Citrus Sinensis ID: 001124
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 | 1149 | 2.2.26 [Sep-21-2011] | |||||||
| Q10233 | 1165 | DNA-directed RNA polymera | yes | no | 0.966 | 0.952 | 0.578 | 0.0 | |
| Q9NW08 | 1133 | DNA-directed RNA polymera | yes | no | 0.966 | 0.980 | 0.578 | 0.0 | |
| P59470 | 1133 | DNA-directed RNA polymera | yes | no | 0.966 | 0.980 | 0.579 | 0.0 | |
| P22276 | 1149 | DNA-directed RNA polymera | yes | no | 0.970 | 0.970 | 0.568 | 0.0 | |
| P25167 | 1137 | DNA-directed RNA polymera | yes | no | 0.974 | 0.985 | 0.537 | 0.0 | |
| Q54IZ9 | 1608 | DNA-directed RNA polymera | yes | no | 0.556 | 0.397 | 0.610 | 0.0 | |
| P31814 | 1122 | DNA-directed RNA polymera | N/A | no | 0.943 | 0.966 | 0.390 | 0.0 | |
| Q8CFI7 | 1174 | DNA-directed RNA polymera | no | no | 0.956 | 0.936 | 0.373 | 0.0 | |
| P30876 | 1174 | DNA-directed RNA polymera | no | no | 0.956 | 0.936 | 0.373 | 0.0 | |
| Q54J75 | 1170 | DNA-directed RNA polymera | no | no | 0.946 | 0.929 | 0.372 | 0.0 |
| >sp|Q10233|RPC2_SCHPO DNA-directed RNA polymerase III subunit RPC2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc2 PE=2 SV=1 | Back alignment and function desciption |
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Score = 1362 bits (3525), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 662/1144 (57%), Positives = 853/1144 (74%), Gaps = 34/1144 (2%)
Query: 19 QKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSI 78
+KLA PV ++ DK+QLLP FLKV+GLVKQHLDS+NYFV+ ++KIV+AN+++ S ++P
Sbjct: 38 KKLADPVPTIEDKWQLLPAFLKVKGLVKQHLDSYNYFVDVDLKKIVQANEKVTSDVEPWF 97
Query: 79 FLRFKDVRIGQPSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
+L++ D+R+G P T D + ++PH CRL D+TY A I V+IEY +G K + +
Sbjct: 98 YLKYLDIRVGAPVRTDADAIQASISPHECRLRDLTYGANIYVDIEYTRG----KQVVRRR 153
Query: 138 DVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRV 197
+V IGR+P+MLRS +CVL GK+E E+A L ECPLDPGGYFI+KGTEKV+L+QEQLSKNR+
Sbjct: 154 NVPIGRMPVMLRSNKCVLSGKNEMEMAALNECPLDPGGYFIVKGTEKVILVQEQLSKNRI 213
Query: 198 IIDTD-KKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESD 256
I++ + KKG ASVTSST KSKT + + GK+YL N IPI+VV+KAMG++SD
Sbjct: 214 IVEAEPKKGLWQASVTSSTHERKSKTYVITKNGKLYLKHNSVADDIPIVVVLKAMGLQSD 273
Query: 257 QEVVQMV-GRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGS----PPNDR 311
QE+ ++V G + Y L PSIEECA L+IYT ++ALEY+ +VK + PP++
Sbjct: 274 QEIFELVAGAEASYQDLFAPSIEECAKLNIYTAQQALEYIGARVKVNRRAGANRLPPHEE 333
Query: 312 EGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLEL 371
A +L V LA++ V N FRPK Y+ +M RR++ AM++ +DD+DYVGNKRLEL
Sbjct: 334 ---ALEVLAAVVLAHINVFNLEFRPKAVYIGIMARRVLMAMVDPLQVDDRDYVGNKRLEL 390
Query: 372 SGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFD-LSQFIVR-DSITVGLERTLST 429
+GQL++LLFEDLFK S+++ +D +L KP R+ FD +Q V D IT G+ R LST
Sbjct: 391 AGQLLALLFEDLFKKFNSDLKLNIDKVLKKPHRTQEFDAYNQLTVHSDHITQGMVRALST 450
Query: 430 GNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCP 489
GN+ +KRFKM R G+T VL+RLS+I LG MTR++ QFEK+RKVSGPR+LQ SQ+GMLC
Sbjct: 451 GNWSLKRFKMERAGVTHVLSRLSYISALGMMTRITSQFEKTRKVSGPRSLQASQFGMLCT 510
Query: 490 CDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIF 549
DTPEGEACGLVKNLALMTH+TTDEEE P+I L Y G+ED+ ++SG ELH+ ++LV
Sbjct: 511 SDTPEGEACGLVKNLALMTHITTDEEEEPIIKLAYAFGIEDIHVISGRELHSHGTYLVYL 570
Query: 550 NGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADK 609
NG ILG R P F RKLRR+GKI F+ +F+N QR V+I++DGGR+CRPL+I
Sbjct: 571 NGAILGISRYPSLFVASFRKLRRSGKISPFIGIFINTHQRAVFISTDGGRICRPLIIVQN 630
Query: 610 GISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEP 669
G+ +++ H++ L +G F+DFL++GL+EY+DVNEEN++LI++YE D TPDTTH+EIEP
Sbjct: 631 GLPKVESKHIRLLKEGKWGFEDFLKQGLVEYVDVNEENDSLISVYERDITPDTTHLEIEP 690
Query: 670 FTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLT 729
FTILG +AGLIPYPHHNQSPRNTYQCAMGKQA+G IA+NQL R+D+LLYL+VYPQ+P++
Sbjct: 691 FTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQLQRIDTLLYLMVYPQQPMVK 750
Query: 730 TRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQK 789
T+TIEL+GYDKL AGQNATVA+MSYSGYDIEDA+V+NKSS+DRGFGRC V K++ I +K
Sbjct: 751 TKTIELIGYDKLPAGQNATVAIMSYSGYDIEDALVLNKSSIDRGFGRCQVFHKHSVIVRK 810
Query: 790 YANSTSDRILRPDR---TGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGS-- 844
Y N T DRI P R TG + +++DDGLA G ++P +Y+NK++P +
Sbjct: 811 YPNGTHDRIGDPQRDPETGEVVWKHGVVEDDGLAGVGCRVQPGQIYVNKQTPTNALDNSI 870
Query: 845 IMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKF 904
+ T +S Y++ TYK P E +D+V L + + IK L+R TRRPELGDKF
Sbjct: 871 TLGHTQTVESGYKATPMTYKAP--EPGYIDKVMLTTTDSDQTLIKVLMRQTRRPELGDKF 928
Query: 905 SSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGR 964
SSRHGQKGVCG IVQQED PF+++GICPD+IMNPHGFPSRMTVGKMIELL GK GV G
Sbjct: 929 SSRHGQKGVCGVIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGKVGVLRGT 988
Query: 965 FHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKL 1024
YG+ FG VE S LV+HG++Y+GKDM+ SGITG L+AYIFMGPIYYQKL
Sbjct: 989 LEYGTCFG-----GTKVEDASRILVEHGYNYSGKDMLTSGITGETLEAYIFMGPIYYQKL 1043
Query: 1025 KHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSS 1084
KHMV+DKMHAR GPR +LTRQPTEGR+R+GGLR+GEMERDCLIAYGAS L+ ERLM+SS
Sbjct: 1044 KHMVMDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASQLLLERLMISS 1103
Query: 1085 DPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRL 1144
D +V VC CGLLGY G C++C++ + M +PYA KLL QEL SMNIVPRL
Sbjct: 1104 DACDVDVCGQCGLLGY------KGWCNSCQSTREVVKMTIPYAAKLLFQELLSMNIVPRL 1157
Query: 1145 KLAE 1148
L +
Sbjct: 1158 ALED 1161
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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 III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol III is composed of mobile elements and RPC2 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|Q9NW08|RPC2_HUMAN DNA-directed RNA polymerase III subunit RPC2 OS=Homo sapiens GN=POLR3B PE=1 SV=2 | Back alignment and function description |
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| >sp|P59470|RPC2_MOUSE DNA-directed RNA polymerase III subunit RPC2 OS=Mus musculus GN=Polr3b PE=2 SV=2 | Back alignment and function description |
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| >sp|P22276|RPC2_YEAST DNA-directed RNA polymerase III subunit RPC2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RET1 PE=1 SV=2 | Back alignment and function description |
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| >sp|P25167|RPC2_DROME DNA-directed RNA polymerase III subunit RPC2 OS=Drosophila melanogaster GN=RpIII128 PE=2 SV=2 | Back alignment and function description |
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| >sp|Q54IZ9|RPC2_DICDI DNA-directed RNA polymerase III subunit rpc2 OS=Dictyostelium discoideum GN=polr3b PE=3 SV=1 | Back alignment and function description |
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| >sp|P31814|RPOB_THECE DNA-directed RNA polymerase subunit B OS=Thermococcus celer GN=rpoB PE=3 SV=1 | Back alignment and function description |
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| >sp|Q8CFI7|RPB2_MOUSE DNA-directed RNA polymerase II subunit RPB2 OS=Mus musculus GN=Polr2b PE=2 SV=2 | Back alignment and function description |
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| >sp|P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 OS=Homo sapiens GN=POLR2B PE=1 SV=1 | Back alignment and function description |
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| >sp|Q54J75|RPB2_DICDI DNA-directed RNA polymerase II subunit rpb2 OS=Dictyostelium discoideum GN=polr2b PE=3 SV=1 | 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 | 1149 | ||||||
| 225464023 | 1142 | PREDICTED: DNA-directed RNA polymerase I | 0.981 | 0.987 | 0.866 | 0.0 | |
| 255569145 | 1139 | DNA-directed RNA polymerase III subunit, | 0.986 | 0.994 | 0.851 | 0.0 | |
| 224132576 | 1141 | predicted protein [Populus trichocarpa] | 0.986 | 0.993 | 0.839 | 0.0 | |
| 449447799 | 1158 | PREDICTED: DNA-directed RNA polymerase I | 0.990 | 0.982 | 0.838 | 0.0 | |
| 297791275 | 1165 | hypothetical protein ARALYDRAFT_917015 [ | 0.987 | 0.974 | 0.798 | 0.0 | |
| 79529842 | 1161 | DNA-directed RNA polymerase III subunit | 0.987 | 0.977 | 0.793 | 0.0 | |
| 9759599 | 1194 | DNA-directed RNA polymerase subunit [Ara | 0.986 | 0.949 | 0.787 | 0.0 | |
| 356520824 | 1152 | PREDICTED: DNA-directed RNA polymerase I | 0.973 | 0.970 | 0.800 | 0.0 | |
| 356495051 | 1166 | PREDICTED: DNA-directed RNA polymerase I | 0.984 | 0.969 | 0.795 | 0.0 | |
| 115453445 | 1155 | Os03g0403100 [Oryza sativa Japonica Grou | 0.979 | 0.974 | 0.731 | 0.0 |
| >gi|225464023|ref|XP_002265454.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2 [Vitis vinifera] | Back alignment and taxonomy information |
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Score = 2066 bits (5354), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 980/1131 (86%), Positives = 1062/1131 (93%), Gaps = 3/1131 (0%)
Query: 22 AAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLR 81
A PVK VDKF LLPEFLKVRGLVKQHLDSFNYFV T I+KIVRANDRIVS +DPSI+LR
Sbjct: 12 ADPVKQAVDKFPLLPEFLKVRGLVKQHLDSFNYFVKTDIKKIVRANDRIVSSVDPSIYLR 71
Query: 82 FKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVI 141
FKDVRIG+PS+TVDG+SEKLNPH CRLSDMTYAAPILVNIEY+ GSH +KT +EKNDVVI
Sbjct: 72 FKDVRIGEPSITVDGISEKLNPHTCRLSDMTYAAPILVNIEYITGSHVQKTRVEKNDVVI 131
Query: 142 GRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDT 201
GR+PIMLRSC CVLY KDEAELARLGECPLDPGGYF++KGTEKV+LIQEQLSKNR+IIDT
Sbjct: 132 GRMPIMLRSCCCVLYKKDEAELARLGECPLDPGGYFVVKGTEKVILIQEQLSKNRIIIDT 191
Query: 202 DKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261
DKKGNINASVTSSTE+ KSKTVI MEK K++L LNQF KIPIM+VMKAMGMESDQEVVQ
Sbjct: 192 DKKGNINASVTSSTESTKSKTVIVMEKEKIWLQLNQFTSKIPIMIVMKAMGMESDQEVVQ 251
Query: 262 MVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRD 321
MVGR+PRYSALLLPS+EECA+ IYTQ++ALE+LE KVK+ F +P ++EGR +ILRD
Sbjct: 252 MVGRNPRYSALLLPSMEECASHGIYTQQQALEFLERKVKKLPFYNPSLEKEGRGMAILRD 311
Query: 322 VFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFE 381
F+ANVPV NNFRPKC YVAVMLRRM++A+LNKDAMDDKDYVGNKRLELSGQL+SLLFE
Sbjct: 312 TFIANVPVRQNNFRPKCLYVAVMLRRMMDAILNKDAMDDKDYVGNKRLELSGQLISLLFE 371
Query: 382 DLFKTMISEVQKTVDIILSKPSRSSRFDLSQ---FIVRDSITVGLERTLSTGNFDVKRFK 438
DLFKTMISEV+KT+D IL+KPSRSSRFD SQ FIVRDSITVGLERTLSTGN+DVKRF+
Sbjct: 372 DLFKTMISEVKKTIDAILAKPSRSSRFDFSQCLRFIVRDSITVGLERTLSTGNWDVKRFR 431
Query: 439 MHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEAC 498
MHRKGM+QV+ARLS+IG+LGHMT++SPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEAC
Sbjct: 432 MHRKGMSQVVARLSYIGSLGHMTKISPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEAC 491
Query: 499 GLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHR 558
GLVKNLALMTHVTTDEEE PLISLCY LGVEDLELLSGEELH PNSFL+IFNGLILGKHR
Sbjct: 492 GLVKNLALMTHVTTDEEESPLISLCYSLGVEDLELLSGEELHTPNSFLIIFNGLILGKHR 551
Query: 559 RPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHH 618
RP+ FA+ +RKLRRAGKIGEFVSVFVNEKQ CVYIASDGGRVCRP+VIADKG SRIKEHH
Sbjct: 552 RPQRFANALRKLRRAGKIGEFVSVFVNEKQHCVYIASDGGRVCRPVVIADKGKSRIKEHH 611
Query: 619 MKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAG 678
MKEL+DGVR+FDDFLR+GLIEYLDVNEENNALIALYE DA P+TTHIEIEPFTILGV AG
Sbjct: 612 MKELIDGVRTFDDFLRDGLIEYLDVNEENNALIALYEADAKPETTHIEIEPFTILGVCAG 671
Query: 679 LIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGY 738
LIP+PHHNQSPRNTYQCAMGKQAMGNIA+NQLCRMDSLLYLLVYPQRPLLTTRTIELVGY
Sbjct: 672 LIPFPHHNQSPRNTYQCAMGKQAMGNIAYNQLCRMDSLLYLLVYPQRPLLTTRTIELVGY 731
Query: 739 DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRI 798
DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIV+KK++A+NQ+Y N+ SDRI
Sbjct: 732 DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVMKKFSAVNQRYENNASDRI 791
Query: 799 LRPDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRS 858
+RP + G AERMQILDDDGLAAPGEIIKPND+YINKESP+ T+G ++SP G DS Y+
Sbjct: 792 VRPLKVGHDAERMQILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISPVGLPDSAYKP 851
Query: 859 ARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIV 918
+RQT+KGP+GE VVDRVALCSDKN +LCIKFLIRHTRRPE+GDKFSSRHGQKGVCGTI+
Sbjct: 852 SRQTFKGPEGEASVVDRVALCSDKNSNLCIKFLIRHTRRPEVGDKFSSRHGQKGVCGTII 911
Query: 919 QQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHA 978
QQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHA
Sbjct: 912 QQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHA 971
Query: 979 DTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSG 1038
D VE+IS+TLVKHGFSY+GKD IYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSG
Sbjct: 972 DKVETISKTLVKHGFSYSGKDFIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSG 1031
Query: 1039 PRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLL 1098
PRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLL
Sbjct: 1032 PRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLL 1091
Query: 1099 GYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAEA 1149
GYYNHKLK GICSTCKNGDNIS+MKLPYACKLL QELQ+MN+VPRLKL EA
Sbjct: 1092 GYYNHKLKIGICSTCKNGDNISTMKLPYACKLLFQELQAMNVVPRLKLTEA 1142
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Source: Vitis vinifera Species: Vitis vinifera Genus: Vitis Family: Vitaceae Order: Vitales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|255569145|ref|XP_002525541.1| DNA-directed RNA polymerase III subunit, putative [Ricinus communis] gi|223535120|gb|EEF36800.1| DNA-directed RNA polymerase III subunit, putative [Ricinus communis] | Back alignment and taxonomy information |
|---|
| >gi|224132576|ref|XP_002321356.1| predicted protein [Populus trichocarpa] gi|222868352|gb|EEF05483.1| predicted protein [Populus trichocarpa] | Back alignment and taxonomy information |
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| >gi|449447799|ref|XP_004141655.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|297791275|ref|XP_002863522.1| hypothetical protein ARALYDRAFT_917015 [Arabidopsis lyrata subsp. lyrata] gi|297309357|gb|EFH39781.1| hypothetical protein ARALYDRAFT_917015 [Arabidopsis lyrata subsp. lyrata] | Back alignment and taxonomy information |
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| >gi|79529842|ref|NP_199327.4| DNA-directed RNA polymerase III subunit C2 [Arabidopsis thaliana] gi|332007826|gb|AED95209.1| DNA-directed RNA polymerase III subunit C2 [Arabidopsis thaliana] | Back alignment and taxonomy information |
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| >gi|9759599|dbj|BAB11387.1| DNA-directed RNA polymerase subunit [Arabidopsis thaliana] | Back alignment and taxonomy information |
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| >gi|356520824|ref|XP_003529060.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|356495051|ref|XP_003516394.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|115453445|ref|NP_001050323.1| Os03g0403100 [Oryza sativa Japonica Group] gi|108708688|gb|ABF96483.1| DNA-directed RNA polymerase III 130 kDa polypeptide, putative, expressed [Oryza sativa Japonica Group] gi|113548794|dbj|BAF12237.1| Os03g0403100 [Oryza sativa Japonica Group] | 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 | 1149 | ||||||
| TAIR|locus:2153323 | 1161 | NRPC2 "nuclear RNA polymerase | 0.997 | 0.987 | 0.778 | 0.0 | |
| POMBASE|SPAC4G9.08c | 1165 | rpc2 "DNA-directed RNA polymer | 0.966 | 0.952 | 0.572 | 0.0 | |
| UNIPROTKB|E1BRJ4 | 1132 | POLR3B "DNA-directed RNA polym | 0.966 | 0.981 | 0.571 | 0.0 | |
| UNIPROTKB|E2RHZ2 | 1133 | POLR3B "DNA-directed RNA polym | 0.966 | 0.980 | 0.571 | 0.0 | |
| RGD|1565311 | 1133 | Polr3b "polymerase (RNA) III ( | 0.966 | 0.980 | 0.573 | 0.0 | |
| UNIPROTKB|E1BPX6 | 1133 | POLR3B "Uncharacterized protei | 0.966 | 0.980 | 0.571 | 0.0 | |
| UNIPROTKB|Q9NW08 | 1133 | POLR3B "DNA-directed RNA polym | 0.966 | 0.980 | 0.571 | 0.0 | |
| MGI|MGI:1917678 | 1133 | Polr3b "polymerase (RNA) III ( | 0.966 | 0.980 | 0.572 | 0.0 | |
| ZFIN|ZDB-GENE-030131-2887 | 1129 | polr3b "polymerase (RNA) III ( | 0.963 | 0.980 | 0.571 | 0.0 | |
| SGD|S000005733 | 1149 | RET1 "Second-largest subunit o | 0.963 | 0.963 | 0.565 | 0.0 |
| TAIR|locus:2153323 NRPC2 "nuclear RNA polymerase C2" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 4787 (1690.2 bits), Expect = 0., P = 0.
Identities = 906/1164 (77%), Positives = 1026/1164 (88%)
Query: 1 MGLMQVE-GSPKDEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTG 59
MGL Q + D+ DK+KL+AP+KS DKFQL+PEFLKVRGLVKQHLDSFNYF+N G
Sbjct: 1 MGLDQEDLDLTNDDHFIDKEKLSAPIKSTADKFQLVPEFLKVRGLVKQHLDSFNYFINVG 60
Query: 60 IRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILV 119
I KIV+AN RI S +DPSI+LRFK VR+G+PS+ E +NPHMCRL+DMTYAAPI V
Sbjct: 61 IHKIVKANSRITSTVDPSIYLRFKKVRVGEPSIINVNTVENINPHMCRLADMTYAAPIFV 120
Query: 120 NIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFII 179
NIEYV GSH K K++V+IGR+PIMLRSCRCVL+GKDE ELARLGECPLDPGGYFII
Sbjct: 121 NIEYVHGSHGNKAKSAKDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFII 180
Query: 180 KGTEKVLLIQEQLSKNRVIIDTDKKGNINAXXXXXXXXXXXXXXIQMEKGKMYLLLNQFV 239
KGTEKVLLIQEQLSKNR+IID+DKKGNINA IQMEK K+YL L++FV
Sbjct: 181 KGTEKVLLIQEQLSKNRIIIDSDKKGNINASVTSSTEMTKSKTVIQMEKEKIYLFLHRFV 240
Query: 240 KKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKV 299
KKIPI++V+KAMGMESDQE+VQMVGRDPR+SA LLPSIEEC + + TQ++AL+YLE KV
Sbjct: 241 KKIPIIIVLKAMGMESDQEIVQMVGRDPRFSASLLPSIEECVSEGVNTQKQALDYLEAKV 300
Query: 300 KRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMD 359
K+ ++G+PP +++GRA SILRD+FLA+VPV +NNFR KCFYV VMLRRM+EAMLNKDAMD
Sbjct: 301 KKISYGTPP-EKDGRALSILRDLFLAHVPVPDNNFRQKCFYVGVMLRRMIEAMLNKDAMD 359
Query: 360 DKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDS- 418
DKDYVGNKRLELSGQL+SLLFEDLFKTM+SE K VD IL+KP R+SRFD SQ + +DS
Sbjct: 360 DKDYVGNKRLELSGQLISLLFEDLFKTMLSEAIKNVDHILNKPIRASRFDFSQCLNKDSR 419
Query: 419 --ITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGP 476
I++GLERTLSTGNFD+KRF+MHRKGMTQVL RLSFIG++G +T++SPQFEKSRKVSGP
Sbjct: 420 YSISLGLERTLSTGNFDIKRFRMHRKGMTQVLTRLSFIGSMGFITKISPQFEKSRKVSGP 479
Query: 477 RALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSG 536
R+LQPSQWGMLCPCDTPEGE+CGLVKNLALMTHVTTDEEEGPL+++CY LGV DLE+LS
Sbjct: 480 RSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTTDEEEGPLVAMCYKLGVTDLEVLSA 539
Query: 537 EELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASD 596
EELH P+SFLVI NGLILGKH RP+ FA+ +R+LRRAGKIGEFVSVF NEKQ CVY+ASD
Sbjct: 540 EELHTPDSFLVILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVYVASD 599
Query: 597 GGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEG 656
GRVCRPLVIADKGISR+K+HHMKEL DGVR+FDDF+R+GLIEYLDVNEENNALIALYE
Sbjct: 600 VGRVCRPLVIADKGISRVKQHHMKELQDGVRTFDDFIRDGLIEYLDVNEENNALIALYES 659
Query: 657 DATP-----------DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNI 705
D T DTTHIEIEPFTILGV+AGLIPYPHHNQSPRNTYQCAMGKQAMGNI
Sbjct: 660 DGTTELDEGAEAAKADTTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGNI 719
Query: 706 AFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVM 765
A+NQL RMD+LLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMS+SGYDIEDAIVM
Sbjct: 720 AYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFSGYDIEDAIVM 779
Query: 766 NKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEI 825
NKSSLDRGFGRCIV+KK A++QKY N T+DRIL P RTGP AE+MQILDDDGLA PGEI
Sbjct: 780 NKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILIPQRTGPDAEKMQILDDDGLATPGEI 839
Query: 826 IKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGD 885
I+PND+YINK+ P++T S +DS+YR AR+ +KGP+GET VVDRVALCSDK G
Sbjct: 840 IRPNDIYINKQVPVDTVTKFTSAL--SDSQYRPAREYFKGPEGETQVVDRVALCSDKKGQ 897
Query: 886 LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRM 945
LCIK++IRHTRRPELGDKFSSRHGQKGVCG I+QQEDFPFSE GICPDLIMNPHGFPSRM
Sbjct: 898 LCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRM 957
Query: 946 TVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGI 1005
TVGKMIELLG KAGVSCGRFHYGSAFGE SGHAD VE+IS TLV+ GFSY+GKD++YSGI
Sbjct: 958 TVGKMIELLGSKAGVSCGRFHYGSAFGERSGHADKVETISATLVEKGFSYSGKDLLYSGI 1017
Query: 1006 TGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERD 1065
+G P++AYIFMGPIYYQKLKHMVLDKMHARGSGPRVM+TRQPTEG+++NGGLRVGEMERD
Sbjct: 1018 SGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERD 1077
Query: 1066 CLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLP 1125
CLIAYGASMLI+ERLM+SSDPFEVQVCR CGLLGYYN+KLK +C+TCKNGDNI++MKLP
Sbjct: 1078 CLIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYNYKLKKAVCTTCKNGDNIATMKLP 1137
Query: 1126 YACKLLIQELQSMNIVPRLKLAEA 1149
YACKLL QELQSMN+VPRLKL EA
Sbjct: 1138 YACKLLFQELQSMNVVPRLKLTEA 1161
|
|
| POMBASE|SPAC4G9.08c rpc2 "DNA-directed RNA polymerase III complex subunit Rpc2" [Schizosaccharomyces pombe (taxid:4896)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|E1BRJ4 POLR3B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|E2RHZ2 POLR3B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] | Back alignment and assigned GO terms |
|---|
| RGD|1565311 Polr3b "polymerase (RNA) III (DNA directed) polypeptide B" [Rattus norvegicus (taxid:10116)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|E1BPX6 POLR3B "Uncharacterized protein" [Bos taurus (taxid:9913)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|Q9NW08 POLR3B "DNA-directed RNA polymerase III subunit RPC2" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
|---|
| MGI|MGI:1917678 Polr3b "polymerase (RNA) III (DNA directed) polypeptide B" [Mus musculus (taxid:10090)] | Back alignment and assigned GO terms |
|---|
| ZFIN|ZDB-GENE-030131-2887 polr3b "polymerase (RNA) III (DNA directed) polypeptide B" [Danio rerio (taxid:7955)] | Back alignment and assigned GO terms |
|---|
| SGD|S000005733 RET1 "Second-largest subunit of RNA polymerase III" [Saccharomyces cerevisiae (taxid:4932)] | 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) |
| P22276 | RPC2_YEAST | 2, ., 7, ., 7, ., 6 | 0.5685 | 0.9704 | 0.9704 | yes | no |
| Q9NW08 | RPC2_HUMAN | 2, ., 7, ., 7, ., 6 | 0.5783 | 0.9669 | 0.9805 | yes | no |
| P59470 | RPC2_MOUSE | 2, ., 7, ., 7, ., 6 | 0.5792 | 0.9669 | 0.9805 | yes | no |
| Q03587 | RPOB_THEAC | 2, ., 7, ., 7, ., 6 | 0.3327 | 0.9408 | 0.9046 | yes | no |
| P25167 | RPC2_DROME | 2, ., 7, ., 7, ., 6 | 0.5376 | 0.9747 | 0.9850 | yes | no |
| Q10233 | RPC2_SCHPO | 2, ., 7, ., 7, ., 6 | 0.5786 | 0.9660 | 0.9527 | yes | no |
| P11513 | RPOB_SULAC | 2, ., 7, ., 7, ., 6 | 0.3692 | 0.9469 | 0.9662 | 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 | 0.963 |
| 4th Layer | 2.7.7.6 | 0.946 |
Prediction of Functionally Associated Proteins
Functionally Associated Proteins Detected by STRING
Original result from the STRING server
Fail to connect to STRING server
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 | 1149 | |||
| PRK08565 | 1103 | PRK08565, PRK08565, DNA-directed RNA polymerase su | 0.0 | |
| COG0085 | 1060 | COG0085, RpoB, DNA-directed RNA polymerase, beta s | 0.0 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 0.0 | |
| TIGR03670 | 599 | TIGR03670, rpoB_arch, DNA-directed RNA polymerase | 0.0 | |
| PRK07225 | 605 | PRK07225, PRK07225, DNA-directed RNA polymerase su | 0.0 | |
| pfam00562 | 373 | pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do | 1e-173 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 1e-122 | |
| PRK09606 | 494 | PRK09606, PRK09606, DNA-directed RNA polymerase su | 1e-100 | |
| pfam04563 | 394 | pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub | 3e-85 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 6e-51 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 6e-45 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 2e-36 | |
| pfam04560 | 78 | pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, do | 1e-32 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 4e-32 | |
| pfam04561 | 185 | pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do | 3e-23 | |
| pfam04565 | 68 | pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do | 2e-20 | |
| pfam04566 | 63 | pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, do | 6e-19 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 8e-16 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 6e-15 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 8e-14 | |
| pfam04567 | 46 | pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, do | 1e-12 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 9e-12 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 1e-10 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 5e-10 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 5e-09 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 1e-08 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 3e-06 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 2e-04 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 0.003 |
| >gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
Score = 1044 bits (2702), Expect = 0.0
Identities = 462/1138 (40%), Positives = 668/1138 (58%), Gaps = 71/1138 (6%)
Query: 38 FLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSM-TVDG 96
+ K +GLV+QHLDS+N F+ G+++IV I + I P + + +R+G+P + DG
Sbjct: 8 YFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADG 66
Query: 97 VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLY 156
+ P RL ++TYAAP+ + + V+ + V IG +PIM++S C L
Sbjct: 67 SERPITPMEARLRNLTYAAPLYLTMIPVENGIEYEPEE----VKIGDLPIMVKSKICPLS 122
Query: 157 GKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNIN---ASVTS 213
G EL +GE P DPGGYFII G+E+V++ QE L+ NRV++D + G+ A V S
Sbjct: 123 GLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVIS 182
Query: 214 STETVKSKTVIQMEK-GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSAL 272
S +++ ++ K G +Y+ KIP +++M+A+G+E+D+++V V DP
Sbjct: 183 SRAGYRAQVTVERRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEIQQE 242
Query: 273 LLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNN 332
LLPS+E+ +++ T E AL+Y+ KR G P R RA IL L ++
Sbjct: 243 LLPSLEQASSIAA-TVEDALDYIG---KRVAIGQPREYRIERAEQILDKYLLPHLGTSPE 298
Query: 333 NFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQ 392
+ K +++ M +++E L + DDKD+ NKRL L+G L++ LF FK ++ +++
Sbjct: 299 DRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLK 358
Query: 393 KTVDIILSKPSRSSRFDLSQFIVR-DSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARL 451
++ + R + DL + IVR D IT + L+TGN+ R G++Q+L R
Sbjct: 359 YQLEKSYA---RGRKLDL-RAIVRPDIITERIRHALATGNW-----VGGRTGVSQLLDRT 409
Query: 452 SFIGTLGHMTRV-------SPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504
+++ TL H+ RV P FE R L +QWG +CP +TPEG CGLVKNL
Sbjct: 410 NYLSTLSHLRRVVSPLSRGQPHFEA-------RDLHGTQWGRICPFETPEGPNCGLVKNL 462
Query: 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFA 564
ALM ++ +E + + Y LGV +E EE + V NG ++G H + A
Sbjct: 463 ALMAQISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELA 520
Query: 565 DVMRKLRRAGKIGEFVSV--FVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKEL 622
+ +R+LRR+GKI + V+V + VY+ D GRV RPL++ + G ++ H+++L
Sbjct: 521 EKIRELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKL 580
Query: 623 LDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPY 682
G +FDD ++ G+IEYLD EE NA +AL D TP+ TH+EI P ILG+ A +IPY
Sbjct: 581 KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEIWPPAILGITASIIPY 640
Query: 683 PHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG 742
P HNQSPRNTYQ AM KQ++G A N R D+ +LL YPQRPL+ TR +E++GY+
Sbjct: 641 PEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRP 700
Query: 743 AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPD 802
AGQNA VAV+SY+GY+IEDAI+MNK+S++RG R + Y +KY D+I P+
Sbjct: 701 AGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPE 760
Query: 803 ---RTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESP----LETRGSIMSPTGQTDS- 854
R G E + LD+DG+ +P +K DV I K SP E + + D+
Sbjct: 761 PNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTS 820
Query: 855 ---RYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQK 911
R+ GE +VD V + G+ +K +R R PELGDKF+SRHGQK
Sbjct: 821 VTVRH-----------GEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQK 869
Query: 912 GVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAF 971
GV G +V QED PF+E GI PDLI+NPH PSRMTVG+++E + GK GRF + F
Sbjct: 870 GVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929
Query: 972 -GEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLD 1030
GEP E + + L+K G+ +G +++Y G TG ++A IF+G +YYQKL HMV D
Sbjct: 930 YGEP------EEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
Query: 1031 KMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQ 1090
K+HAR GP +LTRQPTEGRAR GGLR GEMERDCLI +GA+ML+ ERL+ SSD +
Sbjct: 984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIY 1043
Query: 1091 VCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAE 1148
VC +CG + +Y+ + +C + NIS +++ YA KLL+QEL SM I PRLKL +
Sbjct: 1044 VCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGD 1101
|
Length = 1103 |
| >gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | 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|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6 | Back alignment and domain information |
|---|
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|233685 TIGR02013, rpoB, DNA-directed 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|214330 CHL00001, rpoB, RNA polymerase beta subunit | 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|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed | 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|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3 | Back alignment and domain information |
|---|
| >gnl|CDD|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4 | Back alignment and domain information |
|---|
| >gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | 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|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 | 1149 | |||
| 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 | |
| KOG0216 | 1111 | consensus RNA polymerase I, second largest subunit | 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 | 99.92 | |
| 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 | 99.7 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 99.07 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 98.98 | |
| PF04567 | 48 | RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int | 98.83 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 98.1 | |
| PF06883 | 58 | RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do | 97.54 | |
| PHA03394 | 865 | lef-8 DNA-directed RNA polymerase subunit beta-lik | 95.78 |
| >PRK08565 DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=5e-278 Score=2618.64 Aligned_cols=1090 Identities=41% Similarity=0.696 Sum_probs=999.0
Q ss_pred ccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCCCcEEEEEeEEEEcCCccccCC-cCCCCChhhHhhc
Q 001124 31 KFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLS 109 (1149)
Q Consensus 31 ~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~~~~~l~~~~i~i~~P~~~e~~-~~~~l~P~EcR~r 109 (1149)
.|.++++||+.++|++||++|||+|+++||++++++++||+.. ++++.|+|++++|++|++.+++ ...+|+|+|||+|
T Consensus 1 ~~~li~~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~-~~~~~L~f~~i~l~~P~~~~~~~~~~~l~P~ecR~r 79 (1103)
T PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTE-IPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79 (1103)
T ss_pred CchHHHHHhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEec-CCCEEEEEEEEEECCCcccccccccCCCCHHHHHhc
Confidence 4999999999999999999999999999999999999999764 6789999999999999997665 5678999999999
Q ss_pred CCccCccEEEEEEEEECCcccceeeEEeeEEeeccceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHHh
Q 001124 110 DMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQ 189 (1149)
Q Consensus 110 ~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~~s~~elv~~~E~~~d~GGYFIING~ERVI~~q 189 (1149)
++||+|||+|+|+++.++ ...++++|++|+|||||+|++|||++++|+||++.||||+|+||||||||+|||||+|
T Consensus 80 ~lTYsa~l~v~i~~~~~~----~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIING~ERVI~~q 155 (1103)
T PRK08565 80 NLTYAAPLYLTMIPVENG----IEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQ 155 (1103)
T ss_pred CCCcceEEEEEEEEEECC----eeeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEECCcEEEEEEE
Confidence 999999999999997654 4455668999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCeEEEEeCCCC---cEEEEEEecCCCcc-eEEEEEeeCCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCC
Q 001124 190 EQLSKNRVIIDTDKKG---NINASVTSSTETVK-SKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR 265 (1149)
Q Consensus 190 ~~~s~N~i~~~~~~~g---~~~a~v~s~~~~~~-s~~~~~~k~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~ 265 (1149)
|++++|+++++.+.++ .+.|.++|.++..+ +..+++..+|.++++++++.++||+++||||||++||+||++.|+.
T Consensus 156 ~~~s~n~~~~~~~~~~~~~~~~a~i~s~~~~~~~~~~l~~~~~g~i~~~~~~~~~~IPi~illkALG~~sD~eI~~~i~~ 235 (1103)
T PRK08565 156 EDLAPNRVLVDKGEAGSSITHTAKVISSRAGYRAQVTVERRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSL 235 (1103)
T ss_pred EecCCCEEEEEEecCCCcceEEEEEEeccCCCcceEEEEEecCCeEEEEEcCcccEeeHHHHHHHcCCCCHHHHHHHhcc
Confidence 9999999998765432 36788988876543 3444445678999999987678999999999999999999999976
Q ss_pred chhHHhhhHHhHHHHHhcCC-cCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCccchHHHH
Q 001124 266 DPRYSALLLPSIEECANLDI-YTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVM 344 (1149)
Q Consensus 266 ~~~~~~~l~~~l~~~~~~~i-~t~~~al~yIg~~~r~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~M 344 (1149)
+..+.+.+..+++++. .+ .|+++||.|||++|++. .++.+ ..+.|+++|++++|||++.+..++.+|+++|++|
T Consensus 236 ~~~~~~~l~~~l~~~~--~~~~t~~~al~~ig~~~~~~--~~~~~-~~e~~~~~L~~~ll~Hig~~~~~~~~K~~~L~~M 310 (1103)
T PRK08565 236 DPEIQQELLPSLEQAS--SIAATVEDALDYIGKRVAIG--QPREY-RIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQM 310 (1103)
T ss_pred cHHHHHHHHHHHHHhh--ccccCHHHHHHHHHHhccCC--CCCcc-HHHHHHHHHHhhCcccCCCcccchhHHHHHHHHH
Confidence 6666677777777653 25 79999999999999875 33445 6789999999999999997665567899999999
Q ss_pred HHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHH
Q 001124 345 LRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLE 424 (1149)
Q Consensus 345 i~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~ 424 (1149)
++||+++..|.+.+||+|||+||||+++|+||+.+||++|+++++.+|+++.+.+.+. ..+++..+++++.||++|+
T Consensus 311 i~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~~---~~~~~~~~i~~~~It~~i~ 387 (1103)
T PRK08565 311 ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARG---RKLDLRAIVRPDIITERIR 387 (1103)
T ss_pred HHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc---ccCCHHHhcccchhhHHHH
Confidence 9999999999999999999999999999999999999999999999999998765432 2456777778889999999
Q ss_pred HHhccCCCcccccccccccceEEccccccccccccccccccccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhc
Q 001124 425 RTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504 (1149)
Q Consensus 425 ~~~sTGnw~~~~~~~q~sGvsq~l~rln~ls~LshlRrv~~~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~L 504 (1149)
+|||||||.. |++|+||+|+|+||+|+||||||+++++.+++|.++||+||||||||+||||||||++||||+||
T Consensus 388 ~~~sTGnw~~-----~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~r~~~~~~vR~Lhps~wG~iCPveTPEG~~cGLv~~L 462 (1103)
T PRK08565 388 HALATGNWVG-----GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNL 462 (1103)
T ss_pred HHHhcCcccc-----CCcceEEecccCCHHHHHHHHhhccCCcccCCCCccccccChhhccccCCCCCCCccccchhhhh
Confidence 9999999984 67999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeeccCCCchhHHHHHhhcCceeccccCccccCCCCceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEe
Q 001124 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV 584 (1149)
Q Consensus 505 A~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~ 584 (1149)
|++|+|+++.+..++.++|.++|+.++..+++... ...++|||||+|||++++|..|++.||.+||+|.++.+++|++
T Consensus 463 A~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~--~~~~~V~lnG~~iG~~~~~~~l~~~lR~~Rr~g~i~~~v~I~~ 540 (1103)
T PRK08565 463 ALMAQISVGVDEEEVEEILYELGVVPVEEAREEEY--ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAY 540 (1103)
T ss_pred hcccccccCCChHHHHHHHHHcCCCchhhcCcccC--CCceEEEECCEEEEEECCHHHHHHHHHHHhhcCCCCCeEEEEE
Confidence 99999999888899999999999998765544332 3568999999999999999999999999999999999999999
Q ss_pred cc--cCceEEEecCCCeeeeeEEEeecCcccchhhhHHhhhcCCcchhhhhccCceeEeccccccceEEEeecCCCCCCc
Q 001124 585 NE--KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDT 662 (1149)
Q Consensus 585 ~~--~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~ 662 (1149)
+. ..++|+|+||+||++|||++|++|++.+++++++.++.+..+|++|+++|.|||||++||++++||+.++++...+
T Consensus 541 ~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~~~~~~l~~~g~iEyid~~Ee~~~~Ia~~~~~l~~~~ 620 (1103)
T PRK08565 541 IETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEH 620 (1103)
T ss_pred ccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhccccchhhHhhcCcEEeeCHHHhcCcEEeccccccCcce
Confidence 98 8899999999999999999999999999999999888778899999999999999999999999999999998778
Q ss_pred eeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeechhhhhccCCCCC
Q 001124 663 THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG 742 (1149)
Q Consensus 663 th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~~~~~~p 742 (1149)
||+||+|.+|||++||+|||+||||||||||||||||||||++++|+..|+|++.|+|+|||+|||+|+.++.++++++|
T Consensus 621 th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~KQa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p 700 (1103)
T PRK08565 621 THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRP 700 (1103)
T ss_pred eccccCCccccceeeeccCCcccCcccchhhhhhhhhcccccccccceEeecCCcceeecCceeEEEeccccccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecCCCCCC---CchhhhccCCCCcc
Q 001124 743 AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTG---PGAERMQILDDDGL 819 (1149)
Q Consensus 743 ~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~---~~~~~~~~Ld~dGi 819 (1149)
+|+||+||||||+||||||||||||+|+|||||||+||++|+++++++..+..+.+..|.... .+...|++||+|||
T Consensus 701 ~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi 780 (1103)
T PRK08565 701 AGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGI 780 (1103)
T ss_pred CCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeecCCCCceEEecCCCcccccCchhhhhcCCCCCC
Confidence 999999999999999999999999999999999999999999998876666666676653211 12246899999999
Q ss_pred cCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcEEEEEEEeeecCCC
Q 001124 820 AAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPE 899 (1149)
Q Consensus 820 ~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~~~~~~vkv~~~~~R~p~ 899 (1149)
|++|++|++|||||||++|..+...... .+......+++|++++.+| .|+||+|.++.++++.+.|||++|+.|+|+
T Consensus 781 ~~~G~~v~~gdili~k~~p~~~~~~~~~-~~~~~~~~~~~s~~~~~~e--~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~ 857 (1103)
T PRK08565 781 VSPEVEVKGGDVLIGKTSPPRFLEELEE-LSLGLQERRDTSVTVRHGE--KGIVDTVLITESPEGNKLVKVRVRDLRIPE 857 (1103)
T ss_pred cCCCcEEcCCCEEEEEecCCCCCcchhh-ccccCCccccceEEecCCC--ceEEEEEEEEecCCCcEEEEEEEEEEecCc
Confidence 9999999999999999999753321100 0111234789999999998 999999999988888999999999999999
Q ss_pred ccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeeccCCCCCCC
Q 001124 900 LGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHAD 979 (1149)
Q Consensus 900 iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~ 979 (1149)
||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.|+|||. +.
T Consensus 858 iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~-----~~ 932 (1103)
T PRK08565 858 LGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFY-----GE 932 (1103)
T ss_pred hhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcC-----Cc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999 57
Q ss_pred CHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccCCCceee
Q 001124 980 TVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRV 1059 (1149)
Q Consensus 980 ~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~ 1059 (1149)
.++++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||||+|||||
T Consensus 933 ~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~R~ 1012 (1103)
T PRK08565 933 PEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012 (1103)
T ss_pred hHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCeee
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred echhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHHHHHHhCC
Q 001124 1060 GEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMN 1139 (1149)
Q Consensus 1060 GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~ 1139 (1149)
||||||||+|||||++|+|||+++||++.++||.+||++++.+.+.+..+|+.|+++.++.++.+|||||||+|||+|||
T Consensus 1013 GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm~ 1092 (1103)
T PRK08565 1013 GEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMG 1092 (1103)
T ss_pred ecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccCCCCcceeccCChhHHHHHHHHHhCC
Confidence 99999999999999999999999999999999999999997655555677999999888999999999999999999999
Q ss_pred cccEEEecc
Q 001124 1140 IVPRLKLAE 1148 (1149)
Q Consensus 1140 i~~~l~~~~ 1148 (1149)
|+++|.+++
T Consensus 1093 i~~~l~~~~ 1101 (1103)
T PRK08565 1093 ISPRLKLGD 1101 (1103)
T ss_pred CceEEEeee
Confidence 999999975
|
|
| >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 |
|---|
| >KOG0216 consensus RNA polymerase I, 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 |
|---|
| >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 |
|---|
| >PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >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 |
|---|
| >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 | 1149 | ||||
| 2waq_B | 1131 | The Complete Structure Of The Archaeal 13-Subunit D | 0.0 | ||
| 2pmz_B | 1124 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 0.0 | ||
| 1i3q_B | 1224 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 0.0 | ||
| 3h0g_B | 1210 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 0.0 | ||
| 1ynj_C | 1119 | Taq Rna Polymerase-Sorangicin Complex Length = 1119 | 5e-42 | ||
| 1i6v_C | 1118 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 5e-42 | ||
| 1hqm_C | 1119 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 6e-42 | ||
| 1l9u_C | 1118 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 6e-42 | ||
| 1iw7_C | 1119 | Crystal Structure Of The Rna Polymerase Holoenzyme | 1e-41 | ||
| 3iyd_C | 1342 | Three-Dimensional Em Structure Of An Intact Activat | 3e-25 | ||
| 3lu0_C | 1342 | Molecular Model Of Escherichia Coli Core Rna Polyme | 3e-25 | ||
| 3qqc_A | 436 | Crystal Structure Of Archaeal Spt45 BOUND TO THE RN | 1e-05 |
| >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|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 | Back alignment and structure |
| >pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 | 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|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1119 | Back alignment and structure |
| >pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 | Back alignment and structure |
| >pdb|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|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 |
| >pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >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 |
|---|
Score = 1396 bits (3614), Expect = 0.0
Identities = 427/1216 (35%), Positives = 642/1216 (52%), Gaps = 108/1216 (8%)
Query: 24 PVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIV-----------S 72
+ D + ++ F + L +Q L SF+ FV +++IV + +
Sbjct: 10 ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQG 69
Query: 73 GIDPSIFLRFKDVRIGQPSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT-- 129
+ + F + + +P+MT DG + + P RL ++TY++P+ V++
Sbjct: 70 DVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADS 129
Query: 130 -----------EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFI 178
E+ E + V IG+IPIMLRS C+L G ++EL L ECP D GGYFI
Sbjct: 130 NVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFI 189
Query: 179 IKGTEKVLLIQEQLSKNRVIIDTDKKGNINA--SVTSSTETVKSKTVIQMEK-------- 228
I G+EKV++ QE+ + N V + + A + S S+ + M+
Sbjct: 190 INGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE 249
Query: 229 ---GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDP---RYSALLLPSIEECAN 282
+ L IPI++V +A+G+ D+++++ + DP + ++ P IEE
Sbjct: 250 NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFV 309
Query: 283 LDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVA 342
I ++ AL+Y+ + T G R A IL+ L ++ K F++
Sbjct: 310 --IQDKDIALDYIGKRGS--TTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLG 365
Query: 343 VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKP 402
M+ RM+ L + DD+D+ G KRL+L+G L++ LF LF+ M +V K + +
Sbjct: 366 YMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETN 425
Query: 403 SRSSRFDLSQFIVRDSITVGLERTLSTGNF-DVKRFKMHRKGMTQVLARLSFIGTLGHMT 461
F+L+ + + IT GL +L+TGN+ D KR ++R G++QVL R +F TL H+
Sbjct: 426 RE---FNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLR 482
Query: 462 RVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLIS 521
R + + K++ PR L + WGM+CP +TPEG+ACGLVKNL+LM++V+ P+I
Sbjct: 483 RTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIE 542
Query: 522 LCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVS 581
G+E LE + +PN+ V NG+ LG HR P + +R LRR I VS
Sbjct: 543 FLEEWGLETLEDYNPS--ASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVS 600
Query: 582 VFVNEKQRCVYIASDGGRVCRPLVIAD-------KGISRIKEHHMKELLDGVR------- 627
+ + +++ + + +D GR+CRPL I D +G I++ H+++L++
Sbjct: 601 IVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPE 660
Query: 628 ---SFDDFLREGLIEYLDVNEENNALIALYEGDATPDT---------------------- 662
+ + GLIEYLD EE +IA+ D
Sbjct: 661 QRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAP 720
Query: 663 -------THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDS 715
TH EI P ILG++A +IP+P HNQSPRNTYQ AMGKQAMG N RMD+
Sbjct: 721 NPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDT 780
Query: 716 LLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFG 775
+ +L YPQ+PL TTR++E + + +L AGQNA VA++ YSGY+ ED+I+MN++S+DRG
Sbjct: 781 MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLF 840
Query: 776 RCIVVKKYTAINQKYANSTSDRILRPDR---TGPGAERMQILDDDGLAAPGEIIKPNDVY 832
R I + YT +K + + RP R L+DDGL APG + D+
Sbjct: 841 RSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDII 900
Query: 833 INKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLI 892
I K +P+ + R + E+ +VD+V + +++ G +K +
Sbjct: 901 IGKTAPIPLDHEELGQ-RTQLHAKRDVSTPLRST--ESGIVDQVMVTTNQEGLKFVKVRM 957
Query: 893 RHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIE 952
R TR P++GDKF+SRHGQKG G + ED PFS +GI PD+I+NPH PSRMTV ++E
Sbjct: 958 RSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVE 1017
Query: 953 LLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQA 1012
K G + F + TVE++S+ L HGF G +++Y G TG L A
Sbjct: 1018 CQLSKVSALSGFEGDATPFTD-----VTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVA 1072
Query: 1013 YIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGA 1072
+F+GP YYQ+LKH+V DK+HAR GP +LTRQP EGR+R+GGLR GEMERDC I++G
Sbjct: 1073 QVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGC 1132
Query: 1073 SMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLI 1132
S ++ ERL SD + V VC +CGL+ ++K + C +C+N S + LPYA KLL
Sbjct: 1133 SSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLF 1192
Query: 1133 QELQSMNIVPRLKLAE 1148
QEL SMNI PRL
Sbjct: 1193 QELMSMNIAPRLFTKN 1208
|
| >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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} Length = 188 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1149 | |||
| 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 | 99.96 | |
| 3tbi_B | 228 | DNA-directed RNA polymerase subunit beta; transcri | 99.33 | |
| 3qqc_A | 436 | DNA-directed RNA polymerase subunit B, DNA-direct | 99.12 | |
| 3lti_A | 296 | DNA-directed RNA polymerase subunit beta; BBM2, nu | 98.81 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 96.34 |
| >3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
Probab=100.00 E-value=9.2e-295 Score=2753.36 Aligned_cols=1109 Identities=38% Similarity=0.634 Sum_probs=1009.2
Q ss_pred CCcccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecCC-----------CcEEEEEeEEEEcCCcc
Q 001124 24 PVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGID-----------PSIFLRFKDVRIGQPSM 92 (1149)
Q Consensus 24 ~~~~~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~~-----------~~~~l~~~~i~i~~P~~ 92 (1149)
..++.+|+|.++++||+.++|++|||||||+|+++||++|++++++|+++.+ .++.|+|++++|++|++
T Consensus 10 ~~~~~ed~w~li~aff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~ 89 (1210)
T 3h0g_B 10 ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTM 89 (1210)
T ss_dssp CCCCHHHHHHHHHHHHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCC
T ss_pred ccCCHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHHhccCcEEecCccCcccccccCCceEEEEEEEEEEcCCce
Confidence 3488999999999999999999999999999999999999999999976542 36899999999999999
Q ss_pred ccCC-cCCCCChhhHhhcCCccCccEEEEEEEEECCcc----------c---ceeeEEeeEEeeccceeeccccccCCCC
Q 001124 93 TVDG-VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT----------E---KTTMEKNDVVIGRIPIMLRSCRCVLYGK 158 (1149)
Q Consensus 93 ~e~~-~~~~l~P~EcR~r~lTYsa~l~v~i~~~~~~~~----------~---~~~~~~~~v~lG~IPIMvkS~~C~L~~~ 158 (1149)
.+++ ...++||+|||+|++||+|||+|+|+++.++.. . .......++.||+|||||||++|||+++
T Consensus 90 ~e~d~~~~~l~P~EcRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~ 169 (1210)
T 3h0g_B 90 TEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGV 169 (1210)
T ss_dssp BCTTSCBCCCCTTTTTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSC
T ss_pred ecCCCcccccCHHHHHhcCCccceeEEEEEEEEEcCccccccccccccccccccccccceEEEecCCEEeCCCcccCCCC
Confidence 8877 788999999999999999999999999875421 0 0112235799999999999999999999
Q ss_pred CHHHHHhcCCCCCCCCcEEEEcCchhhhHHhhhccCCeEEEEeCCC---CcEEEEEEecCCCcc----eEEEEEee----
Q 001124 159 DEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKK---GNINASVTSSTETVK----SKTVIQME---- 227 (1149)
Q Consensus 159 s~~elv~~~E~~~d~GGYFIING~ERVI~~q~~~s~N~i~~~~~~~---g~~~a~v~s~~~~~~----s~~~~~~k---- 227 (1149)
+++||+++||||+|+||||||||+||||++|+++++|+|++++++. ..+.|.++|++.+.+ +.++.++.
T Consensus 170 s~~eL~~~gEcp~D~GGYFIING~EKVII~qerla~N~~iv~~~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~ 249 (1210)
T 3h0g_B 170 SDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE 249 (1210)
T ss_dssp CHHHHHHTTCCTTCCCCCBCGGGSCBCCCBCBCCCCSCCCCCCCCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTT
T ss_pred CHHHHHhcCCCCCCCCCEEEEeCEEEEEEechhhccceEEEEeecCCCCceEEEEEEEEecCCccceeEEEEEEEecccc
Confidence 9999999999999999999999999999999999999999986542 246788888877542 22223332
Q ss_pred --CCEEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhC---CchhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcccC
Q 001124 228 --KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG---RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRS 302 (1149)
Q Consensus 228 --~g~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~---~~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r~~ 302 (1149)
++.++++++.++.+||++++|||||.+||+||++.|. .++++.+.|.++++++. .++|+++||+|||+|++..
T Consensus 250 ~~~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~~--~i~tq~~aL~yIG~r~~~~ 327 (1210)
T 3h0g_B 250 NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAF--VIQDKDIALDYIGKRGSTT 327 (1210)
T ss_dssp SCSCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTTS--SCCSSHHHHHTTCCCSSSC
T ss_pred CCCceEEEEEeccccCCcHHHHHHHcCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHhh--hcCCHHHHHHHHHHhcccc
Confidence 5688999999888999999999999999999999994 57889999999998874 4899999999999999853
Q ss_pred CCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHHHH
Q 001124 303 TFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFED 382 (1149)
Q Consensus 303 ~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lfr~ 382 (1149)
..++.+ +++.|+++|++++|||++..+.++.+|+.||++|+|||++++.|.+.+||+|||+||||+++|+||+.+||+
T Consensus 328 -~~~~~~-~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~lfr~ 405 (1210)
T 3h0g_B 328 -GVTREK-RLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRM 405 (1210)
T ss_dssp -CCCHHH-HHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHHHHHH
T ss_pred -CCCchh-HHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHHHHHHH
Confidence 223445 789999999999999999888888899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHHHHhccCCCc-ccccccccccceEEcccccccccccccc
Q 001124 383 LFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFD-VKRFKMHRKGMTQVLARLSFIGTLGHMT 461 (1149)
Q Consensus 383 ~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~-~~~~~~q~sGvsq~l~rln~ls~LshlR 461 (1149)
.|+++++.+++.+++.+.+.+ .+++..+++++.||++|++|||||||+ .++++++++||||+|+|+||+|+|||||
T Consensus 406 ~~~~~~~~i~~~l~k~~~~~~---~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~lShlR 482 (1210)
T 3h0g_B 406 LFRKMTRDVYKYMQKCVETNR---EFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLR 482 (1210)
T ss_dssp HHHHHHHHHHHHHHHHHTTCC---SCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHhhcCC---ccCHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCCHHHHHHHHH
Confidence 999999999999999877642 467777888999999999999999998 5567889999999999999999999999
Q ss_pred ccccccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCccccCC
Q 001124 462 RVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHN 541 (1149)
Q Consensus 462 rv~~~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~ 541 (1149)
|++++|++++|+++||+||||||||+||+|||||++|||+||||++|.||++.+.+||.++|.++||++++.+++...
T Consensus 483 rv~~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le~~~~~~~-- 560 (1210)
T 3h0g_B 483 RTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSAS-- 560 (1210)
T ss_dssp BBCCSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCSCCCSSSS--
T ss_pred hccCchhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHhCCcchhhcCcccC--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999987765543
Q ss_pred CCceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecC-------cccc
Q 001124 542 PNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKG-------ISRI 614 (1149)
Q Consensus 542 ~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~-------~~~~ 614 (1149)
++.++|||||+|||++++|..|++.||.+||+|.|+.+|||+++...++++||||+||+||||++|+|+ ++.+
T Consensus 561 ~~~tkVfvNG~wVGvh~dp~~Lv~~lR~lRR~g~Is~eVSIvrdir~rE~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l 640 (1210)
T 3h0g_B 561 PNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCI 640 (1210)
T ss_dssp SSSCCCCSTTCCCCCCSCHHHHHHHHHHHHTTTSSCTTCCCCCCTTTCCCCCCCSSCCBCCEEEECCCSSCSSSSCCCSS
T ss_pred CCceEEEECCEEEEEeCCHHHHHHHHHHHhhcCCCCCceEEEecCCCCeEEEecCCCcccceEEEEccCCcccccccccc
Confidence 467899999999999999999999999999999999999999999999999999999999999999986 8999
Q ss_pred hhhhHHhhhcC----------CcchhhhhccCceeEeccccccceEEEeecCCCC-------------------------
Q 001124 615 KEHHMKELLDG----------VRSFDDFLREGLIEYLDVNEENNALIALYEGDAT------------------------- 659 (1149)
Q Consensus 615 ~~~~~~~~~~~----------~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~------------------------- 659 (1149)
+++|+++|..+ ..+|++|++.|.|||||++||++++|||+++|+.
T Consensus 641 ~k~hi~~L~~~~~~~~~~~~~~~~w~~Lv~~GvIEylDaeEEet~mIamtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~ 720 (1210)
T 3h0g_B 641 RKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAP 720 (1210)
T ss_dssp CHHHHHHHHHHHTCCCSCTTCCCSSTTTTTTTSEEECCTTTGGGCCEESCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCS
T ss_pred cHHHHHHHhcccccccccccccCCHHHHHhCCCEEEecHhhhhceeEEecHHHhhhhhhhhccccccccccchhhccccC
Confidence 99999988642 4789999999999999999999999999998862
Q ss_pred ----CCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeechhhhh
Q 001124 660 ----PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIEL 735 (1149)
Q Consensus 660 ----~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~ 735 (1149)
..||||||||++|||||||+||||||||||||||||||+|||||++++|+..|+||++|+|+|||+|||+|+.++.
T Consensus 721 ~~~~~~~THcEIhPsmILGIcASiIPFpdHNQSPRNtYQ~aMgKQamG~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~ 800 (1210)
T 3h0g_B 721 NPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEY 800 (1210)
T ss_dssp CCSCCSCSEECSCGGGSSCSSSTTSSSSTTSCSHHHHHHHHHHTTCCSCCCTTTTTSCCSSEEEESSCBCCSSBCTTSTT
T ss_pred CCcccccccccccchhhhhheeecccCccccccchhhhhhhhhcccccccccccccccCccccEeecCcCccccchhHHH
Confidence 3589999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecCCCCCCC---chhhhc
Q 001124 736 VGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGP---GAERMQ 812 (1149)
Q Consensus 736 ~~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~~---~~~~~~ 812 (1149)
++++|+|+|+||+||||||+||||||||||||+|+|||||||+||++|+++++++..+..+.|..|+.+.. +...|+
T Consensus 801 ~~~~elp~G~NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~y~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~ 880 (1210)
T 3h0g_B 801 LKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYD 880 (1210)
T ss_dssp TTCTTSCSCCEECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEEEEECCCCCSSSCCCCCCCCCTTSCCSCCSCCGG
T ss_pred hCCCcccCccceEEEEeccCCCChhhheeeehhheecCceEEEEEEEEEEEeeecCCCceeEEcCCCcchhcccchhhHh
Confidence 99999999999999999999999999999999999999999999999999998876666788888875321 223789
Q ss_pred cCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcEEEEEEE
Q 001124 813 ILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLI 892 (1149)
Q Consensus 813 ~Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~~~~~~vkv~~ 892 (1149)
+||+||||++|++|++|||||||++|......... ++.+...++|+|++++++| .|+||+|.++.+++|.+.|||++
T Consensus 881 ~LD~dGi~~~G~~v~~gDiligK~~p~~~~~~~~~-~~~~~~~~rd~s~~~~~~e--~g~Vd~V~~~~~~~g~~~vkv~~ 957 (1210)
T 3h0g_B 881 KLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELG-QRTQLHAKRDVSTPLRSTE--SGIVDQVMVTTNQEGLKFVKVRM 957 (1210)
T ss_dssp GCCTTSSCCTTCCCCTTCCCCCCCCCC------------CCCCCCCCCCCCCTTC--CCCCCEEEEEECSSSSEEEEEEE
T ss_pred hcCCCCCcCCCCEecCCCEEEEEecCCCCCchhhc-ccccccccceeeEEecCCC--CeEEEEEEEEEecCCCeEEEEEE
Confidence 99999999999999999999999999875432221 2334556899999999999 99999999999999999999999
Q ss_pred eeecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeecc
Q 001124 893 RHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFG 972 (1149)
Q Consensus 893 ~~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~ 972 (1149)
|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.|+|||+
T Consensus 958 ~~~R~~~~GDK~a~RhGqKGvi~~i~~~edmPf~~~G~~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~ 1037 (1210)
T 3h0g_B 958 RSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFT 1037 (1210)
T ss_dssp CCCBCCCTTCEEECTTCCCEEEEEEECTTTSCCBTTTBCCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSC
T ss_pred EEecCCCchhhhhcccCCCceeeEEeccccCCcCCCCCCCeEEECCCcCCCCccchhhhHhHHHHHHHhcCCceeeccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCccccc
Q 001124 973 EPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRA 1052 (1149)
Q Consensus 973 ~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~ 1052 (1149)
+..++++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||+||+||||+|||+.|||||++||+
T Consensus 1038 -----~~~~~~~~~~l~~~g~~~~G~~~l~~g~tg~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~gp~~~~t~QP~~gr~ 1112 (1210)
T 3h0g_B 1038 -----DVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRS 1112 (1210)
T ss_dssp -----SCCHHHHHHHHHTTTSCTTSCBCCBCSSSCCBCSSCBEECCEECEECSCCSTTTCEECSSCCBCSSSCSBCCSST
T ss_pred -----CCcHHHHHHHHHHcCcCCCCCEEEEcCCCCCCccccEEEEehHhhcchhhcccCcEEeccCCCchhccCCccccc
Confidence 789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceeecccccceecccccCCCccccccccHhHHHHH
Q 001124 1053 RNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLI 1132 (1149)
Q Consensus 1053 ~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~ 1132 (1149)
|+|||||||||||||+|||||++|||||+++||.+.++||..||++++.+...+..+|+.|.++.++.++.||||||||+
T Consensus 1113 ~~GG~r~GEME~~~l~a~Gaa~~l~e~l~~~SD~~~~~vC~~cg~~~~~~~~~~~~~c~~c~~~~~i~~~~~p~~~k~l~ 1192 (1210)
T 3h0g_B 1113 RDGGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLF 1192 (1210)
T ss_dssp TCCCCCCCHHHHHHHHHHTBHHHHHHHHHTTTTCCEEEEESSSCCBCCCCSSSCCCCCTTTCCSSCEEEEECCHHHHHHH
T ss_pred ccCCeeeehhhhhhhhhccHHHHHHHHhhcCCCcceeEeecCCCCeeeecccCCceEcCccCCCCccceecCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999998765555667899999999999999999999999
Q ss_pred HHHHhCCcccEEEeccC
Q 001124 1133 QELQSMNIVPRLKLAEA 1149 (1149)
Q Consensus 1133 ~EL~sm~i~~~l~~~~~ 1149 (1149)
|||+||||.+||.++++
T Consensus 1193 ~El~~~~i~~rl~~~~~ 1209 (1210)
T 3h0g_B 1193 QELMSMNIAPRLFTKNH 1209 (1210)
T ss_dssp HHHHTTTCCEECCCSTT
T ss_pred HHHHhCCCceEEEecCC
Confidence 99999999999999875
|
| >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 |
|---|
| >3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli} | 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 |
|---|
| >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 |
| 1149 | ||||
| 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 | 0.0 |
| >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 = 874 bits (2259), Expect = 0.0
Identities = 422/1220 (34%), Positives = 643/1220 (52%), Gaps = 108/1220 (8%)
Query: 19 QKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIV------- 71
+ +AP+ + D + ++ F + +GLV Q LDSFN FV+ ++ I+ + ++
Sbjct: 2 EDESAPI-TAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQH 60
Query: 72 ----SGIDPSIFLRFKDVRIGQPSMTV-DGVSEKLNPHMCRLSDMTYAAPILVNIEYVQG 126
I + F + + +P + DGV+ L P RL ++TY++ + V+++
Sbjct: 61 TTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTY 120
Query: 127 SHTEKTT---------------MEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPL 171
+ E V IGR+PIMLRS C L E++L +L ECP
Sbjct: 121 EAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPF 180
Query: 172 DPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTS--STETVKSKTVIQME-- 227
D GGYFII G+EKVL+ QE+ + N V + + + V S S+ + ++
Sbjct: 181 DMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVK 240
Query: 228 --------KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSA---LLLPS 276
+ L + IPI+++ +A+G+ D E+++ + D +L P
Sbjct: 241 LYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC 300
Query: 277 IEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRP 336
+E+ I +E AL+++ + + G R A IL+ FL ++
Sbjct: 301 VEDG--FVIQDRETALDFIG--RRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESR 356
Query: 337 KCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVD 396
K F++ M+ R++ L++ DD+D+ G KRL+L+G L++ LF+ LFK + ++ + +
Sbjct: 357 KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQ 416
Query: 397 IILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRK-GMTQVLARLSFIG 455
+ F++ I +IT GL+ L+TGN+ ++ M + G++QVL R ++
Sbjct: 417 RT---VEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSS 473
Query: 456 TLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEE 515
TL H+ R + + K++ PR L + WG++CP +TPEG+ACGLVKNL+LM+ ++ +
Sbjct: 474 TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTD 533
Query: 516 EGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGK 575
P+I+ G+E LE +P++ V NG+ G HR P + +R LRR G
Sbjct: 534 PMPIITFLSEWGMEPLEDY--VPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGD 591
Query: 576 IGEFVSVFVNEKQRCVYIASDGGRVCRPLVIAD------KGISRIKEHHMKELLDG---- 625
I VS+ + +++ + I +D GRV RPL I + ++++ H+ +L+
Sbjct: 592 INPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQD 651
Query: 626 ---------VRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTT------------- 663
++ L EGL+EY+D EE + LIA+ D P
Sbjct: 652 IEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKR 711
Query: 664 -----------HIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCR 712
H EI P ILGV A +IP+P HNQSPRNTYQ AMGKQAMG N R
Sbjct: 712 IRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVR 771
Query: 713 MDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDR 772
MD++ +L YPQ+PL TTR +E + + +L AGQNA VA+ YSGY+ ED+++MN+SS+DR
Sbjct: 772 MDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDR 831
Query: 773 GFGRCIVVKKYTAINQKYANS---TSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPN 829
G R + + Y +KY S T ++ R + LDDDGL APG +
Sbjct: 832 GLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGE 891
Query: 830 DVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIK 889
DV I K +P+ GQ + + + E +VD+V + ++++G +K
Sbjct: 892 DVIIGKTTPI---SPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVK 948
Query: 890 FLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGK 949
+R T+ P++GDKF+SRHGQKG G ++ED PF+ GI PDLI+NPH PSRMTV
Sbjct: 949 VRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAH 1008
Query: 950 MIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCP 1009
+IE L K G S F + TVE IS+ L +HG+ G +++Y+G TG
Sbjct: 1009 LIECLLSKVAALSGNEGDASPFTD-----ITVEGISKLLREHGYQSRGFEVMYNGHTGKK 1063
Query: 1010 LQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIA 1069
L A IF GP YYQ+L+HMV DK+HAR GP +LTRQP EGR+R+GGLR GEMERDC+IA
Sbjct: 1064 LMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIA 1123
Query: 1070 YGASMLIFERLMVSSDPFEVQVCRVCGLLGYY-NHKLKAGICSTCKNGDNISSMKLPYAC 1128
+GA+ + ERLM +SD F V +C +CGL+ C C N +I + +PYA
Sbjct: 1124 HGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA 1183
Query: 1129 KLLIQELQSMNIVPRLKLAE 1148
KLL QEL +MNI PRL
Sbjct: 1184 KLLFQELMAMNITPRLYTDR 1203
|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 | Back information, alignment and structure |
|---|
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1149 | |||
| 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: | 84.43 |
| >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=2.7e-259 Score=2508.91 Aligned_cols=1110 Identities=38% Similarity=0.644 Sum_probs=949.1
Q ss_pred CCCcccccccccccccccccchHHHHHHHHHHHHHhCHHHHHHhcccceecC-----------CCcEEEEEeEEEEcCCc
Q 001124 23 APVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-----------DPSIFLRFKDVRIGQPS 91 (1149)
Q Consensus 23 ~~~~~~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fi~~gL~~ii~~~~~I~~~~-----------~~~~~l~~~~i~i~~P~ 91 (1149)
+..++++|.|++|++||+.++|++|||+|||+||++||++|+++.+||.... ...+.|+|++++|++|+
T Consensus 5 ~~~~~~~d~w~~i~~~f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i~kP~ 84 (1207)
T d1twfb_ 5 SAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPM 84 (1207)
T ss_dssp TCCCCTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEEEEE
T ss_pred CCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHCHHHHHHhcCCeEeeccccccccccCCCceEEEEEEEEEEcCCe
Confidence 4667899999999999999999999999999999999999999999985421 23588999999999999
Q ss_pred cccCC-cCCCCChhhHhhcCCccCccEEEEEEEEECCcc---------------cceeeEEeeEEeeccceeeccccccC
Q 001124 92 MTVDG-VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT---------------EKTTMEKNDVVIGRIPIMLRSCRCVL 155 (1149)
Q Consensus 92 ~~e~~-~~~~l~P~EcR~r~lTYsa~l~v~i~~~~~~~~---------------~~~~~~~~~v~lG~IPIMvkS~~C~L 155 (1149)
+.+.+ ...++||+|||+|++||+|||+|+|++...+.. .......++|+||+|||||+|++|||
T Consensus 85 ~~e~~g~~~~l~P~EcR~r~lTYs~~l~v~i~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv~S~~C~L 164 (1207)
T d1twfb_ 85 VNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYL 164 (1207)
T ss_dssp ECCSSSCCEECCHHHHHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTTSGG
T ss_pred EEcCCCcccccCHHHHHhcCCccceEEEEEEEEEEEecccccccccceeecccccccceeeeeEEEEECCEEeCCCcccC
Confidence 98766 778999999999999999999999987532110 00123455799999999999999999
Q ss_pred CCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHHhhhccCCeEEEEeCCCC---cEEEEEEecCCCc----ceEEEEEe-e
Q 001124 156 YGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKG---NINASVTSSTETV----KSKTVIQM-E 227 (1149)
Q Consensus 156 ~~~s~~elv~~~E~~~d~GGYFIING~ERVI~~q~~~s~N~i~~~~~~~g---~~~a~v~s~~~~~----~s~~~~~~-k 227 (1149)
+++++++|++.||||+|+||||||||+||||++|++.++|++++++++++ .+.|.++|...+. .+..+.++ +
T Consensus 165 ~~~~~~~l~~~gEc~~D~GGYFIING~EKVIi~Q~r~~~n~~~v~~~~~~~~~~~~~~irS~~~~~~~~~~~~~~~~~~~ 244 (1207)
T d1twfb_ 165 SEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGR 244 (1207)
T ss_dssp GTCCHHHHHHTTCCTTCCCCSEEETTEEEEECEEEEECSSCCEEEECCTTSSEEEEEEEECCCSSSCCCCCEEEEEEESC
T ss_pred CCcCHHHHHHcCCCCCCCCcEEEECCEEEEEEEEEecCCCeEEEEEcCCCCceEEEEEEEEEeCCCCceeEEEEEEEEEc
Confidence 99999999999999999999999999999999999999999999876543 3568888875433 22233332 2
Q ss_pred CC----EEEEEEceeeccccHHHHHHHhCCCCHHHHHHHhCC---chhHHhhhHHhHHHHHhcCCcCHHHHHHHHhhhcc
Q 001124 228 KG----KMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR---DPRYSALLLPSIEECANLDIYTQEKALEYLEGKVK 300 (1149)
Q Consensus 228 ~g----~i~~r~~~~~~~IPi~ilLrALG~~sD~eI~~~i~~---~~~~~~~l~~~l~~~~~~~i~t~~~al~yIg~~~r 300 (1149)
++ .+.+.+++++.+||+++||||||..+|+||++.+.. +..+.+.+..++++. ..+.|+++|+.|||++++
T Consensus 245 ~~~~~~~i~~~~~~~~~~IPl~illrALG~~sD~eI~~~i~~~~~~~~~~~~l~~~~~~~--~~~~t~e~al~yig~~~~ 322 (1207)
T d1twfb_ 245 EGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDG--FVIQDRETALDFIGRRGT 322 (1207)
T ss_dssp SSCSSCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHT--TTCCSHHHHHHHHHHTTS
T ss_pred CCccceEEEEEeehhcccchHHHHHHHhCCcchhhhhhhcccCchhhHHHHHHHHHHhhc--cchhhHHHHHHHHHhhcc
Confidence 22 578888888788999999999999999999999942 344566666666543 457899999999999877
Q ss_pred cCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCccchHHHHHHHHHHhhcCCCCCCCcccccccEEccccHhHHHHH
Q 001124 301 RSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLF 380 (1149)
Q Consensus 301 ~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NkRv~l~G~Ll~~lf 380 (1149)
.. ..+..+ ..+.|+++|++.+|||++....+...|+.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+|
T Consensus 323 ~~-~~~~~~-~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~~~f 400 (1207)
T d1twfb_ 323 AL-GIKKEK-RIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF 400 (1207)
T ss_dssp CT-TSCHHH-HHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHHHHH
T ss_pred cc-CCCccc-hHHHHHHHHHhhhccccccccchhhhHHHHHHHHHHHHHHhhhcccCCcchhhhccchhhhHHHHHHHHH
Confidence 54 112233 6789999999999999997766677899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHHHHhccCCCccccc-ccccccceEEcccccccccccc
Q 001124 381 EDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRF-KMHRKGMTQVLARLSFIGTLGH 459 (1149)
Q Consensus 381 r~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~-~~q~sGvsq~l~rln~ls~Lsh 459 (1149)
|+.|+++++.+++.+.+...+. ..+++...++++.||++|++||+||||..... ..+++|++|+|+|+||+++|||
T Consensus 401 r~~~~~~~~~i~~~~~~~~~~~---~~~~~~~~~~~~~it~~i~~~~~TGn~~~~~~~~~~~~G~sq~l~r~n~l~~lSh 477 (1207)
T d1twfb_ 401 KTLFKKLTKDIFRYMQRTVEEA---HDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSH 477 (1207)
T ss_dssp HHHHHHHHHHHHHHHHSCCC-----------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSSHHHHHHH
T ss_pred HHHHHHHHHHHHhhhccccccc---cccChhhhhccCcHHHHHHHHHhcCcccccccccccccchhhhhhhcCHHHHHHh
Confidence 9999999999999987654332 34566667788999999999999999986533 3578999999999999999999
Q ss_pred ccccccccccccccCCCCccCCCCCcccccCCCCCCCcchhhhhccceeeeccCCCchhHHHHHhhcCceeccccCcccc
Q 001124 460 MTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEEL 539 (1149)
Q Consensus 460 lRrv~~~f~~~~k~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~~g~~~~~~~~~~~~ 539 (1149)
+||+++++++++|+++||+||||||||+||||||||+|||||||||++|+|+.+.++.++.++|..+|+.++........
T Consensus 478 ~Rrv~~~~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~~~~~~l~~~g~~~~~~~~~~~~ 557 (1207)
T d1twfb_ 478 LRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQS 557 (1207)
T ss_dssp HTEEECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTTCEEGGGCCGGGC
T ss_pred hhcccCCcccccccchhhhcchhhccceeeeeCCCCCcccceeccceeeeeccccccceeeEEeeccCcccceeeeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998776554433
Q ss_pred CCCCceEEEECCeEEEeecChhhHHHHHHHHhhcCCcCceeEEEecccCceEEEecCCCeeeeeEEEeecCcc------c
Q 001124 540 HNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGIS------R 613 (1149)
Q Consensus 540 ~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~rr~g~i~~~v~i~~~~~~~~i~I~td~GRl~RPl~~v~~~~~------~ 613 (1149)
.+..+||+||.|+|+++++..|++.+|.+||.|.++.+++++++....+++|+||+||++|||+.++|+.. .
T Consensus 558 --~~~~~V~~nG~~~G~~~~~~~l~~~lr~~R~~g~i~~~~s~~~~~~~~~i~i~td~Gr~~rPlfi~~nd~~~~~~~~~ 635 (1207)
T d1twfb_ 558 --PDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELK 635 (1207)
T ss_dssp --TTCEEEEETTEEEEEESCHHHHHHHHHHHHHHTSSCTTCEEEEETTTTEEEEECCSCCEEEEEEEEECCCTTSSCEES
T ss_pred --cccceeeeeeeEEEEEcchheeehheeeeeeccCccceeeeeeeccccceEEEecCccccCCceeecchhhhccccee
Confidence 36789999999999999999999999999999999999999999999999999999999999999988742 3
Q ss_pred chhhhHHhhhc-------------CCcchhhhhccCceeEeccccccceEEEeecCCCC---------------------
Q 001124 614 IKEHHMKELLD-------------GVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT--------------------- 659 (1149)
Q Consensus 614 ~~~~~~~~~~~-------------~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~--------------------- 659 (1149)
+.+.++..+.. ...+|.+++..|.|||||++|+++++||+.++++.
T Consensus 636 mqrq~v~~l~~~e~~~v~~~~e~~~~~~~~~~~~~g~ieyid~~E~~~~~Ia~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 715 (1207)
T d1twfb_ 636 VRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVS 715 (1207)
T ss_dssp CCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTTCCEESSGGGGCC---------CCCTTSCCCCC
T ss_pred eeHhhHhhhhccccccccccccchhhccccccccCCceeeecchhcceEEEEecccccccccccccccccccchhheeee
Confidence 33333332211 23578999999999999999999999999988763
Q ss_pred ---CCceeeeecCceeccccccccCCCCCCCCCccccccccccCCcccceeeeccccccceeeecCCCcceeechhhhhc
Q 001124 660 ---PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELV 736 (1149)
Q Consensus 660 ---~~~th~Ei~P~~ilsv~AslIPF~~hNqSpRn~yq~~M~KQa~G~~~~n~~~R~D~~~y~L~ypQ~PlV~t~~~~~~ 736 (1149)
..+||+||+|+.|||++|++|||+||||||||||||||+|||||++++|+..|.|++.|+|+|||+|||+|+.++.+
T Consensus 716 ~~~~~~th~Ei~p~~ilg~~as~iPf~~hNqSpRn~yq~qm~KQa~G~~~~~~~~r~D~~~~~l~~pQ~Plv~t~~~~~~ 795 (1207)
T d1twfb_ 716 HHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYL 795 (1207)
T ss_dssp CCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHHHGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHH
T ss_pred cccccccccccccceEEeeecceEEecccccccceeecccCCcccCCccccccceeccccceeEecCCCceeeccchhhh
Confidence 24799999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCcceEEEEEecCCCCCCCcEEeecccccccceeEEEEEEEEEEeecccCCccceecCCCCCC---Cchhhhcc
Q 001124 737 GYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTG---PGAERMQI 813 (1149)
Q Consensus 737 ~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~---~~~~~~~~ 813 (1149)
+++++|+|+||+||||||+||||||||||||+|++||+|||+||++|+++++++..+..+.+..|.... .....|++
T Consensus 796 ~~~e~p~G~N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 875 (1207)
T d1twfb_ 796 KFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDK 875 (1207)
T ss_dssp TTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGG
T ss_pred hhhcccchhceEEEEEeccCcccccccccchhhhhhcccceeeeEEEEEEeccccccccccccccccccccccchhhhhc
Confidence 999999999999999999999999999999999999999999999999999988877777787765421 12357899
Q ss_pred CCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcEEEEEEEe
Q 001124 814 LDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIR 893 (1149)
Q Consensus 814 Ld~dGi~~~G~~v~~gd~l~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~~~~~~vkv~~~ 893 (1149)
||+||||++|++|++||+||||++|....+..... ......+++.|+.++.++ .|+||+|..+.+.++.+.|||++|
T Consensus 876 Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~-~~~~~~~~~~s~~~~~~~--~g~V~~v~~~~~~~~~~~~kv~i~ 952 (1207)
T d1twfb_ 876 LDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQ-RTAYHSKRDASTPLRSTE--NGIVDQVLVTTNQDGLKFVKVRVR 952 (1207)
T ss_dssp CCTTSBCCTTCEECTTCEEECEECCCC--------------CCBBCCEECCTTC--CEEEEEEEEEECSSSCEEEEEEEE
T ss_pred ccccccccccccccCCceeeeeeeccCCchhhhhh-ccccccccceeEEccCCC--CeEEEEEEEeecccccceeeEEEE
Confidence 99999999999999999999999998765432110 112234689999999988 999999999999999999999999
Q ss_pred eecCCCccccccccCCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCchHHHHHHHhccccccccCceeeeeeccC
Q 001124 894 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGE 973 (1149)
Q Consensus 894 ~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~ 973 (1149)
+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.|+|||+
T Consensus 953 ~~R~p~iGDKfasRhGqKGv~s~i~p~eDMPf~~dG~~pDiI~NP~g~PSRMtiGql~E~~~gk~~~~~g~~~d~t~F~- 1031 (1207)
T d1twfb_ 953 TTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFT- 1031 (1207)
T ss_dssp EEECCCTTCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSS-
T ss_pred EEeccchhhhhhhccCCcceeeeeechhhCCcCCCCCCccEEECCCcCcccCcHHHHHHHHHHHHHHhcCCccccCCCC-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCceEEEeCCCCcEEeeeEeEeeeeecccccccCcccEEecccCcccccccCcccccC
Q 001124 974 PSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRAR 1053 (1149)
Q Consensus 974 ~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~ 1053 (1149)
+..++++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++|||++|||||++|||+
T Consensus 1032 ----~~~~~~~~~~L~~~g~~~~G~e~ly~G~tG~~~~~~i~~G~~yy~rL~HmV~DK~~~Rs~Gp~~~lT~QP~~Gr~~ 1107 (1207)
T d1twfb_ 1032 ----DITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSR 1107 (1207)
T ss_dssp ----SCCHHHHHHHHHTTTSCTTSEECEECTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC--------------
T ss_pred ----CccHHHHHHHHHHcCCCCCCCEEEECCCCCCCccceEEEehhHhhhhhhhhccccEeeccCCCCccccCCCCcccc
Confidence 6889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeechhhhHHHHcccHHHHHHhhccCCCceeeeecccCCcceee-cccccceecccccCCCccccccccHhHHHHH
Q 001124 1054 NGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYY-NHKLKAGICSTCKNGDNISSMKLPYACKLLI 1132 (1149)
Q Consensus 1054 ~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cg~~~~~-~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~ 1132 (1149)
+|||||||||||||+|||||++|||||++|||.+.++||.+||+++.. +.+....+|+.|+++.++.++.+|||||||+
T Consensus 1108 ~GG~R~GEME~dal~a~Gaa~~L~e~l~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~c~~c~~~~~i~~~~iPy~fk~l~ 1187 (1207)
T d1twfb_ 1108 DGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLF 1187 (1207)
T ss_dssp --CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEEEECCHHHHHHH
T ss_pred CCCcceehHHHHHHHHHhHHHHHHHHhhccCCccceeccccCCceEEEecccccceeecCCCCCCCccccCCCHHHHHHH
Confidence 999999999999999999999999999999999999999999999864 3345567799999999999999999999999
Q ss_pred HHHHhCCcccEEEeccC
Q 001124 1133 QELQSMNIVPRLKLAEA 1149 (1149)
Q Consensus 1133 ~EL~sm~i~~~l~~~~~ 1149 (1149)
|||+||||++||.+++.
T Consensus 1188 ~EL~sm~i~~~l~~~~~ 1204 (1207)
T d1twfb_ 1188 QELMAMNITPRLYTDRS 1204 (1207)
T ss_dssp HHHHHTTBCCEEESCSS
T ss_pred HHHHHCCCceEEEecCc
Confidence 99999999999999763
|
| >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 |
|---|