
Q Consensus 837 ~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~ 916 (1131)
.+.|++|.+|+|.||||||||||||||||+.||.+||||| ++|++|||||||||||||||||||+|+||||+||++|..
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 eccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcEEEeeCCCCcEeeeeeeeeceeEEeeccccccceeee
Q 001179 917 MDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVR 996 (1131)
Q Consensus 917 ~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R 996 (1131)
+|+|||..+ ++++++|+||++|+++||||||+|+||||.+|++|+|+||+|+||||||+|||.||+|||
T Consensus 924 ~Datpf~~~-----------E~~t~~dyfg~~L~~~GyNyyGnE~~YSGv~G~e~~adIf~GvVyYQRLrHMv~DKfQVR 992 (1111)
T KOG0216|consen 924 QDATPFIFS-----------EENTAIDYFGEMLKKAGYNYYGNEPMYSGVDGREMRADIFFGVVYYQRLRHMVSDKFQVR 992 (1111)
T ss_pred ccCCceeec-----------CcccHHHHHHHHHHHcCcCccCCcccccccccceeeeeEEEeehhHHHHHHHhcceeeee
Confidence 999999877 777899999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccceeccccccccccccccccccccccccC
Q 001179 997 STGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIG 1076 (1131)
Q Consensus 997 ~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~ 1076 (1131)
+|||++.+|+||++||||+||+||||||||||||||||++|||||++|||.+.++||..||++++..- .....
T Consensus 993 stG~v~~~T~QPvkGRkr~GGiRfGEMERDali~HGtsfllqDRL~~~SD~~~a~vC~~cgsil~~~~-----~l~~~-- 1065 (1111)
T KOG0216|consen 993 STGPVDSLTHQPVKGRKRGGGIRFGEMERDALIAHGTSFLLQDRLLNSSDYTVAEVCRTCGSILSTQQ-----KLIKE-- 1065 (1111)
T ss_pred eccCccccccCCccCcccCCCccccchhhhhHhhcchHhhhhhhhccCcchhHHHHHHHhhhhhhhhh-----hhhcc--
Confidence 99999999999999999999999999999999999999999999999999999999999999998630 00000
Q ss_pred CCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeEEEec
Q 001179 1077 GLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLG 1126 (1131)
Q Consensus 1077 ~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~~~ 1126 (1131)
.....+.-.|+.|+ +..+..|+|||+||||..||+||||+++++++
T Consensus 1066 ---~~~~~~~~~C~~c~-~~~~~~v~~P~vfkYL~aEL~amnIk~~l~l~ 1111 (1111)
T KOG0216|consen 1066 ---PGGSTSTVTCRSCD-GKGVTTVAMPYVFKYLTAELAAMNIKMRLDLE 1111 (1111)
T ss_pred ---cCCCCCceeEEecC-CCceEEEEccHHHHHHHHHHhhCceeEEeccC
Confidence 11233456899995 77899999999999999999999999999875
|
|
| >PRK08565 DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
| >KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >KOG0214 consensus RNA polymerase II, 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 |
|---|
| >PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
| >PRK09606 DNA-directed RNA polymerase subunit B''; Validated | 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 |
|---|
| >PF04560 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; InterPro: IPR007641 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 |
|---|
| >KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] | 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 |
|---|
| >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 |
|---|
| >PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional | 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 | 1131 | ||||
| 2waq_B | 1131 | The Complete Structure Of The Archaeal 13-Subunit D | 9e-89 | ||
| 2pmz_B | 1124 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 2e-88 | ||
| 3h0g_B | 1210 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 2e-81 | ||
| 1i3q_B | 1224 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 8e-80 | ||
| 1iw7_C | 1119 | Crystal Structure Of The Rna Polymerase Holoenzyme | 3e-23 | ||
| 1hqm_C | 1119 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 2e-22 | ||
| 1ynj_C | 1119 | Taq Rna Polymerase-Sorangicin Complex Length = 1119 | 3e-22 | ||
| 1i6v_C | 1118 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 3e-22 | ||
| 1l9u_C | 1118 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 3e-22 | ||
| 3iyd_C | 1342 | Three-Dimensional Em Structure Of An Intact Activat | 1e-19 | ||
| 3lu0_C | 1342 | Molecular Model Of Escherichia Coli Core Rna Polyme | 1e-19 |
| >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|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|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex 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|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 | 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 = 990 bits (2562), Expect = 0.0
Identities = 293/1204 (24%), Positives = 474/1204 (39%), Gaps = 194/1204 (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 DLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVD 943
D+I+NPHA PSRMT+ ++E +A K +L G +DATPF + ++
Sbjct: 910 DVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTP---------------IE 954
Query: 944 ELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQ 1003
+L + G+ EV Y G G ++ I+ G VYYQ+L HMV+DK R+ G +
Sbjct: 955 QLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQI 1014
Query: 1004 ITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTAT 1063
+TRQP +GR R GG+RFGEMERD L+ G A LL DRL SD VC CG +
Sbjct: 1015 LTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWY- 1073
Query: 1064 FIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITL 1123
+ K C + V + Y F+ L EL +M I L
Sbjct: 1074 -----------------DKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRL 1116
Query: 1124 QLGD 1127
L D
Sbjct: 1117 ILED 1120
|
| >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 |
|---|
| >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 |
|---|
| >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 |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1131 | |||
| 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 | 99.87 | |
| 3qqc_A | 436 | DNA-directed RNA polymerase subunit B, DNA-direct | 99.13 | |
| 3lti_A | 296 | DNA-directed RNA polymerase subunit beta; BBM2, nu | 98.77 | |
| 3tbi_B | 228 | DNA-directed RNA polymerase subunit beta; transcri | 98.57 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 91.15 |
| >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=4.4e-272 Score=2540.73 Aligned_cols=1027 Identities=29% Similarity=0.464 Sum_probs=912.7
Q ss_pred ccccchhhHHHHHHHHHHHHHHhHHHHH---------------------------------------------------H
Q 001179 8 DFEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------------------D 36 (1131)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii---------------------------------------------------~ 36 (1131)
+|+..++||+|||||||+|+++||++|+ +
T Consensus 23 aff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~~e~d~~~~~l~P~ 102 (1210)
T 3h0g_B 23 SFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQ 102 (1210)
T ss_dssp HHHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCCBCTTSCBCCCCTT
T ss_pred HHhcccchHHHHHHHHHHHHHHhHHHHHhccCcEEecCccCcccccccCCceEEEEEEEEEEcCCceecCCCcccccCHH
Confidence 4567899999999999999999999876 8
Q ss_pred HHHHcCCeeeEEEEEEEEEEEecCC----------C-----ceEEEEEeecccceeeccCcccCCCCChHHHHhhccccc
Q 001179 37 HCRQAKISYTGKLMADVEFQYLDAG----------S-----PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAA 101 (1131)
Q Consensus 37 ecR~r~~TYsa~l~v~v~~~~~~~~----------~-----~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~~ 101 (1131)
|||+|++||+|||+|+|+++++... . .....++.||+|||||||++|||++++++||+++||||+
T Consensus 103 EcRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~s~~eL~~~gEcp~ 182 (1210)
T 3h0g_B 103 EARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPY 182 (1210)
T ss_dssp TTTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSCCHHHHHHTTCCTT
T ss_pred HHHhcCCccceeEEEEEEEEEcCccccccccccccccccccccccceEEEecCCEEeCCCcccCCCCCHHHHHhcCCCCC
Confidence 9999999999999999999876211 0 112357999999999999999999999999999999999
Q ss_pred cCCcEEEEcCceeEEEEEEeccCCceEEEEeccccCCCcceeeEEEEEeeeecCCCce--EEEEEEEe------CCeEEE
Q 001179 102 EMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSV--TLKLYYLL------NGSVRL 173 (1131)
Q Consensus 102 D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s~--~~~l~~~~------~g~~~l 173 (1131)
||||||||||+||||++|+..++|+|+++ +++++.|+.|++.+||+++++++. ++.+++.. ++.+.+
T Consensus 183 D~GGYFIING~EKVII~qerla~N~~iv~-----~~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~~~~~~i~~ 257 (1210)
T 3h0g_B 183 DQGGYFIINGSEKVIIAQERSAANIVQVF-----KKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRA 257 (1210)
T ss_dssp CCCCCBCGGGSCBCCCBCBCCCCSCCCCC-----CCCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTTSCSCCCCC
T ss_pred CCCCEEEEeCEEEEEEechhhccceEEEE-----eecCCCCceEEEEEEEEecCCccceeEEEEEEEeccccCCCceEEE
Confidence 99999999999999988888888999875 445667889999999999986533 33344443 567777
Q ss_pred EEEEecccccccHhhHHHhccCCCHHHHHHhhccccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhh
Q 001179 174 GFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGE 253 (1131)
Q Consensus 174 ~~~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~ 253 (1131)
+|++.+. +||+++||||||.+||+||++.|+. +.+++.+.+.+..++++.. .++||++||+|||+
T Consensus 258 ~~~~~~~--~IPi~ivlkALg~~sD~EI~~~I~~-----------~~~d~~~~~~l~~slee~~--~i~tq~~aL~yIG~ 322 (1210)
T 3h0g_B 258 TLPYIRS--DIPIVIVFRALGVVPDRDILEHICY-----------DPNDFQMLEMMKPCIEEAF--VIQDKDIALDYIGK 322 (1210)
T ss_dssp CCTTSCS--CCCSHHHHTTTTCCSTTHHHHHHCC-----------SSCCHHHHHTHHHHHHTTS--SCCSSHHHHHTTCC
T ss_pred EEecccc--CCcHHHHHHHcCCCCHHHHHHHHhC-----------CCCcHHHHHHHHHHHHHhh--hcCCHHHHHHHHHH
Confidence 8877664 6999999999999999999999982 1235556677777777653 58999999999999
Q ss_pred cccccccCCCCccHHHHHHHHHHhhhcccCCCc----hhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHH
Q 001179 254 HFQPVIDGLQSESYYAVAETVIRDYIFVHLNDN----NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLIT 329 (1131)
Q Consensus 254 ~~r~~~~~~~~~~~~e~g~~~L~~~ll~Hl~~~----~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~ 329 (1131)
+|+.. ..++.+++++|+++|+++|||||+.. .+||+||++|+||||+++.|++.+||+|||+||||+|+|+||+
T Consensus 323 r~~~~--~~~~~~~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~ 400 (1210)
T 3h0g_B 323 RGSTT--GVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLA 400 (1210)
T ss_dssp CSSSC--CCCHHHHHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHH
T ss_pred hcccc--CCCchhHHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHH
Confidence 99853 13556789999999999999999964 4899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEc
Q 001179 330 IYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQA 409 (1131)
Q Consensus 330 ~lf~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~Gvsqvl 409 (1131)
.+||+.|+++++++++.+++.+.+ ++.+++. .+++ ++.||++|++|||||||+++.+ +++|++||||||
T Consensus 401 ~lfr~~~~~~~~~i~~~l~k~~~~-~~~~~~~------~~i~---~~~It~~l~~~laTGNW~~~kk-~~~~~sGvsqvl 469 (1210)
T 3h0g_B 401 SLFRMLFRKMTRDVYKYMQKCVET-NREFNLT------LAVK---SNIITNGLRYSLATGNWGDQKR-SMVNRVGVSQVL 469 (1210)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTT-CCSCCCT------TSSC---STTTSHHHHHHHSSSCSSTTSS-CCSCCCCSCCBC
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhc-CCccCHH------Hhcc---hhhhHHHHHHHhhcCCcccccc-cccCcCCEEEEc
Confidence 999999999999999999998877 5444432 2342 3589999999999999998766 578999999999
Q ss_pred cccchHHHhhhccccccCCccccccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhh
Q 001179 410 ERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMR 489 (1131)
Q Consensus 410 eRln~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~ 489 (1131)
+|+||+|+|||||||+ +++++++|+++||+||||||||+||+|||||++||||||||++|+||++.+.+
T Consensus 470 ~R~n~~s~lShlRrv~-~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~---------- 538 (1210)
T 3h0g_B 470 NRYTFASTLSHLRRTN-TPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSA---------- 538 (1210)
T ss_dssp CCSSHHHHHHHTTBBC-CSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSS----------
T ss_pred ccCCHHHHHHHHHhcc-CchhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcH----------
Confidence 9999999999999997 57899999999999999999999999999999999999999999999987776
Q ss_pred hHHHHHHHhcCceecCcccccCCCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCC
Q 001179 490 TSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAY 569 (1131)
Q Consensus 490 ~~i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~ 569 (1131)
+|.++|.++||+++. +......++.++|||||+|||++ .++.+|++.||.+||++ .|+..++|+. +...
T Consensus 539 -pI~~~l~~~gme~le-~~~~~~~~~~tkVfvNG~wVGvh--~dp~~Lv~~lR~lRR~g--~Is~eVSIvr-----dir~ 607 (1210)
T 3h0g_B 539 -PIIEFLEEWGLETLE-DYNPSASPNATKVFVNGVWLGVH--RDPAHLTETLRSLRRRL--DISAEVSIVR-----DIRE 607 (1210)
T ss_dssp -HHHHHHHSSSCCCCS-CCCSSSSSSSCCCCSTTCCCCCC--SCHHHHHHHHHHHHTTT--SSCTTCCCCC-----CTTT
T ss_pred -HHHHHHHHhCCcchh-hcCcccCCCceEEEECCEEEEEe--CCHHHHHHHHHHHhhcC--CCCCceEEEe-----cCCC
Confidence 799999999999873 34444456789999999999996 46799999999999998 6887777753 2346
Q ss_pred CeEEEEcCCCcceeeEEEecCC-------CC-------------------------------CCcceeeecccceeeeee
Q 001179 570 PGLYLFTSPPKFVRPVRNISLP-------SE-------------------------------ESQNIELIGPFEQVFMEI 611 (1131)
Q Consensus 570 ~~i~i~td~GRl~RPv~~~~~~-------~~-------------------------------~~g~iE~i~~~Eq~~~~I 611 (1131)
++++||||+||+||||++|+++ +. ..|.|||||++||++++|
T Consensus 608 rE~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l~k~hi~~L~~~~~~~~~~~~~~~~w~~Lv~~GvIEylDaeEEet~mI 687 (1210)
T 3h0g_B 608 KELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMI 687 (1210)
T ss_dssp CCCCCCCSSCCBCCEEEECCCSSCSSSSCCCSSCHHHHHHHHHHHTCCCSCTTCCCSSTTTTTTTSEEECCTTTGGGCCE
T ss_pred CeEEEecCCCcccceEEEEccCCcccccccccccHHHHHHHhcccccccccccccCCHHHHHhCCCEEEecHhhhhceeE
Confidence 8999999999999999999864 10 258999999999999999
Q ss_pred ecCCCCCCC------------------------CCCCCceeEEeecCCCcccceeccccCCCCCCCcccccccccccccc
Q 001179 612 RCPDGGDGG------------------------RRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTM 667 (1131)
Q Consensus 612 a~~~~~~~~------------------------~~~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAi 667 (1131)
|++++|+.. ......||||||||++|||||||+|||||||||||||||||||||||
T Consensus 688 amtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~~~~~~~~THcEIhPsmILGIcASiIPFpdHNQSPRNtYQ~aMgKQam 767 (1210)
T 3h0g_B 688 AMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAM 767 (1210)
T ss_dssp ESCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCSCCSCCSCSEECSCGGGSSCSSSTTSSSSTTSCSHHHHHHHHHHTTCC
T ss_pred EecHHHhhhhhhhhccccccccccchhhccccCCCcccccccccccchhhhhheeecccCccccccchhhhhhhhhcccc
Confidence 999988732 00124589999999999999999999999999999999999999999
Q ss_pred ccccceEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEE
Q 001179 668 GFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747 (1131)
Q Consensus 668 G~~~~n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~ 747 (1131)
|++++|+..|+||++|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+||||||+.+|++
T Consensus 768 G~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~~~~~elp~G~NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~ 847 (1210)
T 3h0g_B 768 GVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRT 847 (1210)
T ss_dssp SCCCTTTTTSCCSSEEEESSCBCCSSBCTTSTTTTCTTSCSCCEECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEE
T ss_pred cccccccccccCccccEeecCcCccccchhHHHhCCCcccCccceEEEEeccCCCChhhheeeehhheecCceEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecccCCCccccccccccCCCC------hhhhcccCCCCCcccCcEEcCCCCeeEEeecCC--------------Cc
Q 001179 748 ETIDLSDDGNKVDRGQKLFRRNKDA------KSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NS 807 (1131)
Q Consensus 748 ~~~~~~~~~~~~~~~~~~f~~~~~~------~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~--------------~~ 807 (1131)
|.+++... .....+.|..|+.. ...+++||+||||.+|+.|++|||||||.+|.. .+
T Consensus 848 y~~~~~~~---~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gDiligK~~p~~~~~~~~~~~~~~~~~r 924 (1210)
T 3h0g_B 848 YTDQEKKI---GMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKR 924 (1210)
T ss_dssp EEECCCCC---SSSCCCCCCCCCTTSCCSCCSCCGGGCCTTSSCCTTCCCCTTCCCCCCCCCC-----------CCCCCC
T ss_pred EEEEeeec---CCCceeEEcCCCcchhcccchhhHhhcCCCCCcCCCCEecCCCEEEEEecCCCCCchhhcccccccccc
Confidence 98764322 12234567777543 235789999999999999999999999987642 24
Q ss_pred EEeeecCCCcceEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEe
Q 001179 808 WRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLII 887 (1131)
Q Consensus 808 ~~~~~~~~~e~g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIi 887 (1131)
+.+++++++|.|+||+|.++.+++ +.+.|+|++|+.|+|++|||||||||||||||+|||+|||||+ +||++|||||
T Consensus 925 d~s~~~~~~e~g~Vd~V~~~~~~~--g~~~vkv~~~~~R~~~~GDK~a~RhGqKGvi~~i~~~edmPf~-~~G~~pDii~ 1001 (1210)
T 3h0g_B 925 DVSTPLRSTESGIVDQVMVTTNQE--GLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFS-AQGIVPDIII 1001 (1210)
T ss_dssp CCCCCCCTTCCCCCCEEEEEECSS--SSEEEEEEECCCBCCCTTCEEECTTCCCEEEEEEECTTTSCCB-TTTBCCSEEC
T ss_pred eeeEEecCCCCeEEEEEEEEEecC--CCeEEEEEEEEecCCCchhhhhcccCCCceeeEEeccccCCcC-CCCCCCeEEE
Confidence 568899999999999999998865 4689999999999999999999999999999999999999999 9999999999
Q ss_pred CCCCCCCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcEEEeeCCC
Q 001179 888 NPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVY 967 (1131)
Q Consensus 888 NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~t 967 (1131)
||||||||||||||+|+++||||++.|.+.|+|||++. .++++++.|.++||+++|+|.||||+|
T Consensus 1002 NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~~~---------------~~~~~~~~l~~~g~~~~G~~~l~~g~t 1066 (1210)
T 3h0g_B 1002 NPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDV---------------TVEAVSKLLRSHGFQSRGFEVMYHGHT 1066 (1210)
T ss_dssp CGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSCSC---------------CHHHHHHHHHTTTSCTTSCBCCBCSSS
T ss_pred CCCcCCCCccchhhhHhHHHHHHHhcCCceeeccCCCC---------------cHHHHHHHHHHcCcCCCCCEEEEcCCC
Confidence 99999999999999999999999999999999999876 588999999999999999999999999
Q ss_pred CcEeeeeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCc
Q 001179 968 GTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDY 1047 (1131)
Q Consensus 968 G~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~ 1047 (1131)
|++|+++||+|++|||||+|||+||+|||++|||+.|||||++||+|+|||||||||||||+|||||++|+|||+.+||.
T Consensus 1067 g~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~gp~~~~t~QP~~gr~~~GG~r~GEME~~~l~a~Gaa~~l~e~l~~~SD~ 1146 (1210)
T 3h0g_B 1067 GRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDA 1146 (1210)
T ss_dssp CCBCSSCBEECCEECEECSCCSTTTCEECSSCCBCSSSCSBCCSSTTCCCCCCCHHHHHHHHHHTBHHHHHHHHHTTTTC
T ss_pred CCCccccEEEEehHhhcchhhcccCcEEeccCCCchhccCCcccccccCCeeeehhhhhhhhhccHHHHHHHHhhcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeccccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeEEEecc
Q 001179 1048 HVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGD 1127 (1131)
Q Consensus 1048 ~~~~vC~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~~~~ 1127 (1131)
+.++||..||+++..+ .+.+.++|+.|+++.++.++.||||||||+|||+||||.+||.+++
T Consensus 1147 ~~~~vC~~cg~~~~~~------------------~~~~~~~c~~c~~~~~i~~~~~p~~~k~l~~El~~~~i~~rl~~~~ 1208 (1210)
T 3h0g_B 1147 YRVIVCDICGLIAIAS------------------YKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTKN 1208 (1210)
T ss_dssp CEEEEESSSCCBCCCC------------------SSSCCCCCTTTCCSSCEEEEECCHHHHHHHHHHHTTTCCEECCCST
T ss_pred ceeEeecCCCCeeeec------------------ccCCceEcCccCCCCccceecCCHHHHHHHHHHHhCCCceEEEecC
Confidence 9999999999998654 2344579999999999999999999999999999999999999987
Q ss_pred C
Q 001179 1128 G 1128 (1131)
Q Consensus 1128 ~ 1128 (1131)
+
T Consensus 1209 ~ 1209 (1210)
T 3h0g_B 1209 H 1209 (1210)
T ss_dssp T
T ss_pred C
Confidence 5
|
| >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 |
|---|
| >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 |
|---|
| >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 |
| 1131 | ||||
| d1twfb_ | 1207 | e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c | 0.0 | |
| d1smyc_ | 1119 | e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop | 1e-140 | |
| d2b5ea2 | 98 | c.47.1.2 (A:142-239) Protein disulfide isomerase, | 0.004 |
| >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 = 624 bits (1609), Expect = 0.0
Identities = 307/1247 (24%), Positives = 481/1247 (38%), Gaps = 201/1247 (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 LESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEV 961
+E + +K +L G DA+PF + V+ + ++LR G+ G EV
Sbjct: 1010 IECLLSKVAALSGNEGDASPFTDIT---------------VEGISKLLREHGYQSRGFEV 1054
Query: 962 LYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFG 1021
+Y+G G +L +IF GP YYQRLRHMV DK R+ G M +TRQP++GR R GG+RFG
Sbjct: 1055 MYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFG 1114
Query: 1022 EMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPA 1081
EMERD ++AHGAA L +RL SD +C +CG L
Sbjct: 1115 EMERDCMIAHGAASFLKERLMEASDAFRVHICGICG--LMTVIAKLNH------------ 1160
Query: 1082 RAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGDG 1128
+ C C + + +PY + L EL AMNI L
Sbjct: 1161 ---NQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRS 1204
|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 | Back information, alignment and structure |
|---|
| >d2b5ea2 c.47.1.2 (A:142-239) Protein disulfide isomerase, PDI {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 98 | 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 | 1131 | |||
| 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: | 96.19 |
| >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=1.7e-242 Score=2340.78 Aligned_cols=1029 Identities=30% Similarity=0.478 Sum_probs=858.5
Q ss_pred cccchhhHHHHHHHHHHHHHHhHHHHH---------------------------------------------------HH
Q 001179 9 FEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------------------DH 37 (1131)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~ii---------------------------------------------------~e 37 (1131)
+...++||+|||||||+||++||++|+ +|
T Consensus 20 ~f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i~kP~~~e~~g~~~~l~P~E 99 (1207)
T d1twfb_ 20 FFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQE 99 (1207)
T ss_dssp HHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEEEEEECCSSSCCEECCHHH
T ss_pred HhCCCCccHHHHHHHHHHHHHCHHHHHHhcCCeEeeccccccccccCCCceEEEEEEEEEEcCCeEEcCCCcccccCHHH
Confidence 446789999999999999999999997 79
Q ss_pred HHHcCCeeeEEEEEEEEEEEec-----------------CCCceEEEEEeecccceeeccCcccCCCCChHHHHhhcccc
Q 001179 38 CRQAKISYTGKLMADVEFQYLD-----------------AGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEA 100 (1131)
Q Consensus 38 cR~r~~TYsa~l~v~v~~~~~~-----------------~~~~~~~~~v~iG~iPIMvkS~~C~L~~ls~~el~~~gE~~ 100 (1131)
||+|++||+|||+|+|++.+.+ .......++|+||+|||||+|++|||+++++++++++||||
T Consensus 100 cR~r~lTYs~~l~v~i~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv~S~~C~L~~~~~~~l~~~gEc~ 179 (1207)
T d1twfb_ 100 ARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECP 179 (1207)
T ss_dssp HHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTTSGGGTCCHHHHHHTTCCT
T ss_pred HHhcCCccceEEEEEEEEEEEecccccccccceeecccccccceeeeeEEEEECCEEeCCCcccCCCcCHHHHHHcCCCC
Confidence 9999999999999999875421 01123356899999999999999999999999999999999
Q ss_pred ccCCcEEEEcCceeEEEEEEeccCCceEEEEeccccCCCcceeeEEEEEeeeecCCCc--eEEEEEEEe-CCe--EEEEE
Q 001179 101 AEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSS--VTLKLYYLL-NGS--VRLGF 175 (1131)
Q Consensus 101 ~D~GGYFIING~EKVIr~qi~~~~N~~~~~~r~s~~~r~~~~t~~~i~iRs~~~~~~s--~~~~l~~~~-~g~--~~l~~ 175 (1131)
+|+||||||||+||||++|+...+|+++++. +++..++.|++.+||+++++.. .++.+.+.. ++. ..+++
T Consensus 180 ~D~GGYFIING~EKVIi~Q~r~~~n~~~v~~-----~~~~~~~~~~~~irS~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 254 (1207)
T d1twfb_ 180 FDMGGYFIINGSEKVLIAQERSAGNIVQVFK-----KAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKA 254 (1207)
T ss_dssp TCCCCSEEETTEEEEECEEEEECSSCCEEEE-----CCTTSSEEEEEEEECCCSSSCCCCCEEEEEEESCSSCSSCCEEE
T ss_pred CCCCcEEEECCEEEEEEEEEecCCCeEEEEE-----cCCCCceEEEEEEEEEeCCCCceeEEEEEEEEEcCCccceEEEE
Confidence 9999999999999999999988899988764 3456778899999999887643 344444332 221 23455
Q ss_pred EEecccccccHhhHHHhccCCCHHHHHHhhccccchhhhcccCCCCChhHHHHHHHHHHHHHhccccCHHHHHHHHhhcc
Q 001179 176 WLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHF 255 (1131)
Q Consensus 176 ~~~k~~~~IPi~ilLkALg~~sD~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~~~~~i~t~~~AL~yIG~~~ 255 (1131)
.+.+...+||+++||||||..||+||++.|+. + ..+..+.+.+...++. ...+.|+++||.|||+++
T Consensus 255 ~~~~~~~~IPl~illrALG~~sD~eI~~~i~~--~---------~~~~~~~~~l~~~~~~--~~~~~t~e~al~yig~~~ 321 (1207)
T d1twfb_ 255 TLPYIKQDIPIVIIFRALGIIPDGEILEHICY--D---------VNDWQMLEMLKPCVED--GFVIQDRETALDFIGRRG 321 (1207)
T ss_dssp ECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCC--C---------TTCHHHHHHHHHHHHH--TTTCCSHHHHHHHHHHTT
T ss_pred EeehhcccchHHHHHHHhCCcchhhhhhhccc--C---------chhhHHHHHHHHHHhh--ccchhhHHHHHHHHHhhc
Confidence 55555568999999999999999999999973 1 1122222333333332 246889999999999987
Q ss_pred cccccCCCCccHHHHHHHHHHhhhcccCCC----chhhHHHHHHHHHHHHhhcCCCCCCCCcccccccEeccchhhHHHH
Q 001179 256 QPVIDGLQSESYYAVAETVIRDYIFVHLND----NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIY 331 (1131)
Q Consensus 256 r~~~~~~~~~~~~e~g~~~L~~~ll~Hl~~----~~~K~~~L~~MvrkLl~l~~G~~~~DD~D~l~NkRv~l~G~Ll~~l 331 (1131)
+.. .+......+.|+++|++.+|||++. +..|+.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+
T Consensus 322 ~~~--~~~~~~~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~~~ 399 (1207)
T d1twfb_ 322 TAL--GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQL 399 (1207)
T ss_dssp SCT--TSCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHHHH
T ss_pred ccc--CCCccchHHHHHHHHHhhhccccccccchhhhHHHHHHHHHHHHHHhhhcccCCcchhhhccchhhhHHHHHHHH
Confidence 642 2345567899999999999999983 4679999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccc
Q 001179 332 LKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAER 411 (1131)
Q Consensus 332 f~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~~GvsqvleR 411 (1131)
|++.|+++++.+++.+.+...+ .+.++ +..+ .+++.||++|++||+||||.++.+ .++|++|++|+|+|
T Consensus 400 fr~~~~~~~~~i~~~~~~~~~~-~~~~~------~~~~---~~~~~it~~i~~~~~TGn~~~~~~-~~~~~~G~sq~l~r 468 (1207)
T d1twfb_ 400 FKTLFKKLTKDIFRYMQRTVEE-AHDFN------MKLA---INAKTITSGLKYALATGNWGEQKK-AMSSRAGVSQVLNR 468 (1207)
T ss_dssp HHHHHHHHHHHHHHHHHSCCC---------------CC---CCTHHHHHHHHHHHHHCCCC----------CCCEEECCC
T ss_pred HHHHHHHHHHHHHhhhcccccc-ccccC------hhhh---hccCcHHHHHHHHHhcCccccccc-ccccccchhhhhhh
Confidence 9999999888887776644322 11111 1111 234589999999999999988765 57899999999999
Q ss_pred cchHHHhhhccccccCCccccccccccccccCCcccccccCCCCCCccccccccccceEEEeeccCCCCcccccchhhhH
Q 001179 412 LNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTS 491 (1131)
Q Consensus 412 ln~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhps~wGfICPveTPEG~~CGLvk~LA~~a~It~~~~~~~~~~~~~~~~~~ 491 (1131)
+||+++|||+||||+| +++++|+++||+||||||||+||+|||||+|||||||||++|+|+...+.. .
T Consensus 469 ~n~l~~lSh~Rrv~~~-~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~-----------~ 536 (1207)
T d1twfb_ 469 YTYSSTLSHLRRTNTP-IGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPM-----------P 536 (1207)
T ss_dssp SSHHHHHHHHTEEECC-C------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCH-----------H
T ss_pred cCHHHHHHhhhcccCC-cccccccchhhhcchhhccceeeeeCCCCCcccceeccceeeeeccccccc-----------e
Confidence 9999999999999986 789999999999999999999999999999999999999999999876665 6
Q ss_pred HHHHHHhcCceecCcccccCCCCCceEEEECCEEEeeecCchHHHHHHHHHHHHhhcCCCCCCCceEEEEeCCCCCCCCe
Q 001179 492 ILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPG 571 (1131)
Q Consensus 492 i~~~L~~lG~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~ 571 (1131)
+.++|..+|+.+.. ........+..+||+||.|+|+++ ++..+++.+|.+|+.| .++...++.+.. ...+
T Consensus 537 ~~~~l~~~g~~~~~-~~~~~~~~~~~~V~~nG~~~G~~~--~~~~l~~~lr~~R~~g--~i~~~~s~~~~~-----~~~~ 606 (1207)
T d1twfb_ 537 IITFLSEWGMEPLE-DYVPHQSPDATRVFVNGVWHGVHR--NPARLMETLRTLRRKG--DINPEVSMIRDI-----REKE 606 (1207)
T ss_dssp HHHHHHHTTCEEGG-GCCGGGCTTCEEEEETTEEEEEES--CHHHHHHHHHHHHHHT--SSCTTCEEEEET-----TTTE
T ss_pred eeEEeeccCcccce-eeeeccccccceeeeeeeEEEEEc--chheeehheeeeeecc--Cccceeeeeeec-----cccc
Confidence 78889999998763 233333456789999999999985 5689999999999999 677666665432 3469
Q ss_pred EEEEcCCCcceeeEEEecCCCC----------------------------------------CCcceeeecccceeeeee
Q 001179 572 LYLFTSPPKFVRPVRNISLPSE----------------------------------------ESQNIELIGPFEQVFMEI 611 (1131)
Q Consensus 572 i~i~td~GRl~RPv~~~~~~~~----------------------------------------~~g~iE~i~~~Eq~~~~I 611 (1131)
++|+||+||++|||+.++++.. ..|.|||||++||+++.|
T Consensus 607 i~i~td~Gr~~rPlfi~~nd~~~~~~~~~mqrq~v~~l~~~e~~~v~~~~e~~~~~~~~~~~~~g~ieyid~~E~~~~~I 686 (1207)
T d1twfb_ 607 LKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILI 686 (1207)
T ss_dssp EEEECCSCCEEEEEEEEECCCTTSSCEESCCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTTCCE
T ss_pred eEEEecCccccCCceeecchhhhcccceeeeHhhHhhhhccccccccccccchhhccccccccCCceeeecchhcceEEE
Confidence 9999999999999998765421 157899999999999999
Q ss_pred ecCCCCCCCCC-------------------CCCceeEEeecCCCcccceeccccCCCCCCCccccccccccccccccccc
Q 001179 612 RCPDGGDGGRR-------------------NAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQ 672 (1131)
Q Consensus 612 a~~~~~~~~~~-------------------~~~~~th~EI~P~~ilsv~AslIPF~~HNqspRn~yqc~M~KQAiG~~~~ 672 (1131)
|+.++++.... ....+||+||+|+.|||++|++|||+||||||||+|||||+|||||++++
T Consensus 687 a~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~th~Ei~p~~ilg~~as~iPf~~hNqSpRn~yq~qm~KQa~G~~~~ 766 (1207)
T d1twfb_ 687 AMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT 766 (1207)
T ss_dssp ESSGGGGCC---------CCCTTSCCCCCCCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHHHGGGBCBCSCT
T ss_pred EecccccccccccccccccccchhheeeecccccccccccccceEEeeecceEEecccccccceeecccCCcccCCcccc
Confidence 99998874310 12348999999999999999999999999999999999999999999999
Q ss_pred eEEEecccceeeecCCCcceeecCcccccCcccCCCCcceEEEEEeccCCCCCceEEeeccccccCceeeeEEEEEEEEe
Q 001179 673 ALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDL 752 (1131)
Q Consensus 673 n~~~R~D~~~y~L~ypQ~PLV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rG~~~~~~y~~~~~~~ 752 (1131)
|+..|.|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+|||+|++++|++|.+++
T Consensus 767 ~~~~r~D~~~~~l~~pQ~Plv~t~~~~~~~~~e~p~G~N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~ 846 (1207)
T d1twfb_ 767 NYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQE 846 (1207)
T ss_dssp TTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECC
T ss_pred ccceeccccceeEecCCCceeeccchhhhhhhcccchhceEEEEEeccCcccccccccchhhhhhcccceeeeEEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998876
Q ss_pred cccCCCccccccccccCCC------ChhhhcccCCCCCcccCcEEcCCCCeeEEeecCC--------------CcEEeee
Q 001179 753 SDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSWRTNS 812 (1131)
Q Consensus 753 ~~~~~~~~~~~~~f~~~~~------~~~~~~~Ld~dGi~~~G~~v~~gdil~~~~~~~~--------------~~~~~~~ 812 (1131)
...+. +..+.|..|.. ....+++||+||+|++|+.|++||+|+||+.+.. .++.+.+
T Consensus 847 ~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~~~~~~~~~~s~~ 923 (1207)
T d1twfb_ 847 KKYGM---SITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTP 923 (1207)
T ss_dssp CCSCT---TCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC-------------CCBBCCEE
T ss_pred ccccc---cccccccccccccccccchhhhhcccccccccccccccCCceeeeeeeccCCchhhhhhccccccccceeEE
Confidence 44332 23334444422 2345689999999999999999999999977643 2345788
Q ss_pred cCCCcceEEEEEEEeccCCCCCCeEEEEEEeeecCCCCCcccccccCCcceeeeeecCCCCCccCCCCCcccEEeCCCCC
Q 001179 813 RKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAF 892 (1131)
Q Consensus 813 ~~~~e~g~Vd~v~~~~~~~~~~~~~~~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dmPf~~~~G~~pDiIiNPh~~ 892 (1131)
++.++.|+||+|.++.+.+ +.+.++|++|+.|+|+||||||||||||||||+|||+|||||| +||++||||||||||
T Consensus 924 ~~~~~~g~V~~v~~~~~~~--~~~~~kv~i~~~R~p~iGDKfasRhGqKGv~s~i~p~eDMPf~-~dG~~pDiI~NP~g~ 1000 (1207)
T d1twfb_ 924 LRSTENGIVDQVLVTTNQD--GLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFT-AEGIVPDLIINPHAI 1000 (1207)
T ss_dssp CCTTCCEEEEEEEEEECSS--SCEEEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTSCEE-TTSCCCSEEECGGGS
T ss_pred ccCCCCeEEEEEEEeeccc--ccceeeEEEEEEeccchhhhhhhccCCcceeeeeechhhCCcC-CCCCCccEEECCCcC
Confidence 8999999999999988765 4689999999999999999999999999999999999999999 999999999999999
Q ss_pred CCccchhHhHHHHHhhhccccCceeccccccccccccCCCCCCCCchhhHHHHHHHHHHCCCCCCCcEEEeeCCCCcEee
Q 001179 893 PSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELT 972 (1131)
Q Consensus 893 PSRMtiGql~E~~~gk~~~~~g~~~d~tpf~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~ 972 (1131)
|||||||||+|+++||||++.|.++|+|||++. .+++++++|.++||+++|+|.||||+||++|+
T Consensus 1001 PSRMtiGql~E~~~gk~~~~~g~~~d~t~F~~~---------------~~~~~~~~L~~~g~~~~G~e~ly~G~tG~~~~ 1065 (1207)
T d1twfb_ 1001 PSRMTVAHLIECLLSKVAALSGNEGDASPFTDI---------------TVEGISKLLREHGYQSRGFEVMYNGHTGKKLM 1065 (1207)
T ss_dssp TTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSC---------------CHHHHHHHHHTTTSCTTSEECEECTTTCCBCS
T ss_pred cccCcHHHHHHHHHHHHHHhcCCccccCCCCCc---------------cHHHHHHHHHHcCCCCCCCEEEECCCCCCCcc
Confidence 999999999999999999999999999999876 58899999999999999999999999999999
Q ss_pred eeeeeeceeEEeeccccccceeeeecccccceeecccCcccccCceeeeehhhhHHhhhchHHHHHHhhccCCCccceec
Q 001179 973 CEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADV 1052 (1131)
Q Consensus 973 ~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lTrQP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~v 1052 (1131)
++||+|++|||||+|||+||+|||+|||+++|||||++||||+|||||||||||||+|||||++|+|||+++||.++++|
T Consensus 1066 ~~i~~G~~yy~rL~HmV~DK~~~Rs~Gp~~~lT~QP~~Gr~~~GG~R~GEME~dal~a~Gaa~~L~e~l~~~SD~~~~~v 1145 (1207)
T d1twfb_ 1066 AQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHI 1145 (1207)
T ss_dssp SCEEEEEEEEEEBSSCGGGTCEEECCCC----------------CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCEEEE
T ss_pred ceEEEehhHhhhhhhhhccccEeeccCCCCccccCCCCccccCCCcceehHHHHHHHHHhHHHHHHHHhhccCCccceec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccccccccccccccccCCCCCCCCCCCeeeccCcCCCCcceecchHhHHHHHHHHHhCCceeEEEeccC
Q 001179 1053 CSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGDG 1128 (1131)
Q Consensus 1053 C~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~klL~~EL~sm~I~~~l~~~~~ 1128 (1131)
|.+||+++... ..+...++|+.|+++.++.++.||||||||+|||+||||.++|.+++.
T Consensus 1146 c~~cg~~~~~~-----------------~~~~~~~~c~~c~~~~~i~~~~iPy~fk~l~~EL~sm~i~~~l~~~~~ 1204 (1207)
T d1twfb_ 1146 CGICGLMTVIA-----------------KLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRS 1204 (1207)
T ss_dssp ESSSCSSCCEE-----------------ETTTTEEEBTTTTBSSSEEEEECCHHHHHHHHHHHHTTBCCEEESCSS
T ss_pred cccCCceEEEe-----------------cccccceeecCCCCCCCccccCCCHHHHHHHHHHHHCCCceEEEecCc
Confidence 99999997643 023446899999999999999999999999999999999999999865
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| >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 |
|---|