Citrus Sinensis ID: 001092
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 | 1159 | 2.2.26 [Sep-21-2011] | |||||||
| Q10233 | 1165 | DNA-directed RNA polymera | yes | no | 0.960 | 0.955 | 0.576 | 0.0 | |
| Q9NW08 | 1133 | DNA-directed RNA polymera | yes | no | 0.961 | 0.983 | 0.575 | 0.0 | |
| P59470 | 1133 | DNA-directed RNA polymera | yes | no | 0.961 | 0.983 | 0.576 | 0.0 | |
| P22276 | 1149 | DNA-directed RNA polymera | yes | no | 0.962 | 0.970 | 0.563 | 0.0 | |
| P25167 | 1137 | DNA-directed RNA polymera | yes | no | 0.968 | 0.987 | 0.535 | 0.0 | |
| Q54IZ9 | 1608 | DNA-directed RNA polymera | yes | no | 0.551 | 0.397 | 0.604 | 0.0 | |
| P31814 | 1122 | DNA-directed RNA polymera | N/A | no | 0.937 | 0.968 | 0.386 | 0.0 | |
| Q8CFI7 | 1174 | DNA-directed RNA polymera | no | no | 0.950 | 0.938 | 0.372 | 0.0 | |
| P30876 | 1174 | DNA-directed RNA polymera | no | no | 0.950 | 0.938 | 0.372 | 0.0 | |
| Q10578 | 1193 | DNA-directed RNA polymera | no | no | 0.945 | 0.918 | 0.371 | 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 = 1357 bits (3513), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 663/1151 (57%), Positives = 854/1151 (74%), Gaps = 38/1151 (3%)
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 YANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPL 849
Y N T DRI P R E +VV +++DDGLA G ++P +Y+NK++P
Sbjct: 811 YPNGTHDRIGDPQRD---PETGEVVWKHG----VVEDDGLAGVGCRVQPGQIYVNKQTPT 863
Query: 850 ETRGS--IMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRR 907
+ + T +S Y++ TYK P E +D+V L + + IK L+R TRR
Sbjct: 864 NALDNSITLGHTQTVESGYKATPMTYKAP--EPGYIDKVMLTTTDSDQTLIKVLMRQTRR 921
Query: 908 PELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGK 967
PELGDKFSSRHGQKGVCG IVQQED PF+++GICPD+IMNPHGFPSRMTVGKMIELL GK
Sbjct: 922 PELGDKFSSRHGQKGVCGVIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGK 981
Query: 968 AGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMG 1027
GV G YG+ FG VE S LV+HG++Y+GKDM+ SGITG L+AYIFMG
Sbjct: 982 VGVLRGTLEYGTCFG-----GTKVEDASRILVEHGYNYSGKDMLTSGITGETLEAYIFMG 1036
Query: 1028 PIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIF 1087
PIYYQKLKHMV+DKMHAR GPR +LTRQPTEGR+R+GGLR+GEMERDCLIAYGAS L+
Sbjct: 1037 PIYYQKLKHMVMDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASQLLL 1096
Query: 1088 ERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQS 1147
ERLM+SSD +V VC CGLLGY G C++C++ + M +PYA KLL QEL S
Sbjct: 1097 ERLMISSDACDVDVCGQCGLLGY------KGWCNSCQSTREVVKMTIPYAAKLLFQELLS 1150
Query: 1148 MNIVPRLKLAE 1158
MNIVPRL L +
Sbjct: 1151 MNIVPRLALED 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|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II subunit RPB2 OS=Caenorhabditis elegans GN=rpb-2 PE=2 SV=2 | Back alignment and function description |
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Close Homologs in the Non-Redundant Database Detected by BLAST
Original result of BLAST against Nonredundant Database
| GI | Alignment Graph | Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 1159 | ||||||
| 225464023 | 1142 | PREDICTED: DNA-directed RNA polymerase I | 0.973 | 0.987 | 0.858 | 0.0 | |
| 255569145 | 1139 | DNA-directed RNA polymerase III subunit, | 0.977 | 0.994 | 0.845 | 0.0 | |
| 224132576 | 1141 | predicted protein [Populus trichocarpa] | 0.978 | 0.993 | 0.832 | 0.0 | |
| 449447799 | 1158 | PREDICTED: DNA-directed RNA polymerase I | 0.981 | 0.982 | 0.831 | 0.0 | |
| 297791275 | 1165 | hypothetical protein ARALYDRAFT_917015 [ | 0.979 | 0.974 | 0.791 | 0.0 | |
| 79529842 | 1161 | DNA-directed RNA polymerase III subunit | 0.979 | 0.977 | 0.786 | 0.0 | |
| 9759599 | 1194 | DNA-directed RNA polymerase subunit [Ara | 0.978 | 0.949 | 0.780 | 0.0 | |
| 356520824 | 1152 | PREDICTED: DNA-directed RNA polymerase I | 0.964 | 0.970 | 0.793 | 0.0 | |
| 356495051 | 1166 | PREDICTED: DNA-directed RNA polymerase I | 0.975 | 0.969 | 0.788 | 0.0 | |
| 115453445 | 1155 | Os03g0403100 [Oryza sativa Japonica Grou | 0.974 | 0.977 | 0.726 | 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 = 2058 bits (5333), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 980/1141 (85%), Positives = 1062/1141 (93%), Gaps = 13/1141 (1%)
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 LRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSP 858
+RP + G AERMQ ILDDDGLAAPGEIIKPND+YINKESP+ T+G ++SP
Sbjct: 792 VRPLKVGHDAERMQ----------ILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISP 841
Query: 859 TGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFSSRH 918
G DS Y+ +RQT+KGP+GE VVDRVALCSDKN +LCIKFLIRHTRRPE+GDKFSSRH
Sbjct: 842 VGLPDSAYKPSRQTFKGPEGEASVVDRVALCSDKNSNLCIKFLIRHTRRPEVGDKFSSRH 901
Query: 919 GQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYG 978
GQKGVCGTI+QQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYG
Sbjct: 902 GQKGVCGTIIQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYG 961
Query: 979 SAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMV 1038
SAFGEPSGHAD VE+IS+TLVKHGFSY+GKD IYSGITGCPLQAYIFMGPIYYQKLKHMV
Sbjct: 962 SAFGEPSGHADKVETISKTLVKHGFSYSGKDFIYSGITGCPLQAYIFMGPIYYQKLKHMV 1021
Query: 1039 LDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFE 1098
LDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFE
Sbjct: 1022 LDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFE 1081
Query: 1099 VQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPRLKLAE 1158
VQVCRVCGLLGYYNHKLK GICSTCKNGDNIS+MKLPYACKLL QELQ+MN+VPRLKL E
Sbjct: 1082 VQVCRVCGLLGYYNHKLKIGICSTCKNGDNISTMKLPYACKLLFQELQAMNVVPRLKLTE 1141
Query: 1159 A 1159
A
Sbjct: 1142 A 1142
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Source: Vitis vinifera Species: Vitis vinifera Genus: Vitis Family: Vitaceae Order: Vitales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|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 |
|---|
| >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 |
|---|
| >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 | 1159 | ||||||
| TAIR|locus:2153323 | 1161 | NRPC2 "nuclear RNA polymerase | 0.988 | 0.987 | 0.765 | 0.0 | |
| POMBASE|SPAC4G9.08c | 1165 | rpc2 "DNA-directed RNA polymer | 0.924 | 0.919 | 0.572 | 0.0 | |
| UNIPROTKB|E1BRJ4 | 1132 | POLR3B "DNA-directed RNA polym | 0.924 | 0.946 | 0.563 | 0.0 | |
| UNIPROTKB|E2RHZ2 | 1133 | POLR3B "DNA-directed RNA polym | 0.924 | 0.946 | 0.564 | 0.0 | |
| UNIPROTKB|E1BPX6 | 1133 | POLR3B "Uncharacterized protei | 0.924 | 0.946 | 0.564 | 0.0 | |
| RGD|1565311 | 1133 | Polr3b "polymerase (RNA) III ( | 0.924 | 0.946 | 0.565 | 0.0 | |
| UNIPROTKB|Q9NW08 | 1133 | POLR3B "DNA-directed RNA polym | 0.924 | 0.946 | 0.564 | 0.0 | |
| MGI|MGI:1917678 | 1133 | Polr3b "polymerase (RNA) III ( | 0.924 | 0.946 | 0.564 | 0.0 | |
| ZFIN|ZDB-GENE-030131-2887 | 1129 | polr3b "polymerase (RNA) III ( | 0.922 | 0.946 | 0.563 | 0.0 | |
| CGD|CAL0002357 | 1157 | orf19.5847 [Candida albicans ( | 0.960 | 0.961 | 0.543 | 0.0 |
| TAIR|locus:2153323 NRPC2 "nuclear RNA polymerase C2" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 4725 (1668.3 bits), Expect = 0., P = 0.
Identities = 899/1174 (76%), Positives = 1021/1174 (86%)
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 NKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHHSNXXXXXXX 825
NKSSLDRGFGRCIV+KK A++QKY N T+DRIL P RTGP AE+MQ++
Sbjct: 780 NKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILIPQRTGPDAEKMQILDDDGL------ 833
Query: 826 XXXXAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDR 885
A PGEII+PND+YINK+ P++T S +DS+YR AR+ +KGP+GET VVDR
Sbjct: 834 ----ATPGEIIRPNDIYINKQVPVDTVTKFTSAL--SDSQYRPAREYFKGPEGETQVVDR 887
Query: 886 VALCSDKNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLI 945
VALCSDK G LCIK++IRHTRRPELGDKFSSRHGQKGVCG I+QQEDFPFSE GICPDLI
Sbjct: 888 VALCSDKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLI 947
Query: 946 MNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSY 1005
MNPHGFPSRMTVGKMIELLG KAGVSCGRFHYGSAFGE SGHAD VE+IS TLV+ GFSY
Sbjct: 948 MNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFGERSGHADKVETISATLVEKGFSY 1007
Query: 1006 NGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNG 1065
+GKD++YSGI+G P++AYIFMGPIYYQKLKHMVLDKMHARGSGPRVM+TRQPTEG+++NG
Sbjct: 1008 SGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNG 1067
Query: 1066 GLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKN 1125
GLRVGEMERDCLIAYGASMLI+ERLM+SSDPFEVQVCR CGLLGYYN+KLK +C+TCKN
Sbjct: 1068 GLRVGEMERDCLIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYNYKLKKAVCTTCKN 1127
Query: 1126 GDNISSMKLPYACKLLIQELQSMNIVPRLKLAEA 1159
GDNI++MKLPYACKLL QELQSMN+VPRLKL EA
Sbjct: 1128 GDNIATMKLPYACKLLFQELQSMNVVPRLKLTEA 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 |
|---|
| UNIPROTKB|E1BPX6 POLR3B "Uncharacterized protein" [Bos taurus (taxid:9913)] | 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|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 |
|---|
| CGD|CAL0002357 orf19.5847 [Candida albicans (taxid:5476)] | 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 | 0.5636 | 0.9620 | 0.9704 | yes | no |
| Q9NW08 | RPC2_HUMAN | 2, ., 7, ., 7, ., 6 | 0.5756 | 0.9611 | 0.9832 | yes | no |
| P59470 | RPC2_MOUSE | 2, ., 7, ., 7, ., 6 | 0.5765 | 0.9611 | 0.9832 | yes | no |
| Q03587 | RPOB_THEAC | 2, ., 7, ., 7, ., 6 | 0.3309 | 0.9352 | 0.9071 | yes | no |
| P25167 | RPC2_DROME | 2, ., 7, ., 7, ., 6 | 0.5352 | 0.9689 | 0.9876 | yes | no |
| Q10233 | RPC2_SCHPO | 2, ., 7, ., 7, ., 6 | 0.5760 | 0.9603 | 0.9553 | yes | no |
| P11513 | RPOB_SULAC | 2, ., 7, ., 7, ., 6 | 0.3670 | 0.9413 | 0.9689 | 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 | 1159 | |||
| 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-171 | |
| 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 | 5e-50 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 3e-44 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 1e-38 | |
| 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 | 3e-20 | |
| pfam04566 | 63 | pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, do | 7e-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 | 1e-11 | |
| 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 | 2e-08 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 3e-06 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 2e-04 |
| >gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
Score = 1039 bits (2690), Expect = 0.0
Identities = 460/1145 (40%), Positives = 666/1145 (58%), Gaps = 75/1145 (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 RTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESP----LETRGSIMSP 858
G + LD+DG+ +P +K DV I K SP E +
Sbjct: 761 PNVRGYRGEEYYRK-------LDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGL 813
Query: 859 TGQTDS----RYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKF 914
+ D+ R+ GE +VD V + G+ +K +R R PELGDKF
Sbjct: 814 QERRDTSVTVRH-----------GEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKF 862
Query: 915 SSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGR 974
+SRHGQKGV G +V QED PF+E GI PDLI+NPH PSRMTVG+++E + GK GR
Sbjct: 863 ASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGR 922
Query: 975 FHYGSAF-GEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQK 1033
F + F GEP E + + L+K G+ +G +++Y G TG ++A IF+G +YYQK
Sbjct: 923 FVDATPFYGEP------EEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQK 976
Query: 1034 LKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVS 1093
L HMV DK+HAR GP +LTRQPTEGRAR GGLR GEMERDCLI +GA+ML+ ERL+ S
Sbjct: 977 LHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDS 1036
Query: 1094 SDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSMNIVPR 1153
SD + VC +CG + +Y+ + +C + NIS +++ YA KLL+QEL SM I PR
Sbjct: 1037 SDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPR 1096
Query: 1154 LKLAE 1158
LKL +
Sbjct: 1097 LKLGD 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 |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1159 | |||
| 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 | |
| TIGR02013 | 1065 | rpoB DNA-directed RNA polymerase, beta subunit. Th | 100.0 | |
| cd00653 | 866 | RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po | 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 | 99.12 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 99.0 | |
| PF04567 | 48 | RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int | 98.84 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 97.72 | |
| PF06883 | 58 | RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do | 97.51 | |
| PHA03394 | 865 | lef-8 DNA-directed RNA polymerase subunit beta-lik | 95.25 |
| >PRK08565 DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=1.6e-278 Score=2625.24 Aligned_cols=1093 Identities=41% Similarity=0.691 Sum_probs=1001.0
Q ss_pred ccccccccccccchHHHHHHHHHHHHHhChHHHHhccCceeecCCCcEEEEEeEEEEcCCccccCC-cCCCCChhhHhhc
Q 001092 31 KFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKLNPHMCRLS 109 (1159)
Q Consensus 31 ~~~~i~~~~~~~~Lv~~qi~SFn~Fl~~gL~~i~~~~~~I~~~~~~~~~l~f~~i~i~~P~~~~~~-~~~~l~P~EcR~r 109 (1159)
.|.++++||+.++|++||+||||+|+++||++++++++||+.. ++++.|+|++++|++|++.+++ ...+|+|+|||+|
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 4999999999999999999999999999999999999999865 6789999999999999997665 6678999999999
Q ss_pred CCccCccEEEEEEEEECCcccceeeEEeeEEEeecceeeccccccCCCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHhh
Q 001092 110 DMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQ 189 (1159)
Q Consensus 110 ~lTYsa~L~v~i~~~~~~~~~~~~i~~~~v~lG~IPIMv~S~~C~L~~ls~~eli~~~E~~~d~GGYFIING~ERVI~~q 189 (1159)
++||+|||+|+|++..++ ..++++++++|+|||||+|++|||++++|+||++.||||+|+||||||||+|||||+|
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 4555668999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCeEEEEeCCCC---cEEEEEEecCCCcc-eEEEEEeeCCEEEEEEcceeccccHHHHHHHhcCCCHHHHHHHhCC
Q 001092 190 EQLSKNRVIIDTDKKG---NINASVTSSTETVK-SKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR 265 (1159)
Q Consensus 190 ~~~s~N~i~~~~~~~g---~~~a~v~s~~~~~~-s~~~~~~~~g~i~~r~~~~~~~IPl~ilLrALG~~sD~eI~~~i~~ 265 (1159)
|++++|+++++.+.++ .+.|.++|.....+ +..+++..||.++++++++.++||+++||||||++||+||++.|+.
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 36788888876543 3444445678999999987678999999999999999999999977
Q ss_pred chhhHhhhhHhHHHHHhcCC-cCHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCcchhHHHH
Q 001092 266 DPRYSALLLPSIEECANLDI-YTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVM 344 (1159)
Q Consensus 266 ~~~~~~~l~~~l~~~~~~~i-~t~~~Al~yIg~r~r~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~M 344 (1159)
++.+.+.+..+++++. .+ .|+++||.|||++|++. .++.+ ..+.|+++|++++|||++.+..++.+|+.+|++|
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 7789999999999999997665567899999999
Q ss_pred HHHHHHhccCCCCCCCcccccCcEEcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHH
Q 001092 345 LRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLE 424 (1159)
Q Consensus 345 i~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~ 424 (1159)
++||+++..|.+.+||+|||+||||+++|+||+.+||++|+++++.+|+++.+.+.+. ..+++..+++++.||++|+
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 2456777788889999999
Q ss_pred HHhccCCCcccccccccccceEEccccccccccccccccccccccccccCCCCccCCCCCccccccCCCCCCcchhhhhc
Q 001092 425 RTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNL 504 (1159)
Q Consensus 425 ~~~sTGnw~~~~~~~q~sGvsq~l~RlN~ls~LshlRrv~s~f~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~L 504 (1159)
+|||||||.. |++|+||+|+|+||+|+||||||+++++.+++|.++||+||||||||+||||||||++||||+||
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 ccceeeccCCCchhHHHHHhhcCCeeccccCccccCCCCcEEEEEcCeEEEeecChhhHHHHHHHHhhcCCCCceeEEEe
Q 001092 505 ALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV 584 (1159)
Q Consensus 505 A~~a~Vt~~~~~~~i~~~l~~lG~~~l~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~Rr~~~i~~~vsi~~ 584 (1159)
|++|+|+.+.+.+++.++|.++|+.++..+++... ...++|||||+|||+++++..|++.||.+||+|.++.+++|++
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 001092 585 NE--KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDT 662 (1159)
Q Consensus 585 ~~--~~~~i~I~td~GRl~RPl~~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~iE~id~~E~~~~~Ia~~~~~~~~~~ 662 (1159)
+. .+++|+|+||+||++|||++|++|++.++++|++.++.+..+|+||+++|.|||||++||++++||+.++++...+
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 8899999999999999999999999999999999888778899999999999999999999999999999997778
Q ss_pred eeeeecCccccccccccccCCCCCCCCccccccccccCCccceeeeeccccccceeeecCCCcceeeeceeeeecCCCCC
Q 001092 663 THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLG 742 (1159)
Q Consensus 663 th~Ei~p~~ilsv~aslIPF~~hNqspRn~yq~~M~KQa~g~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~~~~~~p 742 (1159)
||+||+|.+|||++||+|||+||||||||||||||||||||++++|+..|+|++.|+|+|||+|||+|+.++.++++++|
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 CCcceEEEEEecCCCCCCCcEEeeccccccCceeEEEEEEEEEEeccccCCCcceecCCCCCCCCcccccccccchhhhc
Q 001092 743 AGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLL 822 (1159)
Q Consensus 743 ~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 822 (1159)
+|+||+||||||+||||||||||||+|+|||||||+||++|+++++++..+..+.++.|.....+ .+ +...|+
T Consensus 701 ~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~---~~~~~~ 773 (1103)
T PRK08565 701 AGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRG----YR---GEEYYR 773 (1103)
T ss_pred CCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeecCCCCceEEecCCCcccc----cC---chhhhh
Confidence 99999999999999999999999999999999999999999999887766666777766431111 11 124689
Q ss_pred cCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcEEEEEEE
Q 001092 823 ILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLI 902 (1159)
Q Consensus 823 ~Ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~~~~~~vkv~~ 902 (1159)
+||+||||++|++|++|||||||++|..+..... ..+......+|+|++++.+| .|+||+|.++.+.++.+.|||++
T Consensus 774 ~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~-~~~~~~~~~~~~s~~~~~~e--~g~V~~V~~~~~~~~~~~vkv~i 850 (1103)
T PRK08565 774 KLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELE-ELSLGLQERRDTSVTVRHGE--KGIVDTVLITESPEGNKLVKVRV 850 (1103)
T ss_pred cCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchh-hccccCCccccceEEecCCC--ceEEEEEEEEecCCCcEEEEEEE
Confidence 9999999999999999999999999965322110 01112234789999999999 99999999998888899999999
Q ss_pred eeecCCCcccccccccCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCccHHHHHHHhcccccccCCceeeeeecc
Q 001092 903 RHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFG 982 (1159)
Q Consensus 903 r~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~t~F~ 982 (1159)
|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.|+|||.
T Consensus 851 r~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~ 930 (1103)
T PRK08565 851 RDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFY 930 (1103)
T ss_pred EEEecCchhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcHHHHHHHHHHcCCCCCCceEEEeCCCCceeeeeEeEeeeeeeecccccCcccEEecccCcccccccCccccc
Q 001092 983 EPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRA 1062 (1159)
Q Consensus 983 ~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~ 1062 (1159)
+..++++++.|+++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++|||
T Consensus 931 -----~~~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~ 1005 (1103)
T PRK08565 931 -----GEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRA 1005 (1103)
T ss_pred -----CchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccc
Confidence 677999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCceeeeehhhhHHHHcccHHHHHHhhccCCCcccceeccccccceeecccccceecccccCCCccccccccHhHHHHH
Q 001092 1063 RNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLI 1142 (1159)
Q Consensus 1063 ~~GG~R~GEMErd~l~a~Gas~~L~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~L~ 1142 (1159)
|+|||||||||||||+|||||++|+|||+++||++.++||.+||++++.+.+.+..+|+.|+++.++.++.+|||||||+
T Consensus 1006 ~~GG~R~GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~ 1085 (1103)
T PRK08565 1006 REGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLL 1085 (1103)
T ss_pred cCCCeeeecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccCCCCcceeccCChhHHHHH
Confidence 99999999999999999999999999999999999999999999999865556667899999988999999999999999
Q ss_pred HHHHhCCcccEEEecc
Q 001092 1143 QELQSMNIVPRLKLAE 1158 (1159)
Q Consensus 1143 ~EL~sm~i~~~l~~~~ 1158 (1159)
|||+||||+++|.+++
T Consensus 1086 ~EL~sm~i~~~l~~~~ 1101 (1103)
T PRK08565 1086 QELMSMGISPRLKLGD 1101 (1103)
T ss_pred HHHHhCCCceEEEeee
Confidence 9999999999999975
|
|
| >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 |
|---|
| >TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit | Back alignment and domain information |
|---|
| >cd00653 RNA_pol_B_RPB2 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 | 1159 | ||||
| 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 | ||
| 1i6v_C | 1118 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 8e-40 | ||
| 1hqm_C | 1119 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 9e-40 | ||
| 1ynj_C | 1119 | Taq Rna Polymerase-Sorangicin Complex Length = 1119 | 9e-40 | ||
| 1l9u_C | 1118 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 9e-40 | ||
| 1iw7_C | 1119 | Crystal Structure Of The Rna Polymerase Holoenzyme | 2e-39 | ||
| 3lu0_C | 1342 | Molecular Model Of Escherichia Coli Core Rna Polyme | 3e-25 | ||
| 3iyd_C | 1342 | Three-Dimensional Em Structure Of An Intact Activat | 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|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|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex 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|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 | 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|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 = 1393 bits (3606), Expect = 0.0
Identities = 429/1223 (35%), Positives = 647/1223 (52%), Gaps = 112/1223 (9%)
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 RCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEI 835
R I + YT +K + + RP R+ RM+ + L+DDGL APG
Sbjct: 841 RSIFYRTYTDQEKKIGMTVMEEFERPVRSTTL--RMKHGTYD-----KLEDDGLIAPGTR 893
Query: 836 IKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGD 895
+ D+ I K +P+ + R + E+ +VD+V + +++ G
Sbjct: 894 VSGEDIIIGKTAPIPLDHEELGQ-RTQLHAKRDVSTPLRST--ESGIVDQVMVTTNQEGL 950
Query: 896 LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRM 955
+K +R TR P++GDKF+SRHGQKG G + ED PFS +GI PD+I+NPH PSRM
Sbjct: 951 KFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRM 1010
Query: 956 TVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGI 1015
TV ++E K G + F + TVE++S+ L HGF G +++Y G
Sbjct: 1011 TVAHLVECQLSKVSALSGFEGDATPFTD-----VTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Query: 1016 TGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERD 1075
TG L A +F+GP YYQ+LKH+V DK+HAR GP +LTRQP EGR+R+GGLR GEMERD
Sbjct: 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERD 1125
Query: 1076 CLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLP 1135
C I++G S ++ ERL SD + V VC +CGL+ ++K + C +C+N S + LP
Sbjct: 1126 CQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLP 1185
Query: 1136 YACKLLIQELQSMNIVPRLKLAE 1158
YA KLL QEL SMNI PRL
Sbjct: 1186 YAAKLLFQELMSMNIAPRLFTKN 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 |
|---|
| >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 | 1159 | |||
| 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 | 98.8 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 96.43 |
| >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=3.2e-295 Score=2760.06 Aligned_cols=1110 Identities=38% Similarity=0.629 Sum_probs=1009.9
Q ss_pred CcccccccccccccccccchHHHHHHHHHHHHHhChHHHHhccCceeecCC-----------CcEEEEEeEEEEcCCccc
Q 001092 25 VKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGID-----------PSIFLRFKDVRIGQPSMT 93 (1159)
Q Consensus 25 ~~~~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fl~~gL~~i~~~~~~I~~~~~-----------~~~~l~f~~i~i~~P~~~ 93 (1159)
.++.+|+|.++++||+.++||+|||||||+|+++||++|++++++|+++.+ .++.|+|++++|++|++.
T Consensus 11 ~~~~ed~w~li~aff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~~ 90 (1210)
T 3h0g_B 11 TLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTMT 90 (1210)
T ss_dssp CCCHHHHHHHHHHHHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCCB
T ss_pred cCCHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHHhccCcEEecCccCcccccccCCceEEEEEEEEEEcCCcee
Confidence 378899999999999999999999999999999999999999999976542 368999999999999998
Q ss_pred cCC-cCCCCChhhHhhcCCccCccEEEEEEEEECCcc----------c---ceeeEEeeEEEeecceeeccccccCCCCC
Q 001092 94 VDG-VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT----------E---KTTMEKNDVVIGRIPIMLRSCRCVLYGKD 159 (1159)
Q Consensus 94 ~~~-~~~~l~P~EcR~r~lTYsa~L~v~i~~~~~~~~----------~---~~~i~~~~v~lG~IPIMv~S~~C~L~~ls 159 (1159)
+++ ..+++||+|||+|++||+|||+|+|+++.++.. . .......++.+|+|||||||++|||++++
T Consensus 91 e~d~~~~~l~P~EcRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~s 170 (1210)
T 3h0g_B 91 EADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVS 170 (1210)
T ss_dssp CTTSCBCCCCTTTTTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSCC
T ss_pred cCCCcccccCHHHHHhcCCccceeEEEEEEEEEcCccccccccccccccccccccccceEEEecCCEEeCCCcccCCCCC
Confidence 877 788999999999999999999999999865411 0 01122357999999999999999999999
Q ss_pred HHHHHhcCCCCCCCCcEEEEcCchhhhHhhhhccCCeEEEEeCCC---CcEEEEEEecCCCcc----eEEEEEee-----
Q 001092 160 EAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKK---GNINASVTSSTETVK----SKTVIQME----- 227 (1159)
Q Consensus 160 ~~eli~~~E~~~d~GGYFIING~ERVI~~q~~~s~N~i~~~~~~~---g~~~a~v~s~~~~~~----s~~~~~~~----- 227 (1159)
++||++.||||+|+||||||||+||||++|+++++|+|++++++. ..+.|.++|++.+.+ +.++.++.
T Consensus 171 ~~eL~~~gEcp~D~GGYFIING~EKVII~qerla~N~~iv~~~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~~ 250 (1210)
T 3h0g_B 171 DSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTEN 250 (1210)
T ss_dssp HHHHHHTTCCTTCCCCCBCGGGSCBCCCBCBCCCCSCCCCCCCCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTTS
T ss_pred HHHHHhcCCCCCCCCCEEEEeCEEEEEEechhhccceEEEEeecCCCCceEEEEEEEEecCCccceeEEEEEEEeccccC
Confidence 999999999999999999999999999999999999999986543 246788888876532 22233332
Q ss_pred -CCEEEEEEcceeccccHHHHHHHhcCCCHHHHHHHhC---CchhhHhhhhHhHHHHHhcCCcCHHHHHHHHhhhcccCC
Q 001092 228 -KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG---RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRST 303 (1159)
Q Consensus 228 -~g~i~~r~~~~~~~IPl~ilLrALG~~sD~eI~~~i~---~~~~~~~~l~~~l~~~~~~~i~t~~~Al~yIg~r~r~~~ 303 (1159)
++.++++++.++.+||++++|||||.+||+||++.|. .+.++.+.|.++++++. .++|+++||+|||+|++..
T Consensus 251 ~~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~~--~i~tq~~aL~yIG~r~~~~- 327 (1210)
T 3h0g_B 251 SGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAF--VIQDKDIALDYIGKRGSTT- 327 (1210)
T ss_dssp CSCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTTS--SCCSSHHHHHTTCCCSSSC-
T ss_pred CCceEEEEEeccccCCcHHHHHHHcCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHhh--hcCCHHHHHHHHHHhcccc-
Confidence 5689999999888999999999999999999999994 57788999999998874 4889999999999999853
Q ss_pred CCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCCCcccccCcEEcchhHHHHHHHHHH
Q 001092 304 FGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDL 383 (1159)
Q Consensus 304 ~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lfr~~ 383 (1159)
..++.+ +++.|+++|++++|||++..+.++.+||.||++|+|||++++.|.+.+||+|||+||||+++|+||+.+||+.
T Consensus 328 ~~~~~~-~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~lfr~~ 406 (1210)
T 3h0g_B 328 GVTREK-RLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRML 406 (1210)
T ss_dssp CCCHHH-HHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHHHHHHH
T ss_pred CCCchh-HHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHHHHHHHH
Confidence 234445 7899999999999999998888889999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHHHHhccCCCc-ccccccccccceEEccccccccccccccc
Q 001092 384 FKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFD-VKRFKMHRKGMTQVLARLSFIGTLGHMTR 462 (1159)
Q Consensus 384 l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~-~~~~~~q~sGvsq~l~RlN~ls~LshlRr 462 (1159)
|+++++.+++.+.+.+.+. ..+++..+++++.||++|++|||||||+ .++++++++||||+|+|+||+|+||||||
T Consensus 407 ~~~~~~~i~~~l~k~~~~~---~~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~lShlRr 483 (1210)
T 3h0g_B 407 FRKMTRDVYKYMQKCVETN---REFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRR 483 (1210)
T ss_dssp HHHHHHHHHHHHHHHHTTC---CSCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHHHHHTTB
T ss_pred HHHHHHHHHHHHHHHhhcC---CccCHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCCHHHHHHHHHh
Confidence 9999999999999987764 3567778888999999999999999998 56788899999999999999999999999
Q ss_pred cccccccccccCCCCccCCCCCccccccCCCCCCcchhhhhcccceeeccCCCchhHHHHHhhcCCeeccccCccccCCC
Q 001092 463 VSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNP 542 (1159)
Q Consensus 463 v~s~f~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~lG~~~l~~~~~~~~~~~ 542 (1159)
++++|++++|+++||+||||||||+||+|||||++||||||||++|.||++.+++||.++|.++||++++.+.+... +
T Consensus 484 v~~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le~~~~~~~--~ 561 (1210)
T 3h0g_B 484 TNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSAS--P 561 (1210)
T ss_dssp BCCSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCSCCCSSSS--S
T ss_pred ccCchhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHhCCcchhhcCcccC--C
Confidence 99999999999999999999999999999999999999999999999999999999999999999999987665443 4
Q ss_pred CcEEEEEcCeEEEeecChhhHHHHHHHHhhcCCCCceeEEEecccCceEEEecCCCeeeeeEEEEecC-------cccch
Q 001092 543 NSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKG-------ISRIK 615 (1159)
Q Consensus 543 ~~~~V~lnG~~iG~~~~~~~~~~~lr~~Rr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~~v~~~-------~~~~~ 615 (1159)
+.++|||||+|||+|.+|..|++.||.+||+|.|+.+|||+++...++++||||+||+||||++|+|+ ++.++
T Consensus 562 ~~tkVfvNG~wVGvh~dp~~Lv~~lR~lRR~g~Is~eVSIvrdir~rE~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l~ 641 (1210)
T 3h0g_B 562 NATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIR 641 (1210)
T ss_dssp SSCCCCSTTCCCCCCSCHHHHHHHHHHHHTTTSSCTTCCCCCCTTTCCCCCCCSSCCBCCEEEECCCSSCSSSSCCCSSC
T ss_pred CceEEEECCEEEEEeCCHHHHHHHHHHHhhcCCCCCceEEEecCCCCeEEEecCCCcccceEEEEccCCccccccccccc
Confidence 67899999999999999999999999999999999999999999999999999999999999999986 89999
Q ss_pred hhhHHHhhcC----------CCchhhhhccCceeeeccccccceEEEeecCCCC--------------------------
Q 001092 616 EHHMKELLDG----------VRSFDDFLREGLIEYLDVNEENNALIALYEGDAT-------------------------- 659 (1159)
Q Consensus 616 ~~~~~~~~~~----------~~~~~~l~~~g~iE~id~~E~~~~~Ia~~~~~~~-------------------------- 659 (1159)
++|+++|..+ ..+|++|+++|+|||||++||++++||++++|+.
T Consensus 642 k~hi~~L~~~~~~~~~~~~~~~~w~~Lv~~GvIEylDaeEEet~mIamtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~~ 721 (1210)
T 3h0g_B 642 KEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPN 721 (1210)
T ss_dssp HHHHHHHHHHHTCCCSCTTCCCSSTTTTTTTSEEECCTTTGGGCCEESCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCSC
T ss_pred HHHHHHHhcccccccccccccCCHHHHHhCCCEEEecHhhhhceeEEecHHHhhhhhhhhccccccccccchhhccccCC
Confidence 9999988642 4789999999999999999999999999998862
Q ss_pred ---CcceeeeecCccccccccccccCCCCCCCCccccccccccCCccceeeeeccccccceeeecCCCcceeeeceeeee
Q 001092 660 ---PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELV 736 (1159)
Q Consensus 660 ---~~~th~Ei~p~~ilsv~aslIPF~~hNqspRn~yq~~M~KQa~g~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~ 736 (1159)
..||||||||++|||||||+||||||||||||||||||+|||||++++|+..|+||++|+|+|||+|||+|+.++.+
T Consensus 722 ~~~~~~THcEIhPsmILGIcASiIPFpdHNQSPRNtYQ~aMgKQamG~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~~ 801 (1210)
T 3h0g_B 722 PHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYL 801 (1210)
T ss_dssp CSCCSCSEECSCGGGSSCSSSTTSSSSTTSCSHHHHHHHHHHTTCCSCCCTTTTTSCCSSEEEESSCBCCSSBCTTSTTT
T ss_pred CcccccccccccchhhhhheeecccCccccccchhhhhhhhhcccccccccccccccCccccEeecCcCccccchhHHHh
Confidence 35899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCcceEEEEEecCCCCCCCcEEeeccccccCceeEEEEEEEEEEeccccCCCcceecCCCCCCCCccccccccc
Q 001092 737 GYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHH 816 (1159)
Q Consensus 737 ~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~ 816 (1159)
+++|+|+|+||+||||||+||||||||||||+|+|||||||+||++|+++++++..+..+.|..|+.+... ..+
T Consensus 802 ~~~elp~G~NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~y~~~~~~~~~~~~~~~~~p~~~~~~---~~~--- 875 (1210)
T 3h0g_B 802 KFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTL---RMK--- 875 (1210)
T ss_dssp TCTTSCSCCEECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEEEEECCCCCSSSCCCCCCCCCTTSCC---SCC---
T ss_pred CCCcccCccceEEEEeccCCCChhhheeeehhheecCceEEEEEEEEEEEeeecCCCceeEEcCCCcchhc---ccc---
Confidence 99999999999999999999999999999999999999999999999999988776667888888764321 122
Q ss_pred chhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcE
Q 001092 817 SNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDL 896 (1159)
Q Consensus 817 ~~~~~~~Ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~~~~~ 896 (1159)
...|++||+||||+||++|++|||||||++|+...+..+. ++.+...++|+|++++++| .|+||+|.++.+.+|.+
T Consensus 876 -~~~~~~LD~dGi~~~G~~v~~gDiligK~~p~~~~~~~~~-~~~~~~~~rd~s~~~~~~e--~g~Vd~V~~~~~~~g~~ 951 (1210)
T 3h0g_B 876 -HGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELG-QRTQLHAKRDVSTPLRSTE--SGIVDQVMVTTNQEGLK 951 (1210)
T ss_dssp -SCCGGGCCTTSSCCTTCCCCTTCCCCCCCCCC------------CCCCCCCCCCCCCTTC--CCCCCEEEEEECSSSSE
T ss_pred -hhhHhhcCCCCCcCCCCEecCCCEEEEEecCCCCCchhhc-ccccccccceeeEEecCCC--CeEEEEEEEEEecCCCe
Confidence 2479999999999999999999999999999875432221 2234556899999999999 99999999999999999
Q ss_pred EEEEEEeeecCCCcccccccccCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCccHHHHHHHhcccccccCCcee
Q 001092 897 CIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFH 976 (1159)
Q Consensus 897 ~vkv~~r~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~ 976 (1159)
.|||++|+.|+|++|||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.
T Consensus 952 ~vkv~~~~~R~~~~GDK~a~RhGqKGvi~~i~~~edmPf~~~G~~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~ 1031 (1210)
T 3h0g_B 952 FVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEG 1031 (1210)
T ss_dssp EEEEEECCCBCCCTTCEEECTTCCCEEEEEEECTTTSCCBTTTBCCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCC
T ss_pred EEEEEEEEecCCCchhhhhcccCCCceeeEEeccccCCcCCCCCCCeEEECCCcCCCCccchhhhHhHHHHHHHhcCCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeccCCCCCCCcHHHHHHHHHHcCCCCCCceEEEeCCCCceeeeeEeEeeeeeeecccccCcccEEecccCccccccc
Q 001092 977 YGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQ 1056 (1159)
Q Consensus 977 ~~t~F~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~Q 1056 (1159)
|+|||+ +..++++++.|.++||+++|+|+||||+||++|+++||+|++|||||+|||+||+||||+|||+.||||
T Consensus 1032 ~~tpF~-----~~~~~~~~~~l~~~g~~~~G~~~l~~g~tg~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~gp~~~~t~Q 1106 (1210)
T 3h0g_B 1032 DATPFT-----DVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQ 1106 (1210)
T ss_dssp BCCSSC-----SCCHHHHHHHHHTTTSCTTSCBCCBCSSSCCBCSSCBEECCEECEECSCCSTTTCEECSSCCBCSSSCS
T ss_pred eeccCC-----CCcHHHHHHHHHHcCcCCCCCEEEEcCCCCCCccccEEEEehHhhcchhhcccCcEEeccCCCchhccC
Confidence 999999 789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccccCCceeeeehhhhHHHHcccHHHHHHhhccCCCcccceeccccccceeecccccceecccccCCCccccccccH
Q 001092 1057 PTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPY 1136 (1159)
Q Consensus 1057 P~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erl~~~SD~~~~~vC~~cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy 1136 (1159)
|++||+|+|||||||||||||+|||||++|||||+.+||.+.++||..||++++.+...+..+|+.|+++.++.++.|||
T Consensus 1107 P~~gr~~~GG~r~GEME~~~l~a~Gaa~~l~e~l~~~SD~~~~~vC~~cg~~~~~~~~~~~~~c~~c~~~~~i~~~~~p~ 1186 (1210)
T 3h0g_B 1107 PVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPY 1186 (1210)
T ss_dssp BCCSSTTCCCCCCCHHHHHHHHHHTBHHHHHHHHHTTTTCCEEEEESSSCCBCCCCSSSCCCCCTTTCCSSCEEEEECCH
T ss_pred CcccccccCCeeeehhhhhhhhhccHHHHHHHHhhcCCCcceeEeecCCCCeeeecccCCceEcCccCCCCccceecCCH
Confidence 99999999999999999999999999999999999999999999999999998765556667899999999999999999
Q ss_pred hHHHHHHHHHhCCcccEEEecc
Q 001092 1137 ACKLLIQELQSMNIVPRLKLAE 1158 (1159)
Q Consensus 1137 ~~k~L~~EL~sm~i~~~l~~~~ 1158 (1159)
|||||+|||+||||.+||.+++
T Consensus 1187 ~~k~l~~El~~~~i~~rl~~~~ 1208 (1210)
T 3h0g_B 1187 AAKLLFQELMSMNIAPRLFTKN 1208 (1210)
T ss_dssp HHHHHHHHHHTTTCCEECCCST
T ss_pred HHHHHHHHHHhCCCceEEEecC
Confidence 9999999999999999999876
|
| >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 |
| 1159 | ||||
| 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 = 873 bits (2257), Expect = 0.0
Identities = 423/1227 (34%), Positives = 645/1227 (52%), Gaps = 112/1227 (9%)
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 GFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAP 832
G R + + Y +KY S ++ +P RT + LDDDGL AP
Sbjct: 832 GLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDK-------LDDDGLIAP 884
Query: 833 GEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK 892
G + DV I K +P+ GQ + + + E +VD+V + +++
Sbjct: 885 GVRVSGEDVIIGKTTPI---SPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQ 941
Query: 893 NGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFP 952
+G +K +R T+ P++GDKF+SRHGQKG G ++ED PF+ GI PDLI+NPH P
Sbjct: 942 DGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIP 1001
Query: 953 SRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIY 1012
SRMTV +IE L K G S F + TVE IS+ L +HG+ G +++Y
Sbjct: 1002 SRMTVAHLIECLLSKVAALSGNEGDASPFTD-----ITVEGISKLLREHGYQSRGFEVMY 1056
Query: 1013 SGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEM 1072
+G TG L A IF GP YYQ+L+HMV DK+HAR GP +LTRQP EGR+R+GGLR GEM
Sbjct: 1057 NGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEM 1116
Query: 1073 ERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYY-NHKLKAGICSTCKNGDNISS 1131
ERDC+IA+GA+ + ERLM +SD F V +C +CGL+ C C N +I
Sbjct: 1117 ERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQ 1176
Query: 1132 MKLPYACKLLIQELQSMNIVPRLKLAE 1158
+ +PYA KLL QEL +MNI PRL
Sbjct: 1177 IHIPYAAKLLFQELMAMNITPRLYTDR 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 | 1159 | |||
| 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: | 83.53 |
| >d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} | Back information, alignment and structure |
|---|
class: Multi-domain proteins (alpha and beta) fold: beta and beta-prime subunits of DNA dependent RNA-polymerase superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase family: RNA-polymerase beta domain: RBP2 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Probab=100.00 E-value=5.4e-260 Score=2517.03 Aligned_cols=1113 Identities=38% Similarity=0.638 Sum_probs=952.8
Q ss_pred CCCcccccccccccccccccchHHHHHHHHHHHHHhChHHHHhccCceeecC-----------CCcEEEEEeEEEEcCCc
Q 001092 23 APVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-----------DPSIFLRFKDVRIGQPS 91 (1159)
Q Consensus 23 ~~~~~~~~~~~~i~~~~~~~~Lv~~qi~SFn~Fl~~gL~~i~~~~~~I~~~~-----------~~~~~l~f~~i~i~~P~ 91 (1159)
+..++++|.|.+|++||+.++|++|||||||+||++||++|+++.+||.... ...+.|+|++++|++|+
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 4778899999999999999999999999999999999999999999985421 23588999999999999
Q ss_pred cccCC-cCCCCChhhHhhcCCccCccEEEEEEEEECCcc---------------cceeeEEeeEEEeecceeeccccccC
Q 001092 92 MTVDG-VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT---------------EKTTMEKNDVVIGRIPIMLRSCRCVL 155 (1159)
Q Consensus 92 ~~~~~-~~~~l~P~EcR~r~lTYsa~L~v~i~~~~~~~~---------------~~~~i~~~~v~lG~IPIMv~S~~C~L 155 (1159)
+.+.+ ..++|||+|||+|++||+|||+|+|++...... .......++|+||+|||||+|++|||
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 678999999999999999999999987532100 00123355799999999999999999
Q ss_pred CCCCHHHHHhcCCCCCCCCcEEEEcCchhhhHhhhhccCCeEEEEeCCCC---cEEEEEEecCCCc----ceEEEEEe-e
Q 001092 156 YGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKG---NINASVTSSTETV----KSKTVIQM-E 227 (1159)
Q Consensus 156 ~~ls~~eli~~~E~~~d~GGYFIING~ERVI~~q~~~s~N~i~~~~~~~g---~~~a~v~s~~~~~----~s~~~~~~-~ 227 (1159)
+++++++|++.||||+|+||||||||+||||++|++.++|++++++++.+ .+.|.++|...+. .+....++ +
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 2568888875433 12233333 2
Q ss_pred CC----EEEEEEcceeccccHHHHHHHhcCCCHHHHHHHhCC---chhhHhhhhHhHHHHHhcCCcCHHHHHHHHhhhcc
Q 001092 228 KG----KMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGR---DPRYSALLLPSIEECANLDIYTQEKALEYLEGKVK 300 (1159)
Q Consensus 228 ~g----~i~~r~~~~~~~IPl~ilLrALG~~sD~eI~~~i~~---~~~~~~~l~~~l~~~~~~~i~t~~~Al~yIg~r~r 300 (1159)
++ .+++.+++++.+||+++||||||..+|+||++.+.. +..+.+.+..++++. ..+.|+++|+.|||++++
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 588889988889999999999999999999999942 334566666666543 457899999999999877
Q ss_pred cCCCCCCCCChHHHHHHHHHhhhccCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCCCcccccCcEEcchhHHHHHHH
Q 001092 301 RSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLF 380 (1159)
Q Consensus 301 ~~~~~~~~~~~~e~~~~~L~~~ll~Hl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~NKRv~l~G~Ll~~lf 380 (1159)
.. ..+... ..+.|+++|.+.+|||++....+...|+.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+|
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 122233 6789999999999999997666677899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccccchHHHHHHHhccCCCccccc-ccccccceEEcccccccccccc
Q 001092 381 EDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRF-KMHRKGMTQVLARLSFIGTLGH 459 (1159)
Q Consensus 381 r~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~-~~q~sGvsq~l~RlN~ls~Lsh 459 (1159)
|+.|+++++.+++.+.+...+ ...+++...++++.||++|++||+||||..+.. ..+++|+||+|+|+||+++|||
T Consensus 401 r~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~~~~~~it~~i~~~~~TGn~~~~~~~~~~~~G~sq~l~r~n~l~~lSh 477 (1207)
T d1twfb_ 401 KTLFKKLTKDIFRYMQRTVEE---AHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSH 477 (1207)
T ss_dssp HHHHHHHHHHHHHHHHSCCC-----------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSSHHHHHHH
T ss_pred HHHHHHHHHHHHhhhcccccc---ccccChhhhhccCcHHHHHHHHHhcCcccccccccccccchhhhhhhcCHHHHHHh
Confidence 999999999999998765433 234566677788999999999999999986533 3578999999999999999999
Q ss_pred ccccccccccccccCCCCccCCCCCccccccCCCCCCcchhhhhcccceeeccCCCchhHHHHHhhcCCeeccccCcccc
Q 001092 460 MTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEEL 539 (1159)
Q Consensus 460 lRrv~s~f~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLi~~LA~~a~Vt~~~~~~~i~~~l~~lG~~~l~~~~~~~~ 539 (1159)
+||+++++++++|+++||+||||||||+||||||||+|||||||||++|+|+.+.++.++.++|..+|+.++........
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 99999999999999999999999999999999999999999999999999999999999999999999998876554432
Q ss_pred CCCCcEEEEEcCeEEEeecChhhHHHHHHHHhhcCCCCceeEEEecccCceEEEecCCCeeeeeEEEEecCcc------c
Q 001092 540 HNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGIS------R 613 (1159)
Q Consensus 540 ~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~~Rr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~~v~~~~~------~ 613 (1159)
.+..+||+||.|+|+++++..|++.+|.+||.|.++.+++++++....+++|+||.||++|||+.++|+.. .
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 36789999999999999999999999999999999999999999999999999999999999999998753 3
Q ss_pred chhhhHHHhhc-------------CCCchhhhhccCceeeeccccccceEEEeecCCCC---------------------
Q 001092 614 IKEHHMKELLD-------------GVRSFDDFLREGLIEYLDVNEENNALIALYEGDAT--------------------- 659 (1159)
Q Consensus 614 ~~~~~~~~~~~-------------~~~~~~~l~~~g~iE~id~~E~~~~~Ia~~~~~~~--------------------- 659 (1159)
+.+.++..+.. ...+|.+++..|.|||||++|+++++||+.++++.
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 44444443321 23579999999999999999999999999988763
Q ss_pred ---CcceeeeecCccccccccccccCCCCCCCCccccccccccCCccceeeeeccccccceeeecCCCcceeeeceeeee
Q 001092 660 ---PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIELV 736 (1159)
Q Consensus 660 ---~~~th~Ei~p~~ilsv~aslIPF~~hNqspRn~yq~~M~KQa~g~~~~n~~~R~D~~~y~l~ypQ~Plv~t~~~~~~ 736 (1159)
..+||+||+|++|||++|++|||+||||||||||||||+|||||++++|+..|.|++.|+|+|||+|||+|+.++.+
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 cCCCCCCCcceEEEEEecCCCCCCCcEEeeccccccCceeEEEEEEEEEEeccccCCCcceecCCCCCCCCccccccccc
Q 001092 737 GYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHH 816 (1159)
Q Consensus 737 ~~~~~p~G~N~iVAv~~~~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~ 816 (1159)
+++++|+|+||+||||||+||||||||||||+|++||||||+||++|++++++++.+..+.+..|...... ..+
T Consensus 796 ~~~e~p~G~N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~--- 869 (1207)
T d1twfb_ 796 KFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTL---RMK--- 869 (1207)
T ss_dssp TTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSC---BCC---
T ss_pred hhhcccchhceEEEEEeccCcccccccccchhhhhhcccceeeeEEEEEEecccccccccccccccccccc---ccc---
Confidence 99999999999999999999999999999999999999999999999999998888888888876543221 112
Q ss_pred chhhhccCCCCcccCCCceeCCCCEEEEEecCCCCCCCCCCCCCCCCcccccceeeecCCCCCceEEEEEEEeeCCCCcE
Q 001092 817 SNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDL 896 (1159)
Q Consensus 817 ~~~~~~~Ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~vd~v~~~~~~~~~~ 896 (1159)
...|++||+||||++|++|++||+||||++|....+..... ......++|.|+.++.++ .|+||+|..+.+.++.+
T Consensus 870 -~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~-~~~~~~~~~~s~~~~~~~--~g~V~~v~~~~~~~~~~ 945 (1207)
T d1twfb_ 870 -HGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQ-RTAYHSKRDASTPLRSTE--NGIVDQVLVTTNQDGLK 945 (1207)
T ss_dssp -SSCGGGCCTTSBCCTTCEECTTCEEECEECCCC--------------CCBBCCEECCTTC--CEEEEEEEEEECSSSCE
T ss_pred -hhhhhcccccccccccccccCCceeeeeeeccCCchhhhhh-ccccccccceeEEccCCC--CeEEEEEEEeecccccc
Confidence 35889999999999999999999999999998765432110 112234689999999998 99999999999999999
Q ss_pred EEEEEEeeecCCCcccccccccCCccEEEeeeccCCCCCCCCCCCCcEEeCCCCCCCCccHHHHHHHhcccccccCCcee
Q 001092 897 CIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFH 976 (1159)
Q Consensus 897 ~vkv~~r~~R~p~iGDKf~sRhGqKGvvs~i~~~eDmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~g~~~ 976 (1159)
.|||++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||||++.|.+.
T Consensus 946 ~~kv~i~~~R~p~iGDKfasRhGqKGv~s~i~p~eDMPf~~dG~~pDiI~NP~g~PSRMtiGql~E~~~gk~~~~~g~~~ 1025 (1207)
T d1twfb_ 946 FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEG 1025 (1207)
T ss_dssp EEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCE
T ss_pred eeeEEEEEEeccchhhhhhhccCCcceeeeeechhhCCcCCCCCCccEEECCCcCcccCcHHHHHHHHHHHHHHhcCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeccCCCCCCCcHHHHHHHHHHcCCCCCCceEEEeCCCCceeeeeEeEeeeeeeecccccCcccEEecccCccccccc
Q 001092 977 YGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQ 1056 (1159)
Q Consensus 977 ~~t~F~~~~~~~~~~~~~~~~l~~~g~~~~G~e~ly~G~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~Q 1056 (1159)
|+|||+ +..++++++.|.++||+++|+|+||||+||++|+++||+|++|||||+|||+||+|||++|||++||||
T Consensus 1026 d~t~F~-----~~~~~~~~~~L~~~g~~~~G~e~ly~G~tG~~~~~~i~~G~~yy~rL~HmV~DK~~~Rs~Gp~~~lT~Q 1100 (1207)
T d1twfb_ 1026 DASPFT-----DITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQ 1100 (1207)
T ss_dssp ECCSSS-----SCCHHHHHHHHHTTTSCTTSEECEECTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC-------
T ss_pred ccCCCC-----CccHHHHHHHHHHcCCCCCCCEEEECCCCCCCccceEEEehhHhhhhhhhhccccEeeccCCCCccccC
Confidence 999999 788999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccccCCceeeeehhhhHHHHcccHHHHHHhhccCCCcccceeccccccceee-cccccceecccccCCCcccccccc
Q 001092 1057 PTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYY-NHKLKAGICSTCKNGDNISSMKLP 1135 (1159)
Q Consensus 1057 P~~Gr~~~GG~R~GEMErd~l~a~Gas~~L~erl~~~SD~~~~~vC~~cg~~~~~-~~~~~~~~C~~c~~~~~~~~v~iP 1135 (1159)
|++||||+|||||||||||||+|||||++|||||++|||.+.++||.+||+++.. +.+....+|+.|+++.++.++.+|
T Consensus 1101 P~~Gr~~~GG~R~GEME~dal~a~Gaa~~L~e~l~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~c~~c~~~~~i~~~~iP 1180 (1207)
T d1twfb_ 1101 PVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIP 1180 (1207)
T ss_dssp ---------CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEEEECC
T ss_pred CCCccccCCCcceehHHHHHHHHHhHHHHHHHHhhccCCccceeccccCCceEEEecccccceeecCCCCCCCccccCCC
Confidence 9999999999999999999999999999999999999999999999999999864 334556789999999999999999
Q ss_pred HhHHHHHHHHHhCCcccEEEeccC
Q 001092 1136 YACKLLIQELQSMNIVPRLKLAEA 1159 (1159)
Q Consensus 1136 y~~k~L~~EL~sm~i~~~l~~~~~ 1159 (1159)
||||||+|||+||||.+||.+++.
T Consensus 1181 y~fk~l~~EL~sm~i~~~l~~~~~ 1204 (1207)
T d1twfb_ 1181 YAAKLLFQELMAMNITPRLYTDRS 1204 (1207)
T ss_dssp HHHHHHHHHHHHTTBCCEEESCSS
T ss_pred HHHHHHHHHHHHCCCceEEEecCc
Confidence 999999999999999999999763
|
| >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 |
|---|