RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 001092
(1159 letters)
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
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
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 969 bits (2508), Expect = 0.0
Identities = 349/1162 (30%), Positives = 532/1162 (45%), Gaps = 149/1162 (12%)
Query: 30 DKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQ 89
D F +PEFL + LV+ LDS+N F G++++ R I S + + L + R+G+
Sbjct: 13 DSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIES-YNGNTELEYGSYRLGE 71
Query: 90 PSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEK-NDVVIGRIPIML 148
P K P CRL +TY+AP+ V + V E K +V +G IP+M
Sbjct: 72 P--------PKFYPEECRLRGLTYSAPLYVKLRLV---VNETGEEIKEQEVYMGDIPLMT 120
Query: 149 RSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVII-DTDKKGNI 207
R GGYFII GTE+V++ QE S + + DK G+
Sbjct: 121 R------------------------GGYFIINGTERVIVSQEHRSPGVIFVEKKDKTGSK 156
Query: 208 NASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG--- 264
V S + + + +KIP+ ++++A+G+E+D+E+++ G
Sbjct: 157 VLYVARVIPYRGSWLEFEFDPKDNLYVRIDRKRKIPVTILLRALGLETDEEIIEAFGGDE 216
Query: 265 ----RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGR---AFS 317
P LL EE I + ALE + +V + +EGR A
Sbjct: 217 LTDLVPPEGEEALLEIYEEAKGEKITARN-ALELIGSRVFV---VKRYDAKEGRYKRAKY 272
Query: 318 ILRDVFLANV----PVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSG 373
+L L ++ ++ + K + M++ ++E L K DD D++GN+RL L G
Sbjct: 273 VLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVG 332
Query: 374 QLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVR-DSITVGLERTLSTGNF 432
+L+ LF M +V++ R + D +V D I L TG F
Sbjct: 333 ELLENLFRVGLSRMERDVKE----------RLEKADKRDTLVPQDLINAKPIHALITGFF 382
Query: 433 DVKRFKMHRKGMTQVLARLSFIGTLGHMTRVS-PQFEKSRKVSGPRALQPSQWGMLCPCD 491
R ++Q + + + + L H R+S + R R + P+ +G +CP +
Sbjct: 383 G-------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVRDVHPTHYGRICPIE 435
Query: 492 TPEGEACGLVKNLALMTHVT-TDEEEGPLISLCY-CLGVEDLELLSGEELHNPNSFLVIF 549
TPEG GL+K+LAL + E P + L V+++E LS +E V
Sbjct: 436 TPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEIEYLSADE------EDVYV 489
Query: 550 NGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQR----CVYIASDGGRVCRPLV 605
G G P + + + RR VSV E GR P +
Sbjct: 490 IGQANGTLDEPGELVEELVECRR--GGSGEVSVADPEGVDYMDVSPKQVVSVGRSLIPFL 547
Query: 606 IADKGISRIKEHHMKELLDG-VRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTH 664
D + +M+ +R+ + G +EYLD + A+IA G TH
Sbjct: 548 EHDDANRALMGSNMQRQAVPLLRTEAPLVGTG-MEYLDAEDSGAAVIAKRPGV----VTH 602
Query: 665 IEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQ 724
+EI P ILG+ A LIPYP HNQSP N Y+ A QA G + R D++ LVY
Sbjct: 603 VEISPIVILGIEASLIPYPEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLVYAD 662
Query: 725 RPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYT 784
P + T +L GQNA VA M ++GY+ EDAI++++ S++R I +++Y
Sbjct: 663 GPSVDT--------GELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFTSIHIEEYE 714
Query: 785 AINQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYIN 844
+ + P+ E ++ LD+DG+ G +K D+ +
Sbjct: 715 TEARDTKLGPEEIRDIPNV---SEEALRN----------LDEDGIIRIGAEVKGGDILVG 761
Query: 845 KESPLETRGSIMSPTGQTD----SRYRSARQTYKGPDGETCVVDRVALCSDKNGDL---- 896
K +P + ++P + + R P GE +VD V + + ++GD
Sbjct: 762 KVTP--KGETELTPEERLLRIFGEKVRDTSLRV--PHGEEGIVDDVQVFTREDGDPGVNK 817
Query: 897 CIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMT 956
+K + R+P++GDK + RHG KGV IV QED PF E G PD+I+NP G PSRM
Sbjct: 818 LVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMN 877
Query: 957 VGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGIT 1016
+G+++E GKA G F E I E L + GF Y+GK+++Y G T
Sbjct: 878 IGQILETHLGKAAALLGIPVDTPVFDGAP-----EEDIRELLKEAGFPYSGKEVLYDGRT 932
Query: 1017 GCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDC 1076
G P A IF+G +YYQKL HMV DK+HAR +GP ++T+QP G+A+ GG R GEME
Sbjct: 933 GEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 992
Query: 1077 LIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPY 1136
L AYGA+ + ERL V SD VCG + Y C G+NI + +P
Sbjct: 993 LEAYGAAYTLQERLTVKSD-------DVCGRIKIYE-------CIVK--GENIPEVGIPE 1036
Query: 1137 ACKLLIQELQSMNIVPRLKLAE 1158
+ K+L++EL+S+ I RL+L +
Sbjct: 1037 SFKVLLKELRSLGIDVRLELED 1058
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit. RNA polymerases
catalyse the DNA dependent polymerization of RNA.
Prokaryotes contain a single RNA polymerase compared to
three in eukaryotes (not including mitochondrial. and
chloroplast polymerases). Each RNA polymerase complex
contains two related members of this family, in each case
they are the two largest subunits.The clamp is a mobile
structure that grips DNA during elongation.
Length = 866
Score = 737 bits (1904), Expect = 0.0
Identities = 245/499 (49%), Positives = 312/499 (62%), Gaps = 28/499 (5%)
Query: 660 PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYL 719
+ THIEI P IL V A LIP+P HNQSPRN YQ M KQA+G A NQ RMD+ LYL
Sbjct: 393 KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYL 452
Query: 720 LVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIV 779
L+YPQ+PL+ T E + + +L GQNA VAVMSYSGY+ EDAI++NKSS+DRGF R I
Sbjct: 453 LLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIH 512
Query: 780 VKKYTAINQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPN 839
KKY +K N + R + + S L LD+DG+ PG ++P
Sbjct: 513 YKKYEIELRKTKNGPEEIT-----------RGDIPNVSEEKLKNLDEDGIIRPGARVEPG 561
Query: 840 DVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGD---L 896
D+ + K +P S G+ R Y G GE +VD V + S + D
Sbjct: 562 DILVGKITPKGETESTP-IFGEKARDVRDTSLKYPG--GEKGIVDDVKIFSRELNDGGNK 618
Query: 897 CIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMT 956
+K IR R+P++GDKF+SRHGQKGV I+ QED PF+E GI PD+I+NPHGFPSRMT
Sbjct: 619 LVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMT 678
Query: 957 VGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGIT 1016
+G+++E L GKAG G+F + F E ISE L + G +Y GK+++Y G T
Sbjct: 679 IGQLLESLLGKAGALLGKFGDATPFDG-----AEEEDISELLGEAGLNYYGKEVLYDGRT 733
Query: 1017 GCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDC 1076
G PL+A IF+GP+YYQ+LKHMV DK+HAR +GP +LTRQP +GR+R GG R GEMERD
Sbjct: 734 GEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDA 793
Query: 1077 LIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPY 1136
LIA+GA+ L+ ERL + SD +VC CG++ N C CK G NIS + +PY
Sbjct: 794 LIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPY 847
Query: 1137 ACKLLIQELQSMNIVPRLK 1155
A KLL QELQSMNI PRLK
Sbjct: 848 AFKLLFQELQSMNIDPRLK 866
Score = 397 bits (1023), Expect = e-122
Identities = 161/470 (34%), Positives = 232/470 (49%), Gaps = 91/470 (19%)
Query: 44 LVKQHLDSFNYFVNTGIRKIVRANDRIVSGI-DPSIFLRFKDVRIGQPSMTVDGVSEKLN 102
LVKQ +DSFNYF+N G+++IV++ I D + L+F D+ +G+P + GV+ KL
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLT 60
Query: 103 PHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAE 162
P+ CRL D+TY+AP+ V+I +K +++ +V IG IPIMLRS C L G E
Sbjct: 61 PNECRLRDLTYSAPLYVDIRLT---VNDKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEE 117
Query: 163 LARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKT 222
L +LGECPLDPGGYFII GTEKV++ QEQ S N +I++ D KG + TS S
Sbjct: 118 LIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSKGKRIYTKTSIPSY--SPY 174
Query: 223 VIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECAN 282
+ K ++ +I
Sbjct: 175 RGSWLEVKSDKKKDRIYVRI---------------------------------------- 194
Query: 283 LDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVA 342
D+ QE+AL+Y+ + +
Sbjct: 195 -DLKRQEEALKYIGKRF---------------------------------------EDLI 214
Query: 343 VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKP 402
M+R+++ +L K +DD D++GNKR+ L+G+L+ LF K + EV++ + LSK
Sbjct: 215 YMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK- 273
Query: 403 SRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTR 462
I IT G++ L+TGN+ KRF M R G++QVL RL+ + L H R
Sbjct: 274 --KKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRR 331
Query: 463 VS-PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVT 511
+S + RK R L PS WG +CP +TPEGE CGLVKNLALM ++
Sbjct: 332 ISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B. This
model represents the archaeal version of DNA-directed RNA
polymerase subunit B (rpoB) and is observed in all
archaeal genomes.
Length = 599
Score = 687 bits (1774), Expect = 0.0
Identities = 286/617 (46%), Positives = 387/617 (62%), Gaps = 23/617 (3%)
Query: 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVI 606
V NG ++G H P+ + +RKLRR+GK+ + V+V E+ VYI D GR+ RPL++
Sbjct: 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIV 60
Query: 607 ADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIE 666
+ G ++ H+++L +G ++DD +++G+IEYLD EE NA IAL + TP+ TH+E
Sbjct: 61 VENGKPKLTREHVEKLKEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLE 120
Query: 667 IEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRP 726
I+P ILG+IA IPYP HNQSPRNT AM KQ++G A N R+D+ +LL YPQ+P
Sbjct: 121 IDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKP 180
Query: 727 LLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAI 786
L+ TR +EL+GYD AGQN VAVMSY GY+IEDA++MNK+S++RG R + Y A
Sbjct: 181 LVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
Query: 787 NQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKE 846
++Y DR P+ G + H LD+DG+ P +K DV I K
Sbjct: 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKH-------LDEDGIVYPEVEVKGGDVLIGKT 293
Query: 847 SP---LETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIR 903
SP LE + T R R T + GE +VD+V + + G+ +K +R
Sbjct: 294 SPPRFLEELRELGLVT----ERRRDTSVTVR--HGEKGIVDKVIITETEEGNKLVKVRVR 347
Query: 904 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIEL 963
R PELGDKF+SRHGQKGV G IV QED PF+E GI PDLI+NPH PSRMTVG+++E+
Sbjct: 348 DLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM 407
Query: 964 LGGKAGVSCGRFHYGSAF-GEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQA 1022
+ GK GR G+ F GEP E + + L+K GF +GK+++Y GITG L+A
Sbjct: 408 IAGKVAALEGRRVDGTPFEGEP------EEELRKELLKLGFKPDGKEVMYDGITGEKLEA 461
Query: 1023 YIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGA 1082
IF+G IYYQKL HMV DK+HAR GP +LTRQPTEGRAR GGLR GEMERD LI +GA
Sbjct: 462 EIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGA 521
Query: 1083 SMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLI 1142
+ML+ ERL+ SD + V VC CG + + + + C C +IS +++ YA KLL+
Sbjct: 522 AMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLL 581
Query: 1143 QELQSMNIVPRLKLAEA 1159
EL+S+ I PRL+L +
Sbjct: 582 DELKSLGISPRLELGDK 598
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 673 bits (1738), Expect = 0.0
Identities = 285/617 (46%), Positives = 382/617 (61%), Gaps = 23/617 (3%)
Query: 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVI 606
V NG ++G H P+ + +R+ RR+G+I E V+V E+ V I +D GR RPL++
Sbjct: 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIV 66
Query: 607 ADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIE 666
+ G + E H+++L +G +FDD +++G+IEYLD EE NA IA+YE D T + TH+E
Sbjct: 67 VENGEPLLTEEHIEKLKNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLE 126
Query: 667 IEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRP 726
I+P ILG+ AG+IPYP HN SPR T M KQ++G A N R D+ +LL YPQ P
Sbjct: 127 IDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVP 186
Query: 727 LLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAI 786
L+ T+T E++G+D+ AGQN VAVMSY GY+IEDA++MNK+S++RG GR + Y
Sbjct: 187 LVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
Query: 787 NQKYANSTSDRILRPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKE 846
++Y DR PD+ G + H LD+DGL P +K DV I K
Sbjct: 247 ERRYPGGQEDRFEIPDKDVRGYRGEEAYRH-------LDEDGLVNPETEVKEGDVLIGKT 299
Query: 847 SP---LETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIR 903
SP LE G + + R T + GE +VD V L + G +K +R
Sbjct: 300 SPPRFLEE----PDDFGISPEKRRETSVTMR--SGEEGIVDTVILTETEEGSRLVKVRVR 353
Query: 904 HTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIEL 963
R PELGDKF+SRHGQKGV G IV QED PF+E G+ PDLI+NPH PSRMTVG ++E+
Sbjct: 354 DLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM 413
Query: 964 LGGKAGVSCGRFHYGSAF-GEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQA 1022
+GGK G GR G+AF GE E + E L K GF + GK+++Y GITG ++A
Sbjct: 414 IGGKVGSLEGRRVDGTAFSGED------EEDLREALEKLGFEHTGKEVMYDGITGEKIEA 467
Query: 1023 YIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGA 1082
IF+G IYYQKL HMV +K+HAR GP +LTRQPTEGRAR GGLR GEMERD LI +GA
Sbjct: 468 EIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGA 527
Query: 1083 SMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACKLLI 1142
+ML+ ERL+ SD E+ VC CG++ Y+ K C C +I +++ YA KLL+
Sbjct: 528 AMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLL 587
Query: 1143 QELQSMNIVPRLKLAEA 1159
EL+S+ I PRL+L +
Sbjct: 588 DELKSLGIAPRLELEDK 604
>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase compared
to three in eukaryotes (not including mitochondrial. and
chloroplast polymerases). This domain represents the
hybrid binding domain and the wall domain. The hybrid
binding domain binds the nascent RNA strand / template
DNA strand in the Pol II transcription elongation
complex. This domain contains the important structural
motifs, switch 3 and the flap loop and binds an active
site metal ion. This domain is also involved in binding
to Rpb1 and Rpb3. Many of the bacterial members contain
large insertions within this domain, as region known as
dispensable region 2 (DRII).
Length = 373
Score = 510 bits (1315), Expect = e-171
Identities = 177/391 (45%), Positives = 238/391 (60%), Gaps = 19/391 (4%)
Query: 674 GVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTI 733
G++A LIP+ HNQSPR TYQCAMGKQA+G N+ R D YLL YPQ+PL+ T +
Sbjct: 1 GIVASLIPFVDHNQSPRITYQCAMGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAV 60
Query: 734 ELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANS 793
E G+ +L GQNA VAVMSY+GY+ EDAI++NKSS+DRG I +K+Y +K
Sbjct: 61 EKGGFGELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHIKEYEIEARKTKLG 120
Query: 794 TSDRILR-PDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETR 852
+ I R P A R LD+DG+ G +KP D+ + K +P +
Sbjct: 121 PIEEITRDPPNVSEEAYR------------KLDEDGIVRVGAEVKPGDILVGKITPKGEK 168
Query: 853 GSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGD 912
+ + G+ + K GE VD V + + G +K IR R+P++GD
Sbjct: 169 L-LRAIFGEKARDVKDTSLKVKH--GEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQVGD 225
Query: 913 KFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSC 972
KF+SRHGQKGV I+ QED PF+E GI PD+I+NPHG PSRMT+G+++E L GKA
Sbjct: 226 KFASRHGQKGVVSKILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLESLLGKAAALL 285
Query: 973 GRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQ 1032
G+F + F S + VE I E L + G++ GK+++Y G TG P +A IF+GPIYYQ
Sbjct: 286 GKFIDATPFDGAS---EDVEDIGELLKEAGYNAYGKEVLYDGRTGEPFKAPIFVGPIYYQ 342
Query: 1033 KLKHMVLDKMHARGSGPRVMLTRQPTEGRAR 1063
KLKHMV DK+HAR +GP +LT+QP GR+R
Sbjct: 343 KLKHMVDDKIHARSTGPYSLLTQQPLGGRSR 373
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 326 bits (838), Expect = e-100
Identities = 175/517 (33%), Positives = 278/517 (53%), Gaps = 45/517 (8%)
Query: 29 VDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIG 88
D+ L + K LV+ H+DS+N FV+ G++KI+ I + I+ +++ +R+G
Sbjct: 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVG 62
Query: 89 QP-SMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIM 147
+P DG ++ P RL ++TY+AP+ + + V+G E+ +V IG +P+M
Sbjct: 63 KPVVKEADGSEREIYPMEARLRNLTYSAPLYLEMSPVEGGEEEEPE----EVYIGELPVM 118
Query: 148 LRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNI 207
+ S C LYG E EL +GE PLDPGGYFI+ G+E+VL+ E L+ N+++++ D++
Sbjct: 119 VGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGD 178
Query: 208 N---ASVTSSTETVKSKTVIQMEKGKMYLLLNQF---VKKIPIMVVMKAMGMESDQEVVQ 261
A V S ++ + E+ + LL F IP +++M+A+G+E+D+E+V+
Sbjct: 179 RIEVAKVFSQRRGYRALVTV--ERNRDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVE 236
Query: 262 MVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRD 321
V DP +L ++EE ++ TQE+ALEY+ KR G R RA ++
Sbjct: 237 AVSDDPEIVKFMLENLEE---AEVDTQEEALEYIG---KRVAPGQTKEYRIKRAEYVIDR 290
Query: 322 VFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFE 381
L ++ V R K Y+ M E L + DDKD+ NKRL+L+G L+ E
Sbjct: 291 YLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLM----E 346
Query: 382 DLFKTMISEVQKTVDIILSKPSRSSRFDLS-QFIVR-DSITVGLERTLSTGNFDVKRFKM 439
DLF+ + + + V L + + +R +LS + VR D +T LE ++TGN +
Sbjct: 347 DLFRVAFNRLARDVKYQLERANMRNR-ELSIKTAVRSDVLTERLEHAMATGN-----WVG 400
Query: 440 HRKGMTQVLARLSFIGTLGHMTRV-------SPQFEKSRKVSGPRALQPSQWGMLCPCDT 492
R G++Q+L R ++ TL H+ RV P FE R L P+QWG +CP +T
Sbjct: 401 GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEA-------RDLHPTQWGRICPSET 453
Query: 493 PEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVE 529
PEG CGLVKN A M ++T E+E + + LGVE
Sbjct: 454 PEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This domain
forms one of the two distinctive lobes of the Rpb2
structure. This domain is also known as the protrusion
domain. The other lobe (pfam04561) is nested within this
domain.
Length = 394
Score = 282 bits (723), Expect = 3e-85
Identities = 118/400 (29%), Positives = 189/400 (47%), Gaps = 18/400 (4%)
Query: 43 GLVKQHLDSFNYFVNTGIRKIVRANDRIVS-GIDPSIFLRFKDVRIGQPSMTV-DGVSEK 100
GLV+Q LDSFN+F++ G+++ + I +P L+ +++ +P + DG + +
Sbjct: 1 GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDEEPEFSLKVGQIKLAKPKIKESDGKTRE 60
Query: 101 LNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDE 160
+ P RL ++TY++P+ V E +EK V IG+IP+MLRS C+L G E
Sbjct: 61 IYPREARLRNLTYSSPLYVPAELTVN---NTEEIEKEKVFIGKIPLMLRSNACILNGASE 117
Query: 161 AELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVI-IDTDKKGNINASVTSSTETVK 219
+EL +LGECPLDPGGYFI+ G+EKV++ Q Q S N DK G S + + +
Sbjct: 118 SELVKLGECPLDPGGYFIVNGSEKVIINQIQRSPNIYYVFKKDKNGIRIYSASIISNRGR 177
Query: 220 SKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEV-VQMVGRDPRYSALLLPSIE 278
S + KGK+Y +N K I ++++ + + + + D + + E
Sbjct: 178 SLRLEITSKGKIYARINSGAKLIMFVLLLALGLNLVEIILNLLVPEVDLEIQDDIGINDE 237
Query: 279 ECANLDI--------YTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVH 330
E L Q + + S G P R A IL L ++ V
Sbjct: 238 EDEFLTDKPELEEQFVIQTQDEALDYIGGRGSAKGFPRERRILGAVGILDLNLLPHLGVS 297
Query: 331 NNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISE 390
N K + M+ R++ L + +DD D++GNKRL L+G+L+ F L + +
Sbjct: 298 ENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGELLQSQFRILLNRLERD 357
Query: 391 VQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTG 430
V++ + L K F L + IT G+ L TG
Sbjct: 358 VRERIQKCLKKK---FDFTLQNLVNSKPITSGIRYFLGTG 394
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit. This
model describes orthologs of the beta subunit of
Bacterial RNA polymerase. The core enzyme consists of two
alpha chains, one beta chain, and one beta' subunit
[Transcription, DNA-dependent RNA polymerase].
Length = 1065
Score = 192 bits (491), Expect = 5e-50
Identities = 142/434 (32%), Positives = 208/434 (47%), Gaps = 71/434 (16%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKK--YTAIN-QKYANSTSDR 797
L G+N VA M ++GY+ EDAI+++ +R +VK +T+I+ ++Y D
Sbjct: 671 LALGRNVLVAFMPWNGYNYEDAILIS----ER------LVKDDVFTSIHIEEYEVEARD- 719
Query: 798 ILRPDRTGPGAERM--QVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSI 855
T G E + + + S L LD++G+ G +K D+ + K
Sbjct: 720 ------TKLGPEEITRDIPNVSEDALRNLDENGIVRIGAEVKAGDILVGK---------- 763
Query: 856 MSPTGQTDS-------------RYRSARQT-YKGPDGETCVVDRVALCSDKNGD------ 895
++P G+T+ + R R T + P G V V + S K GD
Sbjct: 764 VTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKEGDELPPGV 823
Query: 896 -LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSR 954
+K I R+ ++GDK + RHG KGV I+ ED PF E G D+++NP G PSR
Sbjct: 824 NKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883
Query: 955 MTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSG 1014
M +G+++E G AG GR G P + E I E L K G +GK +Y G
Sbjct: 884 MNIGQILETHLGWAGKKLGR--KGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDG 941
Query: 1015 ITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMER 1074
TG + +G +Y KL H+V DKMHAR +GP ++T+QP G+A+ GG R GEME
Sbjct: 942 RTGEQFDNPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1001
Query: 1075 DCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKL 1134
L AYGA+ + E L V SD V G Y +K G+N+ +
Sbjct: 1002 WALEAYGAAYTLQEMLTVKSDD-------VTGRTKAYEAIVK---------GENVPEPGI 1045
Query: 1135 PYACKLLIQELQSM 1148
P + +LI+ELQS+
Sbjct: 1046 PESFNVLIKELQSL 1059
Score = 82.8 bits (205), Expect = 8e-16
Identities = 115/533 (21%), Positives = 212/533 (39%), Gaps = 147/533 (27%)
Query: 32 FQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDP---SIF--------- 79
F +PE L+V L++ LDS+++F+ R G++ SIF
Sbjct: 8 FGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKE----EGLEEVFKSIFPIEDYTGNM 63
Query: 80 -LRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKND 138
L + +G+P V+ C+ +TY+ P+ V + + +++ +
Sbjct: 64 ELEYLSYELGEPKYDVE---------ECKERGLTYSVPLKVKLRLINKEEDGTKEIKEQE 114
Query: 139 VVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVI 198
V +G IP+M G FII G E+V++ Q S V
Sbjct: 115 VYMGDIPLMTDR------------------------GTFIINGAERVVVSQLHRSPG-VF 149
Query: 199 IDTDKKGNINASVTSSTETVKSK-TVIQME---KGKMYLLLNQFVKKIPIMVVMKAMGME 254
++K + N V S + + + ++ E K +Y+ +++ +K+P V+++A+G
Sbjct: 150 FSSEKDTHKNGKVLYSARIIPYRGSWLEFETDKKDLVYVRIDR-KRKLPATVLLRALGYT 208
Query: 255 SDQEVVQMVGRDPRYSALLL---PSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDR 311
D + VG S L + + A L+IY + E P
Sbjct: 209 IDTLKLNRVGSYEYISNTLRKDPTNSRDEALLEIYRVLRPGE--------------PPTV 254
Query: 312 EGRAFSILRDVF-------LANVPVHNNNFR---PKCFYVAVM--------LRRMVEAML 353
E A S+L ++F L V + N + + V+ ++ +++
Sbjct: 255 EA-ARSLLENLFFDPKRYDLGRVGRYKMNKKLGLDVPEDIGVLTKEDIIATIKYLIKLRN 313
Query: 354 NKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTV---------------DII 398
K +DD D++GN+R+ G+L+ ++ F+ ++ +++ V D+I
Sbjct: 314 GKGEVDDIDHLGNRRIRSVGELL----QNQFRVGLARMERIVRERMTTQDTDTLTPQDLI 369
Query: 399 LSKPSRSS------RFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLS 452
+KP ++ LSQF+ D E T H++ RLS
Sbjct: 370 NAKPISAAIKEFFGSSQLSQFM--DQTNPLAELT-------------HKR-------RLS 407
Query: 453 FIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLA 505
+G G +TR FE R + P+ +G +CP +TPEG GL+ +L+
Sbjct: 408 ALGP-GGLTRERAGFEV-------RDVHPTHYGRICPIETPEGPNIGLINSLS 452
Score = 32.4 bits (74), Expect = 1.9
Identities = 25/101 (24%), Positives = 41/101 (40%), Gaps = 28/101 (27%)
Query: 624 DGVRSFDDFLREGLIEYLDVNEENNALIA-------------------LYEGD---ATPD 661
DG D + YL +EE+N +IA Y G+ +P+
Sbjct: 472 DGKVVVTD-----EVVYLTADEEDNYVIAQANAPLDENGRFVGDLVPARYRGEISLVSPE 526
Query: 662 T-THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQA 701
++++ P I+ V A LIP+ H+ + R M +QA
Sbjct: 527 QVDYMDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQA 567
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 174 bits (444), Expect = 3e-44
Identities = 128/431 (29%), Positives = 202/431 (46%), Gaps = 55/431 (12%)
Query: 744 GQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN-QKYANSTSDRILRPD 802
GQN VA M + GY+ EDAI++NK R + +T+I+ +KY + LR
Sbjct: 647 GQNVLVAYMPWEGYNFEDAILINK--------RLVYEDLFTSIHIEKY-----EIELRQT 693
Query: 803 RTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQT 862
+ G + + S L LD++G+ + G + D+ + K +P S P G+
Sbjct: 694 KLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGE--SDQLPEGKL 751
Query: 863 -----DSRYRSARQT-YKGPDGETCVVDRVALCSDKNGD-------LCIKFLIRHTRRPE 909
+ + + T + P+G V +V + S GD L I+ I R+ +
Sbjct: 752 LRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQ 811
Query: 910 LGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAG 969
+GDK + RHG KG+ I+ ++D P+ G PD+I+NP G PSRM VG++ E L G AG
Sbjct: 812 VGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAG 871
Query: 970 VSCGRFHYGSAFGEPSGHA----------DTVESISETLVKHGFSYNGKDMIYSGITGCP 1019
+ + F E G + + + GK ++ G TG
Sbjct: 872 DNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYK 931
Query: 1020 LQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIA 1079
+ + +G Y KL H+V DK+HAR +GP ++T+QP G+A++GG R GEME L A
Sbjct: 932 FKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEA 991
Query: 1080 YGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKNGDNISSMKLPYACK 1139
+GA+ + E L + SD + + N L A G I P + K
Sbjct: 992 FGAAYTLKELLTIKSDDMQGR-----------NETLNA-----IVKGQPIPKPGTPESFK 1035
Query: 1140 LLIQELQSMNI 1150
+L++ELQS+ +
Sbjct: 1036 VLMRELQSLGL 1046
Score = 69.3 bits (170), Expect = 1e-11
Identities = 96/479 (20%), Positives = 182/479 (37%), Gaps = 86/479 (17%)
Query: 50 DSFNYFVNTGIRKIVRANDRIVSGIDPS----IFLRFKDVRIGQPSMTVDGVSEKLNPHM 105
SF +F+N G+ + + +I D + + L K+ ++ P K N
Sbjct: 16 TSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFGKNYKLKYP---------KYNLLS 63
Query: 106 CRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELAR 165
+ D Y+ I + ++ T K ++ + +IG +P M +
Sbjct: 64 AKSYDSNYSIQIYLPLK-FINLKTNK--IKFINYLIGNLPKMTQR--------------- 105
Query: 166 LGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVII---DTDKKGNINASVTSSTETVKSKT 222
G FII G E+V I Q+ ++ I + K N S T
Sbjct: 106 ---------GTFIINGLERV--IVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIK 154
Query: 223 VIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVGRDPRYSALLL------PS 276
+ ++++ +++ +K P+++ +KA+G+ +DQ++ + + L
Sbjct: 155 FELDKNKEIWIRIDK-NRKKPLIIFLKALGL-TDQDIYSRLTKSEFLKKLKPILLNSNSY 212
Query: 277 IEECANLDIYTQEKALEYLEGKVKR----STFGSPPNDREGRA--FSILRDVFLANVPVH 330
E L+IY +E S F P N G+ + I + L N+P
Sbjct: 213 TNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNL-NIPER 271
Query: 331 NNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISE 390
N + + +++ +NK DD D++ N+R+ G+L+ F K +
Sbjct: 272 VRNLTYEDILSI--IDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERI 329
Query: 391 VQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLAR 450
++ + I D+ + I L F + ++Q + +
Sbjct: 330 LRNRMTI----------CDIDSLSKFNLINPKPLIALIREFFGSSQ-------LSQYMDQ 372
Query: 451 LSFIGTLGHMTRVS----PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLA 505
+ + L H R+S +K R R + PS +G +CP +TPEG CGL+ +LA
Sbjct: 373 TNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
Score = 30.1 bits (68), Expect = 8.8
Identities = 33/135 (24%), Positives = 50/135 (37%), Gaps = 40/135 (29%)
Query: 665 IEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQ 724
I I P + + LIP+ HN + R MG M L+YP+
Sbjct: 510 IAISPIQVFSIAESLIPFLEHNDANR----ALMGS------------NMQRQAVPLLYPE 553
Query: 725 RPLLTTRTIELVGYDK-LGAGQNATVA------VMSYSGYDIEDAIVMNKSSLDRGFGRC 777
+P++ T GY+K + T+ V+S S Y I I+ + R
Sbjct: 554 KPIVGT------GYEKQIALDSGMTIISLTEGIVVSVSAYKI---IIQDD------NNRY 598
Query: 778 IV--VKKYTAINQKY 790
I ++KY NQ
Sbjct: 599 IHYYLQKYQRSNQNT 613
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 156 bits (397), Expect = 1e-38
Identities = 124/387 (32%), Positives = 183/387 (47%), Gaps = 56/387 (14%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN-QKYANSTSDRIL 799
L G+N VA M + GY+ EDA+++++ R + YT+ + +KY T
Sbjct: 649 LALGKNVLVAYMPWEGYNFEDAVLISE--------RLVYEDIYTSFHIRKYEIQTH---- 696
Query: 800 RPDRTGPGAERM--QVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS 857
T G ER+ ++ H LL LD +G+ G ++ D+ + K +P E S +
Sbjct: 697 ---VTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYA 753
Query: 858 PTGQT-----DSRYRSARQT-YKGPDGETCVVDRVALCSDKNGDL----CIKFLIRHTRR 907
P G+ + ++++T K P G V V K G I I R
Sbjct: 754 PEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKRE 813
Query: 908 PELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGK 967
++GDK + RHG KG+ I+ ++D P+ + G D+++NP G PSRM VG++ E L G
Sbjct: 814 IQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGL 873
Query: 968 AGVSCGRFHYGSA-FGEPSGHADTVESISETLVKHGFS------------------YNGK 1008
AG R HY A F E + S LV FS Y GK
Sbjct: 874 AGDLLNR-HYRIAPFDERYE-----QEASRKLV---FSELYEASKQTANPWVFEPEYPGK 924
Query: 1009 DMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLR 1068
++ G TG P + + +G Y KL H V DK+HAR SGP ++T+QP GR++ GG R
Sbjct: 925 SRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQR 984
Query: 1069 VGEMERDCLIAYGASMLIFERLMVSSD 1095
VGEME L +G + ++ E L SD
Sbjct: 985 VGEMEVWALEGFGVAYILQEMLTYKSD 1011
Score = 58.8 bits (143), Expect = 2e-08
Identities = 105/540 (19%), Positives = 187/540 (34%), Gaps = 171/540 (31%)
Query: 35 LPEFLKVRGLVKQHLDSFNYFVNTGIR-------KIVRANDRIVSGIDPSIFLRFKDVRI 87
+P F +++ + F F++ G+ KI + I L + ++
Sbjct: 12 IPGFNQIQ------FEGFCRFIDQGLTEELSKFPKIEDTDQEI------EFQLFVETYQL 59
Query: 88 GQPSMTV-DGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPI 146
+P + D V E L TY++ + V + + M++ V IG IP+
Sbjct: 60 VEPLIKERDAVYESL----------TYSSELYVPAGLIW---KKSRDMQEQTVFIGNIPL 106
Query: 147 MLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQ----------EQLSKNR 196
M + G FII G +V++ Q +L N
Sbjct: 107 M------------------------NSLGTFIINGIYRVVINQILRSPGIYYRSELDHNG 142
Query: 197 VII---------------DTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKK 241
+ + + D+K I A V S+ +K
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKARIWARV--------SR-----------------KQK 177
Query: 242 IPIMVVMKAMGMESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKR 301
I I+V++ AMG+ E++ V Y + L + + I ++E A+ LE +
Sbjct: 178 ISILVLLSAMGLNLR-EILDNV----CYPEIFLSFLNDKEKKKIGSKENAI--LEFYQQF 230
Query: 302 STFGSPPNDREGRAFSILRDVFLA-------------------NVPVHNNNFRPKCFYVA 342
+ G P E L+ F ++P +N P+ A
Sbjct: 231 ACVGGDPVFSES-LCKELQKKFFQQRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAA 289
Query: 343 VMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKP 402
++ +DD D++ NKR+ + V+ L +D F ++ ++ V +
Sbjct: 290 A--DYLIGMKFGMGTLDDIDHLKNKRI----RSVADLLQDQFGLALNRLENAVRGTICGA 343
Query: 403 SRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVL------------AR 450
R Q +V + L T + F F H ++Q L +
Sbjct: 344 IRRKLIPTPQNLV---TSTPLTTTYES--F----FGSHP--LSQFLDQTNPLTEIVHGRK 392
Query: 451 LSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
LS +G G +T + F R + PS +G +CP DT EG GL+ +LA+ +
Sbjct: 393 LSSLGP-GGLTGRTASFRV-------RDIHPSHYGRICPIDTSEGINAGLIGSLAIHARI 444
>gnl|CDD|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase compared
to three in eukaryotes (not including mitochondrial. and
chloroplast polymerases). Rpb2 is the second largest
subunit of the RNA polymerase. This domain comprised of
the structural domains anchor and clamp. The clamp region
(C-terminal) contains a zinc-binding motif. The clamp
region is named due to its interaction with the clamp
domain found in Rpb1. The domain also contains a region
termed "switch 4". The switches within the polymerase are
thought to signal different stages of transcription.
Length = 78
Score = 120 bits (304), Expect = 1e-32
Identities = 35/92 (38%), Positives = 44/92 (47%), Gaps = 15/92 (16%)
Query: 1065 GGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCK 1124
GG R GEME L AYGA+ + ERL + SD VC CG CK
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVCGRCGAYAAI-----------CK 45
Query: 1125 NGDNISSMKLPYACKLLIQELQSMNIVPRLKL 1156
I +P + KLL+QEL+S+ + RL L
Sbjct: 46 GKTIIEPGDIPESFKLLLQELRSLGLDIRLFL 77
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 135 bits (343), Expect = 4e-32
Identities = 76/186 (40%), Positives = 104/186 (55%), Gaps = 7/186 (3%)
Query: 911 GDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGV 970
GDK + RHG KGV I+ ED P+ E G D+++NP G PSRM +G+++E G A
Sbjct: 883 GDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAK 942
Query: 971 SCGRFHYGS-AFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPI 1029
G + + F E I E L + G +GK +Y G TG P + +G +
Sbjct: 943 GLGI-KFATPVFDGAKE-----EEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYM 996
Query: 1030 YYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFER 1089
Y KL H+V DK+HAR +GP ++T+QP G+A+ GG R GEME L AYGA+ + E
Sbjct: 997 YMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1056
Query: 1090 LMVSSD 1095
L V SD
Sbjct: 1057 LTVKSD 1062
Score = 60.5 bits (148), Expect = 5e-09
Identities = 64/261 (24%), Positives = 114/261 (43%), Gaps = 89/261 (34%)
Query: 32 FQLLPEFLKVRGLVKQHLDSFNYFV-------NTGIRKIVRANDRIVSGIDPSIF----- 79
F + E L++ L++ LDSF++F+ + G+ ++ R SIF
Sbjct: 15 FGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFR-----------SIFPIEDF 63
Query: 80 -----LRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTM 134
L F +G+P V+ E C+ +TY+AP+ V + + + E +
Sbjct: 64 NGNLSLEFVSYELGEPKYDVE---E------CKERGLTYSAPLRVKLRLI---NKETGEI 111
Query: 135 EKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSK 194
++ +V +G IP+M G FII GTE+V I QL
Sbjct: 112 KEQEVYMGDIPLM------------------------TENGTFIINGTERV--IVSQL-- 143
Query: 195 NR---VIIDTDKKGNINASVTSSTETVKSKTVIQ-----ME-----KGKMYLLLNQFVKK 241
+R V D DK TSS + + S +I +E K +Y+ +++ +K
Sbjct: 144 HRSPGVYFDHDK------DKTSSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDR-RRK 196
Query: 242 IPIMVVMKAMGMESDQEVVQM 262
+P+ V+++A+G SD+E++ +
Sbjct: 197 LPVTVLLRALGY-SDEEILDL 216
Score = 37.0 bits (87), Expect = 0.070
Identities = 12/23 (52%), Positives = 18/23 (78%)
Query: 744 GQNATVAVMSYSGYDIEDAIVMN 766
GQN VA M ++GY+ EDAI+++
Sbjct: 716 GQNVLVAFMPWNGYNFEDAILIS 738
Score = 34.7 bits (81), Expect = 0.33
Identities = 49/196 (25%), Positives = 81/196 (41%), Gaps = 76/196 (38%)
Query: 341 VAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTV----- 395
+A + + ++ K +DD D++GN+R+ G+L+ ++ F+ +S +++ V
Sbjct: 347 IATI-KYLINLRNGKGEVDDIDHLGNRRVRSVGELL----QNQFRIGLSRMERAVRERMS 401
Query: 396 ----------DIILSKPSR--------SSRFDLSQFIVRDSITVGLERTLSTGNFDVKRF 437
D+I +KP SS+ LSQF
Sbjct: 402 LQDLDTLTPQDLINAKPVVAAIKEFFGSSQ--LSQF------------------------ 435
Query: 438 KMHRKGMTQV--LA------RLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCP 489
M Q L+ RLS +G G +TR FE V R + P+ +G +CP
Sbjct: 436 ------MDQTNPLSELTHKRRLSALGP-GGLTRERAGFE----V---RDVHPTHYGRICP 481
Query: 490 CDTPEGEACGLVKNLA 505
+TPEG GL+ +LA
Sbjct: 482 IETPEGPNIGLINSLA 497
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain forms one of the two distinctive lobes of the
Rpb2 structure. This domain is also known as the lobe
domain. DNA has been demonstrated to bind to the concave
surface of the lobe domain, and plays a role in
maintaining the transcription bubble. Many of the
bacterial members contain large insertions within this
domain, as region known as dispensable region 1 (DRI).
Length = 185
Score = 97.8 bits (244), Expect = 3e-23
Identities = 50/186 (26%), Positives = 82/186 (44%), Gaps = 9/186 (4%)
Query: 193 SKNRVIIDTDK-KGNINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVK-KIPIMVVMKA 250
N + ++ + K I A+ TSS + + + GK + K KIPI++ +KA
Sbjct: 1 RSNGIYVEKELDKNGIGATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKA 60
Query: 251 MGMESDQEVVQMV-GRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPP- 308
+G+ SD+E++ + L L E +IYTQE+AL+Y+ GK G P
Sbjct: 61 LGLVSDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYI-GKGFALRRGEEPR 119
Query: 309 --NDREGRAFSILRDVFLA--NVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYV 364
RE + + N R K + M+ R++ L + DD D++
Sbjct: 120 LQRAREILYSRDPKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHL 179
Query: 365 GNKRLE 370
GNKR+
Sbjct: 180 GNKRVR 185
>gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Domain 3, s
also known as the fork domain and is proximal to
catalytic site.
Length = 68
Score = 85.4 bits (212), Expect = 3e-20
Identities = 29/68 (42%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 446 QVLARLSFIGTLGHMTRVS--PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKN 503
QVL + +++ L H RV+ K RK R L PSQ+G +CP +TPEG CGLV +
Sbjct: 1 QVLDQTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNS 60
Query: 504 LALMTHVT 511
LAL +
Sbjct: 61 LALYARIN 68
>gnl|CDD|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Domain 4,
is also known as the external 2 domain.
Length = 63
Score = 81.2 bits (201), Expect = 7e-19
Identities = 29/62 (46%), Positives = 41/62 (66%)
Query: 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVI 606
V NG ++G HR P+ + +R+LRR GKI VSV N +QR + I +D GR+CRPL+I
Sbjct: 1 VYVNGKLVGTHRNPEELVETLRELRRKGKISPEVSVVRNIRQREIRINTDAGRICRPLII 60
Query: 607 AD 608
+
Sbjct: 61 VE 62
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 80.0 bits (197), Expect = 6e-15
Identities = 49/143 (34%), Positives = 73/143 (51%), Gaps = 16/143 (11%)
Query: 1006 NGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNG 1065
+GK +Y G TG ++ + +G +Y KL H+V +K+HAR +GP ++T QP G+A G
Sbjct: 1239 DGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFG 1298
Query: 1066 GLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKAGICSTCKN 1125
G R GEME L AYGA+ + E L + SD G Y K
Sbjct: 1299 GQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR-------GRENAYRAIAK--------- 1342
Query: 1126 GDNISSMKLPYACKLLIQELQSM 1148
G+ + ++P +L +ELQS+
Sbjct: 1343 GEQVGESEIPETFYVLTKELQSL 1365
Score = 64.2 bits (156), Expect = 5e-10
Identities = 29/77 (37%), Positives = 46/77 (59%)
Query: 898 IKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTV 957
+K I R+ ++GDK + RHG KG+ IV D P++ G D+++NP G PSRM +
Sbjct: 1078 VKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNI 1137
Query: 958 GKMIELLGGKAGVSCGR 974
G+++E+ G G G+
Sbjct: 1138 GQILEMHLGLVGKEFGK 1154
Score = 45.7 bits (108), Expect = 2e-04
Identities = 39/159 (24%), Positives = 76/159 (47%), Gaps = 15/159 (9%)
Query: 354 NKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQF 413
N+ +DD+D++GN+R+ G+L++ + + + ++QKT+ L+ S + +
Sbjct: 450 NQGKIDDRDHLGNRRIRAVGELLA----NELHSGLVKMQKTIKDKLTTMSGAFDSLMPHD 505
Query: 414 IVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVL--ARLSFIGTLGHMTRVSPQFEKSR 471
+V + G + +F +++V RLS +G G + + FE
Sbjct: 506 LVNSKMITSTIMEFFMGG-QLSQFMDQTNPLSEVTHKRRLSALGE-GGLVKDRVGFEA-- 561
Query: 472 KVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
R + P+ +G +CP +TPEG+ GL+ L+ T V
Sbjct: 562 -----RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV 595
Score = 37.2 bits (86), Expect = 0.073
Identities = 48/254 (18%), Positives = 99/254 (38%), Gaps = 66/254 (25%)
Query: 32 FQLLPEFLKVRGLVKQHLDSFNYFV------NTGIRKIVRANDRIVSGIDPSIFLRFKDV 85
F P L+V L+ DS++ F+ +GI K+ ++ I + I L +
Sbjct: 15 FTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHN-RITLEYAGC 73
Query: 86 RIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTT-------MEKND 138
G+ TV E+ +TY+ P+ + + + K+ +++
Sbjct: 74 EFGKSKYTVREAMER---------GITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQS 124
Query: 139 VVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVI 198
+ I IP+M FII G E+V++ QL ++ +
Sbjct: 125 IFIREIPLMTERTS------------------------FIINGVERVVV--NQLHRSPGV 158
Query: 199 IDTDKKGNINASVTSSTETVKSKTVIQME----------KGKMYLLLNQFVKKIPIMVVM 248
I +++ S TS + + + +I K +Y +N+ +K+P+ ++
Sbjct: 159 IFKEEE-----SSTSLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINK-RRKVPVTILF 212
Query: 249 KAMGMESDQEVVQM 262
+AM Q++++M
Sbjct: 213 RAMDY-QKQDIIKM 225
Score = 33.7 bits (77), Expect = 0.81
Identities = 26/114 (22%), Positives = 42/114 (36%), Gaps = 22/114 (19%)
Query: 740 KLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL 799
+L G+N VA M ++GY+ EDAIV+++ I Y R L
Sbjct: 803 ELALGKNVRVAFMPWNGYNFEDAIVVSE---------RITKDDIFTSTHIYEKEVDAREL 853
Query: 800 RP-----DRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESP 848
+ P + + H LD+ G+ G + + + K SP
Sbjct: 854 KHGVEEFTADIPDVKEEALAH--------LDESGIVKVGTYVSAGMILVGKTSP 899
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 76.6 bits (188), Expect = 8e-14
Identities = 50/157 (31%), Positives = 80/157 (50%), Gaps = 16/157 (10%)
Query: 992 ESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRV 1051
E I++ G +G+ ++Y G +G + +G +Y KL H+V K+HAR GP
Sbjct: 1283 EQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYS 1342
Query: 1052 MLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYY 1111
++T+QP G++ GG R GEME L AYGA+ + E L V SD + G + Y
Sbjct: 1343 LVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDD-------INGRVKIY 1395
Query: 1112 NHKLKAGICSTCKNGDNISSMKLPYACKLLIQELQSM 1148
+K GD+ +P + ++I+EL+S+
Sbjct: 1396 ESIIK---------GDSNFECGIPESFNVMIKELRSL 1423
Score = 65.8 bits (160), Expect = 1e-10
Identities = 29/61 (47%), Positives = 41/61 (67%), Gaps = 2/61 (3%)
Query: 902 IRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMI 961
++H+ +P GDK + RHG KGV +V ED P+ E G D+I+NP G PSRM VG+++
Sbjct: 1077 VKHSLQP--GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQIL 1134
Query: 962 E 962
E
Sbjct: 1135 E 1135
Score = 51.5 bits (123), Expect = 3e-06
Identities = 43/169 (25%), Positives = 86/169 (50%), Gaps = 17/169 (10%)
Query: 344 MLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPS 403
++R++V + ++DD D++GN+R+ G+ + E+ F+T + ++++ V +S S
Sbjct: 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFI----ENQFRTGLLKLERAVVDSMSTSS 504
Query: 404 RSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVL--ARLSFIGTLGHMT 461
+ S FI +T L ++ + +F ++++ RLS +G G +T
Sbjct: 505 LD-KVSPSDFINPKVLTNVLRDFFNSSQ--LSQFMDQTNPLSEITHKRRLSALGP-GGLT 560
Query: 462 RVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
R FE R + P+ +G +CP +TPEG+ GL+ +LA+ +
Sbjct: 561 RERAGFEV-------RDVHPTHYGRICPIETPEGQNIGLINSLAIYARI 602
Score = 40.0 bits (93), Expect = 0.010
Identities = 28/109 (25%), Positives = 50/109 (45%), Gaps = 12/109 (11%)
Query: 740 KLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL 799
+L GQN VA MS+ GY+ ED+I+++ + + I ++++ + S++I
Sbjct: 813 ELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHD-TPLGSEKI- 870
Query: 800 RPDRTGPGAERMQVVHHSNLLLLILDDDGLAAPGEIIKPNDVYINKESP 848
R PG + H LDD G+ G + P + + K +P
Sbjct: 871 --TRAIPGVNEENLYH--------LDDSGIVKIGTRVGPGYILVGKVTP 909
Score = 33.1 bits (75), Expect = 1.2
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 17/92 (18%)
Query: 175 GYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQME------- 227
G FII G EKV++ Q S V D+DK N S + + S VI
Sbjct: 154 GTFIINGVEKVIVSQMHRSPG-VFFDSDKGKTYN-----SGKLIYSARVIPYRGSWLDIE 207
Query: 228 ---KGKMYLLLNQFVKKIPIMVVMKAMGMESD 256
K +Y +++ +K+PI V++KA+G+ ++
Sbjct: 208 FDVKDHLYFRIDR-KRKLPISVLLKALGLSNN 238
>gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Domain 5,
is also known as the external 2 domain.
Length = 46
Score = 62.6 bits (153), Expect = 1e-12
Identities = 23/46 (50%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 629 FDDFLREGLIEYLDVNEENNALIALYEGD-----ATPDTTHIEIEP 669
F D L+EG+IEYLD EE A+IA+ D T TTH EI P
Sbjct: 1 FVDLLKEGVIEYLDAEEEETAMIAMSPEDLRLEDITKTTTHCEIHP 46
>gnl|CDD|146144 pfam03356, Pox_LP_H2, Viral late protein H2. All Members of this
family show similarity to the vaccinia virus late
protein H2. This protein is often referred to by its
gene name of H2R. Members from this family all belong to
the viral taxon Poxviridae.
Length = 189
Score = 34.2 bits (79), Expect = 0.20
Identities = 18/59 (30%), Positives = 30/59 (50%)
Query: 176 YFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKMYLL 234
+F++ VLL Q S N V+ + K I ++ S V+SKT I+ ++G+ L
Sbjct: 34 FFVLILLISVLLFWFQTSDNSVLSELAKYARIKNNIKSWKPLVESKTKIESDRGRALAL 92
>gnl|CDD|237796 PRK14712, PRK14712, conjugal transfer nickase/helicase TraI;
Provisional.
Length = 1623
Score = 34.8 bits (79), Expect = 0.36
Identities = 20/65 (30%), Positives = 30/65 (46%)
Query: 648 NALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAF 707
+A+ + G A P T + PFT L + G + P H+ S T ++ + AM N
Sbjct: 610 DAMTVVVPGRAEPATLPVSDSPFTALKLENGWVETPGHSVSDSATVFASVTQMAMDNATL 669
Query: 708 NQLCR 712
N L R
Sbjct: 670 NGLAR 674
>gnl|CDD|222970 PHA03072, PHA03072, putative viral membrane protein; Provisional.
Length = 190
Score = 32.3 bits (74), Expect = 0.97
Identities = 18/56 (32%), Positives = 30/56 (53%)
Query: 176 YFIIKGTEKVLLIQEQLSKNRVIIDTDKKGNINASVTSSTETVKSKTVIQMEKGKM 231
+F+I VLL+ Q S N V + K I +V S V+SKT ++ ++G++
Sbjct: 34 FFVIILAISVLLLWFQTSDNSVFSELTKYARIKNNVKSWRPLVESKTKLESDRGRL 89
>gnl|CDD|223465 COG0388, COG0388, Predicted amidohydrolase [General function
prediction only].
Length = 274
Score = 31.3 bits (71), Expect = 3.0
Identities = 21/97 (21%), Positives = 31/97 (31%), Gaps = 5/97 (5%)
Query: 492 TPEGEACGLVKNLALMTHVTTDEEEGPLIS-LCYCLGVEDLELLSGEELHNP----NSFL 546
PE G L E + L + ++ G N+ L
Sbjct: 41 FPELFLTGYPCEDDLFLEEAAAEAGEETLEFLAALAEEGGVIIVGGPLPEREKLYNNAAL 100
Query: 547 VIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVF 583
+ +G ILGK+R+ F + R E V VF
Sbjct: 101 IDPDGEILGKYRKLHLFDAFYEERRFFTPGDEGVVVF 137
>gnl|CDD|227944 COG5657, CSE1, CAS/CSE protein involved in chromosome segregation
[Cell division and chromosome partitioning].
Length = 947
Score = 31.3 bits (71), Expect = 3.4
Identities = 23/145 (15%), Positives = 50/145 (34%), Gaps = 9/145 (6%)
Query: 326 NVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDY--VGNKRLELSGQLVSLLFEDL 383
++P + K L +L KD ++D Y + E+ L + + ++
Sbjct: 217 DIPEFFEDNLDKFMEHFCKLLSYSNPVLQKDCLEDCVYFKLKGSICEIF-NLYTTKYPEV 275
Query: 384 FKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKG 443
+I + + V +L+ +R D +V S+TV K ++
Sbjct: 276 ITYLIYDFVEIVWNLLTTITRPYIRDY---LVSKSLTV---LINVIKYPIRKTAEVLSNV 329
Query: 444 MTQVLARLSFIGTLGHMTRVSPQFE 468
++ L + L ++ E
Sbjct: 330 SENLINNLVDLLILPNLILREEDLE 354
>gnl|CDD|223073 PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like
protein; Provisional.
Length = 865
Score = 31.4 bits (72), Expect = 3.5
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 911 GDKFSSRHGQKGVCGTIVQQEDFP--FSERGICPDLIMNPHGFPSRMT 956
G K HGQKGV ED +E G + ++P + SR T
Sbjct: 711 GLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISYLSRQT 755
>gnl|CDD|206419 pfam14251, DUF4346, Domain of unknown function (DUF4346). This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 127 and 502 amino acids in length. There are two
conserved sequence motifs: LDP and DHA. Many members of
this family have been annotated as dihydropteroate
synthases, however no experimental evidence can be found
for this and MJ0107 has been shown not to possess
dihydropteroate synthase activity.
Length = 119
Score = 29.5 bits (67), Expect = 4.1
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 171 LDPGGYFIIK 180
LDP GYF+I
Sbjct: 14 LDPAGYFLIY 23
>gnl|CDD|131508 TIGR02455, TreS_stutzeri, trehalose synthase, Pseudomonas stutzeri
type. Trehalose synthase catalyzes a one-step
conversion of maltose to trehalose. This is an
alternative to the OtsAB and TreYZ pathways. This family
includes a characterized example from Pseudomonas
stutzeri plus very closely related sequences from other
Pseudomonads. Cutoff scores are set to find a more
distantly related sequence from Desulfovibrio vulgaris,
likely to be functionally equivalent, between trusted
and noise limits [Energy metabolism, Biosynthesis and
degradation of polysaccharides, Cellular processes,
Adaptations to atypical conditions].
Length = 688
Score = 30.3 bits (68), Expect = 8.1
Identities = 23/82 (28%), Positives = 29/82 (35%), Gaps = 10/82 (12%)
Query: 730 TRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGR----CIVVKKYTA 785
TR I GYD A + G A+ SL +KK A
Sbjct: 534 TRWIHRGGYDLADLAPEAEASA---EGLPKARALY---GSLAEQLDEPDSFACKLKKILA 587
Query: 786 INQKYANSTSDRILRPDRTGPG 807
+ Q Y + S +IL PD PG
Sbjct: 588 VRQAYDIAASKQILIPDVQAPG 609
>gnl|CDD|214431 MTH00142, COX1, cytochrome c oxidase subunit I; Provisional.
Length = 511
Score = 30.1 bits (68), Expect = 9.3
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 428 STGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEK 469
S G+ D+ F +H G++ +L ++FI T+ +M +FE+
Sbjct: 137 SGGSVDLAIFSLHLAGVSSILGAINFITTVINMRAGGMKFER 178
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.407
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 59,236,947
Number of extensions: 5982434
Number of successful extensions: 4328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4233
Number of HSP's successfully gapped: 57
Length of query: 1159
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1051
Effective length of database: 6,147,370
Effective search space: 6460885870
Effective search space used: 6460885870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 65 (28.7 bits)