RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 001050
(1173 letters)
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 744 bits (1924), Expect = 0.0
Identities = 407/1207 (33%), Positives = 587/1207 (48%), Gaps = 194/1207 (16%)
Query: 32 SFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVE-PGYDPSKKGEGEWRYASMRFGQ 90
++F E GLV ++SYN+FI+ GLQ+ D FGE E PG + G+
Sbjct: 7 AYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLK-------------IVLGK 53
Query: 91 VTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQ 150
+ + +P +G + + P ARL+N+TY++ + + + G E
Sbjct: 54 IRVGEPEIKEADGSERP-ITPMEARLRNLTYAAPLYLTMIPVE------------NGIEY 100
Query: 151 YIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFDHGGYFIIKGAEKV 204
E + IG +P+MVKS +C + G +E G+ D GGYFII G+E+V
Sbjct: 101 ---------EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERV 151
Query: 205 FVAQEQICLKRLWVSNSMGWTVAYKSE-----------NKRNRLIVRLVDMSKFEDIKGG 253
V+QE + R+ V A S R ++ V E K G
Sbjct: 152 IVSQEDLAPNRVLV----DKGEAGSSITHTAKVISSRAGYRAQVTV--------ERRKDG 199
Query: 254 EKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDE 313
+S + +IP IL ALG+ +D++IV + D I L S+ A
Sbjct: 200 TIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSL---DPEIQQELLPSLEQAS---SI 253
Query: 314 FRKGRNALKYVDKLIKGTTFPPG-------ESTEECMNTYLFPSLHGT-----KQKARFL 361
+AL Y+ K + G E E+ ++ YL P L GT +KA FL
Sbjct: 254 AATVEDALDYIGKRVA-----IGQPREYRIERAEQILDKYLLPHL-GTSPEDRIKKAYFL 307
Query: 362 GYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYG 421
G M LL+ Y GRR+ D++D + NKRL LAG+LL +V K + L++
Sbjct: 308 GQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEK--SY 365
Query: 422 DRTVRP-IEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLR 480
R + + + I+T + A +TG W RT G+ L R N L TL LR
Sbjct: 366 ARGRKLDLRAIVRPDIITERIRHALATGNW--VGGRT----GVSQLLDRTNYLSTLSHLR 419
Query: 481 R-----TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILE 535
R +R Q + +AR H + WG+IC TP+G NCGLVKNL + +S + E
Sbjct: 420 RVVSPLSRGQPHF-----EARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDE 474
Query: 536 -PIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPT 594
+ E L+ G+ + + +V+++G IG D ++R RR ++
Sbjct: 475 EEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISD 534
Query: 595 QVEIK--RDELQSEVRIFMDAGRILRPLLVVENMGKIK-------SLEGKNYTFQALLDH 645
+V + +EV + D+GR+ RPL+VVEN GK K L+ TF L+
Sbjct: 535 EVNVAYIETGEINEVYVNCDSGRVRRPLIVVEN-GKPKLTREHVEKLKKGELTFDDLVKM 593
Query: 646 GIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDH 705
G+IE + EEEE+ Y+ D ED P + TH E+ +LG++ IIP+ H+
Sbjct: 594 GVIEYLDAEEEENA-------YVALDPEDLTP-EHTHLEIWPPAILGITASIIPYPEHNQ 645
Query: 706 ARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHI 765
+ R YQ+ + Q++G N IR DT H L YPQRPL +T + +G Y
Sbjct: 646 SPRNTYQAAM-AKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIG---YND--- 698
Query: 766 LPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVK 825
RP GQNA+VAV + GYN ED+++MN+AS+ERG+ RS R+Y+ E + K
Sbjct: 699 --RPA---GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETE-ERKYP--- 749
Query: 826 RRSSDDMVNFGKIQSKIGRVDS-------------LDDDGFPFIGANLQSGDIVIGK--- 869
G + KI + LD+DG ++ GD++IGK
Sbjct: 750 ----------GGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSP 799
Query: 870 ------YADSGA------DHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLG 917
+ D S+ ++H E+G+V V+++ + +G V +R +R P LG
Sbjct: 800 PRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELG 859
Query: 918 DKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAA 977
DKF+S HGQKGV+G L QE+ PFT GIVPD++INPHA PSR T GQLLE+ GK A
Sbjct: 860 DKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAAL 919
Query: 978 LGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTF 1037
G+ + ATPF + + ++L + G+ GTE +YDGRTGE +++ IFIG +
Sbjct: 920 EGRFV------DATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVY 973
Query: 1038 YQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERL 1097
YQ+L HM DK+ R GPV LTRQP R R GG++FGEMERDCLI HGAA L ERL
Sbjct: 974 YQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERL 1033
Query: 1098 FTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQ 1157
SD +++C C ++A R+ C I +I V Y KLL Q
Sbjct: 1034 LDSSDKTTIYVCELCGHIAWY-------DRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQ 1086
Query: 1158 ELFSMGI 1164
EL SMGI
Sbjct: 1087 ELMSMGI 1093
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 658 bits (1700), Expect = 0.0
Identities = 312/1206 (25%), Positives = 484/1206 (40%), Gaps = 234/1206 (19%)
Query: 32 SFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQV 91
F + LV Q++SYN F GLQ+ F + P + + +G
Sbjct: 20 EFLDLPNLVEIQLDSYNAFFLEGLQEVFRE-----IFPIESYNGN-------TELEYGSY 67
Query: 92 TLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQY 151
L +P F +P RL+ +TYS+ + VK++ V
Sbjct: 68 RLGEPPKF----------YPEECRLRGLTYSAPLYVKLRLVVNETGEEI----------- 106
Query: 152 IQKEVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQI 211
+ + +G IP+M + GGYFII G E+V V+QE
Sbjct: 107 --------KEQEVYMGDIPLMTR------------------GGYFIINGTERVIVSQEHR 140
Query: 212 CLKRLWVSNSMGWTVAYKSENKRNRL------IVRLVDMSKFEDIKGGEKVLSVYFLSTE 265
S G K + +++ I +FE + + +
Sbjct: 141 ---------SPGVIFVEKKDKTGSKVLYVARVIPYRGSWLEFE-FDPKDNLYVRIDRKRK 190
Query: 266 IPIWILFFALGVSSDKEIVNLIDFTC----EDCSILNILFASIHDADNKCDEFRKGRNAL 321
IP+ IL ALG+ +D+EI+ L +A + R +
Sbjct: 191 IPVTILLRALGLETDEEIIEAFGGDELTDLVPPEGEEALLEIYEEAKGEKITARNALELI 250
Query: 322 KYVDKLIKGTTFPPG--ESTEECMNTYLFPSLHGTKQ--------KARFLGYMVKCLLQA 371
++K G + + ++ L P L + KA+ + M+K L++
Sbjct: 251 GSRVFVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIEL 310
Query: 372 YSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDL---YGDRTVRPI 428
G+ + D+ D N+RL L GELLE +V + RM + ++ L T+ P
Sbjct: 311 RLGKGEEDDIDHLGNRRLRLVGELLENLFRVGL----SRMERDVKERLEKADKRDTLVP- 365
Query: 429 EYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRR------T 482
++ A TG + S + + + NPL L RR +
Sbjct: 366 -----QDLINAKPIHALITGFFGR--------SQLSQFMDQTNPLSELSHKRRLSALGLS 412
Query: 483 RQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVS--TSILEPIFEQ 540
R++ + R HP+H+G+IC + TP+G N GL+K+L + ++ + P +
Sbjct: 413 RER-----AGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKV 467
Query: 541 LFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQV--EI 598
L + D+ Y + V+V G G + V EL RR V
Sbjct: 468 LD---GSLVVDEIEYLSADEEDVYVIGQANGTLDEPGELVEELVECRRGGSGEVSVADPE 524
Query: 599 KRDELQSEVRIFMDAGRILRPLLVV---------ENMGKIKSLEGKNYTFQALLDHGIIE 649
D + + + GR L P L NM + T L+ G+ E
Sbjct: 525 GVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQA--VPLLRTEAPLVGTGM-E 581
Query: 650 LVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRV 709
+ E+ A K+P TH E+ +LG+ +IP+ H+ +
Sbjct: 582 YLDAEDSGAAVIA------------KRPGVVTHVEISPIVILGIEASLIPYPEHNQSPYN 629
Query: 710 LYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRP 769
LY+ + S+QA G R DT+ L Y P T
Sbjct: 630 LYKFAR-SNQATGINQRPLVKRGDTVEKGLVYADGPSVDT-------------------G 669
Query: 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSS 829
EL GQNA+VA GYN ED+++++ S+ER +F S HI Y+ E K
Sbjct: 670 ELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFTSIHIEEYETE----ARDTKLGPE 725
Query: 830 D--DMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGA------------ 875
+ D+ N + + +LD+DG IGA ++ GDI++GK G
Sbjct: 726 EIRDIPNVSEEALR-----NLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRI 780
Query: 876 ------DHSIKLKHTERGMVQKVVLSSNDDGKN----FSVVSLRQVRSPCLGDKFSSMHG 925
D S+++ H E G+V V + + +DG V + Q R P +GDK + HG
Sbjct: 781 FGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHG 840
Query: 926 QKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSG 985
KGV+ + QE+ PF G PDI++NP PSR GQ+LE LGK G
Sbjct: 841 NKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHLGKA------AALLG 894
Query: 986 LKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMS 1045
+ F + I E L AGF G E LYDGRTGE + IF+G +YQ+L HM
Sbjct: 895 IPVDTPVFDGAPEEDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMV 954
Query: 1046 EDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQ 1105
+DK+ R+TGP +T+QP+ + +FGG +FGEME L A+GAA L ERL SD
Sbjct: 955 DDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVKSDDVC 1014
Query: 1106 MHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGIT 1165
I + + C + G++I + +P K+L +EL S+GI
Sbjct: 1015 GRIK--------IYE-------------CIVK--GENIPEVGIPESFKVLLKELRSLGID 1051
Query: 1166 LKFDTE 1171
++ + E
Sbjct: 1052 VRLELE 1057
>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 = 601 bits (1553), Expect = 0.0
Identities = 210/509 (41%), Positives = 281/509 (55%), Gaps = 54/509 (10%)
Query: 679 KFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQ 738
+ TH E+ S +L ++ +IPF H+ + R LYQS QA+G P N R+DT +
Sbjct: 394 EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQK-QAVGTPALNQQYRMDTKLYL 452
Query: 739 LFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRA 798
L YPQ+PL T I + + EL GQNAIVAV + GYN ED++++N++
Sbjct: 453 LLYPQKPLVGTGIEEYIA-----------FGELPLGQNAIVAVMSYSGYNFEDAIIINKS 501
Query: 799 SLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGA 858
S++RG FRS H + Y+ E+ + + + D+ N ++ +LD+DG GA
Sbjct: 502 SVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPN-----VSEEKLKNLDEDGIIRPGA 556
Query: 859 NLQSGDIVIGKY---------------ADSGADHSIKLKHTERGMVQKVVLSS---NDDG 900
++ GDI++GK A D S+K E+G+V V + S ND G
Sbjct: 557 RVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGG 616
Query: 901 KNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSR 960
V +RQ R P +GDKF+S HGQKGV+ + QE+ PFT GI PDI++NPH FPSR
Sbjct: 617 NKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSR 676
Query: 961 QTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYD 1020
T GQLLE+ LGK A LGK ATPF + I+E L AG + +G E LYD
Sbjct: 677 MTIGQLLESLLGKAGALLGK------FGDATPFDGAEEEDISELLGEAGLNYYGKEVLYD 730
Query: 1021 GRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEME 1080
GRTGE + + IF+GP +YQRL HM +DK+ R+TGP LTRQP+ R R GG +FGEME
Sbjct: 731 GRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEME 790
Query: 1081 RDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSG 1140
RD LIAHGAA L ERL SD +C KC + + CR+C G
Sbjct: 791 RDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN-------------LCRLCKKG 837
Query: 1141 DDIVKANVPYGAKLLCQELFSMGITLKFD 1169
+I K +PY KLL QEL SM I +
Sbjct: 838 TNISKVGIPYAFKLLFQELQSMNIDPRLK 866
Score = 289 bits (742), Expect = 6e-83
Identities = 130/507 (25%), Positives = 198/507 (39%), Gaps = 125/507 (24%)
Query: 39 LVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSF 98
LV QI+S+N F+ GLQ+ S + ++FG + L KP
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTD----------DDGRLKLKFGDIYLGKPKV 50
Query: 99 FAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLS 158
GG + P RL+++TYS+ + V ++ V + K K
Sbjct: 51 E--EGGVTRKLTPNECRLRDLTYSAPLYVDIRLTVNDK-----GKIKE------------ 91
Query: 159 DETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFDHGGYFIIKGAEKVFVAQEQIC 212
+ IG IP+M++S LC + G ++ G+C D GGYFII G EKV + QEQ
Sbjct: 92 ---QEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQ-- 146
Query: 213 LKRLWVSNSMGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEKVLSVYFLSTEIPIWILF 272
N +IV ED KG I
Sbjct: 147 -------------------RSPNVIIV--------EDSKG---------------KRIYT 164
Query: 273 FALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTT 332
S + ++ + + ++ I ++ ALKY+ K
Sbjct: 165 KTSIPSYSPYRGSWLEV--KSDKKKDRIYVRID--------LKRQEEALKYIGKRF---- 210
Query: 333 FPPGESTEECMNTYLFPSLHGTKQKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELA 392
L YM++ L+ G+ K D+ D NKR+ LA
Sbjct: 211 --------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLA 244
Query: 393 GELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSH 452
GELL+ + + + + + LQ+ L + + P +++ +T+G+ +TG W
Sbjct: 245 GELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQ-LLINSKPITSGIKEFLATGNWGS 303
Query: 453 PFKRTERISGIVANLGRANPLQTLVDLRRT-RQQVQYTGKVGDARYPHPSHWGKICFLST 511
+R SG+ L R NPL L RR + K + R HPSHWG+IC + T
Sbjct: 304 KRFLMQR-SGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIET 362
Query: 512 PDGENCGLVKNLGVTGLVSTSILEPIF 538
P+GENCGLVKNL + +S I P
Sbjct: 363 PEGENCGLVKNLALMARISGRIERPYR 389
>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 = 506 bits (1305), Expect = e-167
Identities = 242/631 (38%), Positives = 342/631 (54%), Gaps = 71/631 (11%)
Query: 563 VFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLV 622
V+++G IG D V E+R+ RR +L +V + E +EV I DAGRI RPL+V
Sbjct: 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIV 60
Query: 623 VENMGK-------IKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDK 675
VEN GK ++ L+ T+ L+ G+IE + EEEE+ Y+ D E+
Sbjct: 61 VEN-GKPKLTREHVEKLKEGELTWDDLVKQGVIEYLDAEEEENA-------YIALDPEEL 112
Query: 676 KPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTL 735
P + TH E+D S +LG+ IP+ H+ + R + + Q++G N IR+DT
Sbjct: 113 TP-EHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAM-AKQSLGLYAANYRIRLDTR 170
Query: 736 SHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVM 795
H L YPQ+PL +T + + +G Y RP GQN +VAV + GYN ED+L+M
Sbjct: 171 GHLLHYPQKPLVKTRVLELIG---YDD-----RPA---GQNFVVAVMSYEGYNIEDALIM 219
Query: 796 NRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGR-------VDSL 848
N+AS+ERG+ RS R+Y+AE +RR + +I R L
Sbjct: 220 NKASIERGLARSTFFRTYEAE--------ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHL 271
Query: 849 DDDGFPFIGANLQSGDIVIGK---------YADSGA------DHSIKLKHTERGMVQKVV 893
D+DG + ++ GD++IGK + G D S+ ++H E+G+V KV+
Sbjct: 272 DEDGIVYPEVEVKGGDVLIGKTSPPRFLEELRELGLVTERRRDTSVTVRHGEKGIVDKVI 331
Query: 894 LSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVIN 953
++ ++G V +R +R P LGDKF+S HGQKGV+G + QE+ PFT GIVPD++IN
Sbjct: 332 ITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIIN 391
Query: 954 PHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKW 1013
PHA PSR T GQLLE GK A G+ + TPF + + ++L + GF
Sbjct: 392 PHAIPSRMTVGQLLEMIAGKVAALEGRRV------DGTPFEGEPEEELRKELLKLGFKPD 445
Query: 1014 GTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGG 1073
G E +YDG TGE + + IFIG +YQ+L HM DK+ R+ GPV LTRQP R R GG
Sbjct: 446 GKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGG 505
Query: 1074 IKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPY 1133
++FGEMERD LI HGAA L ERL SD Y +++C C ++A ++ Y
Sbjct: 506 LRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWE-------DKRKGTAY 558
Query: 1134 CRICDSGDDIVKANVPYGAKLLCQELFSMGI 1164
C +C DI + Y KLL EL S+GI
Sbjct: 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGI 589
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 496 bits (1278), Expect = e-162
Identities = 237/639 (37%), Positives = 333/639 (52%), Gaps = 85/639 (13%)
Query: 562 KVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLL 621
KV+V+G IG D V E+R RR E+ +V + E +EV I DAGR RPL+
Sbjct: 6 KVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLI 65
Query: 622 VVENMGK-------IKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIED 674
VVEN G+ I+ L+ TF L+ G+IE + EEEE+ Y+ ED
Sbjct: 66 VVEN-GEPLLTEEHIEKLKNGELTFDDLVKQGVIEYLDAEEEENA-------YIAVYEED 117
Query: 675 KKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDT 734
+ TH E+D S +LG+ G+IP+ H+ + R+ + Q++G P N +R DT
Sbjct: 118 LTE-EHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGA-GMIKQSLGLPAANYKLRPDT 175
Query: 735 LSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLV 794
H L YPQ PL +T + +G + RP GQN +VAV + GYN ED+L+
Sbjct: 176 RGHLLHYPQVPLVKTQTQEIIG---FDE-----RPA---GQNFVVAVMSYEGYNIEDALI 224
Query: 795 MNRASLERGMFRSEHIRSYKAE--------VDNKEMQVKR----RSSDDMVNFGKIQSKI 842
MN+AS+ERG+ RS R+Y+ E D E+ K R + +
Sbjct: 225 MNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRH-------- 276
Query: 843 GRVDSLDDDGFPFIGANLQSGDIVIGK---------YADSGA------DHSIKLKHTERG 887
LD+DG ++ GD++IGK D G + S+ ++ E G
Sbjct: 277 -----LDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEG 331
Query: 888 MVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIV 947
+V V+L+ ++G V +R +R P LGDKF+S HGQKGV+G + QE+ PFT G+V
Sbjct: 332 IVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVV 391
Query: 948 PDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHR 1007
PD++INPHA PSR T G +LE GK + +L G + T F+ + + E L +
Sbjct: 392 PDLIINPHAIPSRMTVGHVLEMIGGK-VGSL-----EGRRVDGTAFSGEDEEDLREALEK 445
Query: 1008 AGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVAD 1067
GF G E +YDG TGE + + IF+G +YQ+L HM +K+ R+ GPV LTRQP
Sbjct: 446 LGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEG 505
Query: 1068 RKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVA--NVIQRVVGG 1125
R R GG++FGEMERD LI HGAA L ERL SD ++++C KC +A + +
Sbjct: 506 RAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRK-- 563
Query: 1126 GRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGI 1164
YC IC DI + Y KLL EL S+GI
Sbjct: 564 -------YCPICGEETDIYPVEMSYAFKLLLDELKSLGI 595
>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 = 420 bits (1083), Expect = e-137
Identities = 161/397 (40%), Positives = 220/397 (55%), Gaps = 42/397 (10%)
Query: 692 GLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMI 751
G+ +IPF +H+ + R+ YQ QAIG T N R D ++ L YPQ+PL +T
Sbjct: 1 GIVASLIPFVDHNQSPRITYQCA-MGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGA 59
Query: 752 SDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIR 811
+ G EL GQNA+VAV + GYNQED++++N++S++RG+F S HI+
Sbjct: 60 VEKGG-----------FGELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHIK 108
Query: 812 SYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDS-LDDDGFPFIGANLQSGDIVIGK- 869
Y+ E K + + LD+DG +GA ++ GDI++GK
Sbjct: 109 EYEIEAR------KTKLGPIEEITRDPPNVSEEAYRKLDEDGIVRVGAEVKPGDILVGKI 162
Query: 870 --------YADSGA------DHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPC 915
A G D S+K+KH E G V V + N G V +RQ R P
Sbjct: 163 TPKGEKLLRAIFGEKARDVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQ 222
Query: 916 LGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGI 975
+GDKF+S HGQKGV+ + QE+ PFT GI PDI++NPH PSR T GQLLE+ LGK
Sbjct: 223 VGDKFASRHGQKGVVSKILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLESLLGKAA 282
Query: 976 AALGKGICSGLKRYATPF--ATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFI 1033
A LGK ATPF A+ V+ I E L AG++ +G E LYDGRTGE ++ IF+
Sbjct: 283 ALLGK------FIDATPFDGASEDVEDIGELLKEAGYNAYGKEVLYDGRTGEPFKAPIFV 336
Query: 1034 GPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKR 1070
GP +YQ+L HM +DK+ R+TGP LT+QP+ R R
Sbjct: 337 GPIYYQKLKHMVDDKIHARSTGPYSLLTQQPLGGRSR 373
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 232 bits (595), Expect = 2e-66
Identities = 157/556 (28%), Positives = 256/556 (46%), Gaps = 112/556 (20%)
Query: 32 SFFNEYGLVSHQINSYNEFIKNGLQKAFDSFG--ETIVEPGYDPSKKGEGEWRYASMRFG 89
++F E+ LV H I+SYN+F+ NGLQK D G ET +E G + G
Sbjct: 11 AYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGV-------------YVELG 57
Query: 90 QVTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGRE 149
++ + KP +G E +++P ARL+N+TYS+ + + + + G E
Sbjct: 58 KIRVGKPVVKEADGS-EREIYPMEARLRNLTYSAPLYL--EMSPV----------EGGEE 104
Query: 150 QYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFDHGGYFIIKGAEK 203
+ E + IG +PVMV S +C + G +E G+ D GGYFI+ G+E+
Sbjct: 105 E---------EPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSER 155
Query: 204 VFVAQEQICLKRLWVSNSMGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEKV------- 256
V + E + ++ V +++ ++++K + G +
Sbjct: 156 VLMTLEDLAPNKILV--------------EKDERYGDRIEVAKVFSQRRGYRALVTVERN 201
Query: 257 ----LSVYF--LSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNK 310
L V F + IP IL ALG+ +D+EIV + +D I+ + ++ +A+
Sbjct: 202 RDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVS---DDPEIVKFMLENLEEAEVD 258
Query: 311 CDEFRKGRNALKYVDKLIKGTTFPPGESTE-------ECMNTYLFPSLHGTKQ----KAR 359
E AL+Y+ K + PG++ E ++ YL P L + KA
Sbjct: 259 TQE-----EALEYIGKRVA-----PGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAH 308
Query: 360 FLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDL 419
+LG M + + GRR+ D++D + NKRL+LAG+L+E +V + + L+R
Sbjct: 309 YLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERAN 368
Query: 420 YGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDL 479
+R + I+ + + +LT L A +TG W R +G+ L R + + TL L
Sbjct: 369 MRNRELS-IKTAVRSDVLTERLEHAMATGNW-----VGGR-TGVSQLLDRTDYMATLSHL 421
Query: 480 RR-----TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI- 533
RR +R Q + +AR HP+ WG+IC TP+G NCGLVKN +ST
Sbjct: 422 RRVVSPLSRSQPHF-----EARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGED 476
Query: 534 LEPIFEQLFNSGMEKL 549
E + E L G+E
Sbjct: 477 EEEVKEILKELGVEPE 492
>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 = 174 bits (442), Expect = 3e-47
Identities = 101/441 (22%), Positives = 168/441 (38%), Gaps = 77/441 (17%)
Query: 38 GLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPS 97
GLV Q++S+N F+ GLQ+ D F E E + S++ GQ+ L KP
Sbjct: 1 GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDE---------EPEF-SLKVGQIKLAKPK 50
Query: 98 FFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVL 157
+G +++PR ARL+N+TYSS + V +
Sbjct: 51 IKESDG-KTREIYPREARLRNLTYSSPLYVPAE--------------------LTVNNTE 89
Query: 158 SDETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFDHGGYFIIKGAEKVFVAQEQI 211
E + IG+IP+M++S+ C + G V+ G+C D GGYFI+ G+EKV + Q Q
Sbjct: 90 EIEKEKVFIGKIPLMLRSNACILNGASESELVKLGECPLDPGGYFIVNGSEKVIINQIQR 149
Query: 212 CLKRLWVSN-SMGWTVAYK-----SENKRNRLIVRLVDM-----SKFEDIKGGEKVLSVY 260
+V Y + + RL + + + +L++
Sbjct: 150 SPNIYYVFKKDKNGIRIYSASIISNRGRSLRLEITSKGKIYARINSGAKLIMFVLLLALG 209
Query: 261 FLSTEIPIWILFFA-LGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEF----- 314
EI + +L D +N + I D D
Sbjct: 210 LNLVEIILNLLVPEVDLEIQDDIGINDEEDEFLTDKPELEEQFVIQTQDEALDYIGGRGS 269
Query: 315 RKGRNALKYV--DKLIKGTTFPPGESTEECMNTYLFPSLHGTKQKARFLGYMVKCLLQAY 372
KG + + I P E + KA+ +GYM+ LL
Sbjct: 270 AKGFPRERRILGAVGILDLNLLPHLGVSE----------NTRTLKAQDIGYMIHRLLLLA 319
Query: 373 SGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTV-RPIEYY 431
GR D+ D NKRL LAGELL+ + ++ R+ + ++ + + + + ++
Sbjct: 320 LGRGPLDDIDHLGNKRLRLAGELLQSQFRI----LLNRLERDVRERI--QKCLKKKFDFT 373
Query: 432 LD----ASILTNGLSRAFSTG 448
L + +T+G+ TG
Sbjct: 374 LQNLVNSKPITSGIRYFLGTG 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 = 181 bits (461), Expect = 2e-46
Identities = 135/427 (31%), Positives = 204/427 (47%), Gaps = 67/427 (15%)
Query: 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQV-KRRS 828
EL G+N +VA GYN ED+++++ ++ +F S HI Y EV+ ++ ++
Sbjct: 670 ELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEY--EVEARDTKLGPEEI 727
Query: 829 SDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGA------------- 875
+ D+ N + + +LD++G IGA +++GDI++GK G
Sbjct: 728 TRDIPNVSE-----DALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAI 782
Query: 876 ---------DHSIKLKHTERGMVQKVVLSSNDDGK------NFSV-VSLRQVRSPCLGDK 919
D S+++ G V V + S +G N V V + Q R +GDK
Sbjct: 783 FGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKEGDELPPGVNKLVKVYIAQKRKIQVGDK 842
Query: 920 FSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALG-KGIAAL 978
+ HG KGV+ + E+ PF G DIV+NP PSR GQ+LE LG G
Sbjct: 843 MAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKKLG 902
Query: 979 GKGICSGLKRYATP-FATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTF 1037
KG+ ATP F S + I E L +AG + G RLYDGRTGE + + +G +
Sbjct: 903 RKGVP-----IATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDNPVTVGYMY 957
Query: 1038 YQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERL 1097
+L H+ +DK+ R+TGP +T+QP+ + +FGG +FGEME L A+GAA L E L
Sbjct: 958 MLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1017
Query: 1098 FTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQ 1157
SD V G K Y I G+++ + +P +L +
Sbjct: 1018 TVKSDD-------------------VTGRTKA---YEAIVK-GENVPEPGIPESFNVLIK 1054
Query: 1158 ELFSMGI 1164
EL S+G+
Sbjct: 1055 ELQSLGL 1061
Score = 75.9 bits (187), Expect = 1e-13
Identities = 117/536 (21%), Positives = 204/536 (38%), Gaps = 151/536 (28%)
Query: 39 LVSHQINSYNEFIKN----------GLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRF 88
L+ Q++SY+ F++ GL++ F S + P D + E E Y S
Sbjct: 20 LLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKS-----IFPIEDYTGNMELE--YLSYEL 72
Query: 89 GQVTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGR 148
G+ D + + +TYS +KVK++ +
Sbjct: 73 GEPKYD----------------VEECKERGLTYSVPLKVKLRLINKEEDGT--------- 107
Query: 149 EQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQ 208
KE+ E + +G IP+M G FII GAE+V V+Q
Sbjct: 108 -----KEIKEQE---VYMGDIPLMTDR------------------GTFIINGAERVVVSQ 141
Query: 209 EQICLKRLWVSNSMGWTVAYKSE---NKRNRLI--VRLVDMS----KFE-DIKGGEKVLS 258
L R S G V + SE +K +++ R++ +FE D K ++
Sbjct: 142 ----LHR-----SPG--VFFSSEKDTHKNGKVLYSARIIPYRGSWLEFETDKK---DLVY 187
Query: 259 VYFLST-EIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNK--CDEFR 315
V ++P +L ALG + D +N + I N L ++ ++ + +R
Sbjct: 188 VRIDRKRKLPATVLLRALGYTIDTLKLNRVG---SYEYISNTLRKDPTNSRDEALLEIYR 244
Query: 316 KGRNA----LKYVDKLIKGTTFPP-----GESTEECMNTYL---FPSLHGTKQKARFLGY 363
R ++ L++ F P G MN L P G K +
Sbjct: 245 VLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKMNKKLGLDVPEDIGVLTKEDIIAT 304
Query: 364 MVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDR 423
+ K L++ +G+ + D+ D N+R+ GELL+ + +V +A RM + ++ +
Sbjct: 305 I-KYLIKLRNGKGEVDDIDHLGNRRIRSVGELLQNQFRVGLA----RMERIVRERM---- 355
Query: 424 TVRPIEYYLDASI-----LTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVD 478
T + + + ++ + F + S +T NPL L
Sbjct: 356 TTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQT-------------NPLAELTH 402
Query: 479 LRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGV 525
RR TR++ + + R HP+H+G+IC + TP+G N GL+ +L
Sbjct: 403 KRRLSALGPGGLTRERAGF-----EVRDVHPTHYGRICPIETPEGPNIGLINSLST 453
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 158 bits (401), Expect = 4e-39
Identities = 126/444 (28%), Positives = 195/444 (43%), Gaps = 81/444 (18%)
Query: 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVD-NKEMQVKRRS 828
EL GQN +VA GYN ED++++N+ + +F S HI Y+ E+ K +
Sbjct: 643 ELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITR 702
Query: 829 SDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGK----------------YAD 872
+ V+ +++ LD++G IG+ + +GDI++GK A
Sbjct: 703 NIPNVSEYSLKN-------LDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAI 755
Query: 873 SGA------DHSIKLKHTERGMVQKVVL---SSNDDGKNFSVVSLR----QVRSPCLGDK 919
G D S+++ + G V KV + S D+ K + +R Q+R +GDK
Sbjct: 756 FGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDK 815
Query: 920 FSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALG 979
+ HG KG++ + +++ P+ G PDI++NP PSR GQL E LG L
Sbjct: 816 LAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLN 875
Query: 980 KGICSGLKRYATPF-----ATPSVDAITEQLHRAGF---SKW-------GTERLYDGRTG 1024
K PF + S I +L++A W G L DGRTG
Sbjct: 876 KRFKI------LPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTG 929
Query: 1025 EMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCL 1084
++ + +G + +LIH+ +DK+ R TGP +T+QP+ + + GG +FGEME L
Sbjct: 930 YKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWAL 989
Query: 1085 IAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIV 1144
A GAA L E L SD + N I G I
Sbjct: 990 EAFGAAYTLKELLTIKSD-----DMQGRNETLNAI------------------VKGQPIP 1026
Query: 1145 KANVPYGAKLLCQELFSMGITLKF 1168
K P K+L +EL S+G+ ++
Sbjct: 1027 KPGTPESFKVLMRELQSLGLDIEA 1050
Score = 57.0 bits (138), Expect = 6e-08
Identities = 93/512 (18%), Positives = 169/512 (33%), Gaps = 118/512 (23%)
Query: 39 LVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSF 98
+ Q S+ F+ GL + + F +D + E + L P +
Sbjct: 10 FLEIQRTSFCWFLNEGLNEELNIF-----SKIFDYTGNLE-----LLLFGKNYKLKYPKY 59
Query: 99 FAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLS 158
A+ + YS ++ + ++F +
Sbjct: 60 N-----------LLSAKSYDSNYSIQIYLPLKFI-----------NLKTNKIKFI----- 92
Query: 159 DETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV 218
N +IG +P M + G FII G E+V V+Q +
Sbjct: 93 ----NYLIGNLPKMTQR------------------GTFIINGLERVIVSQ---------I 121
Query: 219 SNSMGWTVAYKSENKRN-------RLIVRLVDMSKFEDIKGGEKVLSVYFLSTEIPIWIL 271
S G + +K E K+N LI KFE K E + + + + P+ I
Sbjct: 122 IRSPG--IYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEIWIRI-DKNRKKPLIIF 178
Query: 272 FFALGVSSDKEIVNLIDFTCEDCSILNILF-ASIHDADNKCDEFRKGRNALKYVDKLIKG 330
ALG++ L +L S + + + ++
Sbjct: 179 LKALGLTDQDIYSRLTKSEFLKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQ 238
Query: 331 TTFPP---------GESTEECMNTYLFPSLHGTKQKARFLGYM--VKCLLQAYSGRRKCD 379
F G+ +N L ++ + + + + L+ + D
Sbjct: 239 NLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFD 298
Query: 380 NRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTN 439
+ D +N+R+ GELL+ + ++ + K L+R L T+ I+ +++
Sbjct: 299 DIDHLKNRRVRSVGELLQNQFRIGL--------KRLERILRNRMTICDIDSLSKFNLINP 350
Query: 440 GLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQVQYTGKVGDARYP- 498
A + S + + + NPL L RR + G G +
Sbjct: 351 KPLIAL--------IREFFGSSQLSQYMDQTNPLSELTHKRR----ISILGPGGLDKDRI 398
Query: 499 -------HPSHWGKICFLSTPDGENCGLVKNL 523
HPSH+G+IC + TP+G NCGL+ +L
Sbjct: 399 SFAVRDIHPSHYGRICPIETPEGPNCGLIGSL 430
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 141 bits (358), Expect = 6e-34
Identities = 139/445 (31%), Positives = 207/445 (46%), Gaps = 91/445 (20%)
Query: 770 ELYNGQNAIVAV---NVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEV-DNK---EM 822
EL GQN +VA N GYN ED+++++ ++ +F S HI Y+ E D K E
Sbjct: 712 ELALGQNVLVAFMPWN---GYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPE- 767
Query: 823 QVKRRSSDDMVNFGKIQSKIGRVDS---LDDDGFPFIGANLQSGDIVIGK---------- 869
++ R D+ N + ++ LD+ G IGA ++ GDI++GK
Sbjct: 768 EITR----DIPNVSE--------EALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELT 815
Query: 870 ---------YADSGADH---SIKLKHTERGMVQKV-VLSSNDDGKNFSVVSLRQVR---- 912
+ + D S+++ H E G V V V + + G + V+
Sbjct: 816 PEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIA 875
Query: 913 -----SPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLL 967
GDK + HG KGV+ + E+ P+ G DIV+NP PSR GQ+L
Sbjct: 876 QKRKIQV--GDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQIL 933
Query: 968 EAALGKGIAALGKGICSGLKRYATP-FATPSVDAITEQLHRAGFSKWGTERLYDGRTGEM 1026
E LG AA G GI ++ATP F + I E L AG + G LYDGRTGE
Sbjct: 934 ETHLG--WAAKGLGI-----KFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEP 986
Query: 1027 VRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIA 1086
+ +G + +L H+ +DK+ R+TGP +T+QP+ + +FGG +FGEME L A
Sbjct: 987 FDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1046
Query: 1087 HGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKA 1146
+GAA L E L SD +V+ R KV Y I G++I +
Sbjct: 1047 YGAAYTLQEMLTVKSD--------------DVVGRT-----KV---YEAIVK-GENIPEP 1083
Query: 1147 NVPYGAKLLCQELFSMGITLKFDTE 1171
+P +L +EL S+G+ ++ E
Sbjct: 1084 GIPESFNVLVKELQSLGLDVELLDE 1108
Score = 50.5 bits (122), Expect = 6e-06
Identities = 37/177 (20%), Positives = 66/177 (37%), Gaps = 68/177 (38%)
Query: 39 LVSHQINSYNEFI-------KNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQV 91
L+ Q++S++ F+ GL++ F S + P D + S+ F
Sbjct: 27 LLEIQLDSFDWFLQLDVPPEDEGLEEVFRS-----IFPIEDFNGN-------LSLEFVSY 74
Query: 92 TLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQY 151
L +P + D + + +TYS+ ++VK++ + +EQ
Sbjct: 75 ELGEPKY------DV-----EECKERGLTYSAPLRVKLRLINKETGEI--------KEQ- 114
Query: 152 IQKEVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQ 208
EV +G IP+M ++ G FII G E+V V+Q
Sbjct: 115 ---EVY--------MGDIPLMTEN------------------GTFIINGTERVIVSQ 142
Score = 35.8 bits (84), Expect = 0.16
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 499 HPSHWGKICFLSTPDGENCGLVKNLGV 525
HP+H+G+IC + TP+G N GL+ +L
Sbjct: 472 HPTHYGRICPIETPEGPNIGLINSLAT 498
Score = 30.8 bits (71), Expect = 5.2
Identities = 14/50 (28%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 365 VKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKA 414
+K L+ +G+ + D+ D N+R+ GELL+ + ++ ++ RM +A
Sbjct: 350 IKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLS----RMERA 395
>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 = 102 bits (258), Expect = 2e-26
Identities = 34/100 (34%), Positives = 44/100 (44%), Gaps = 22/100 (22%)
Query: 1072 GGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRG 1131
GG +FGEME L A+GAA L ERL SD +C +C A
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVCGRCGAYAA-------------- 42
Query: 1132 PYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171
IC I ++P KLL QEL S+G+ ++ E
Sbjct: 43 ----ICKGKTIIEPGDIPESFKLLLQELRSLGLDIRLFLE 78
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 110 bits (277), Expect = 2e-24
Identities = 113/396 (28%), Positives = 175/396 (44%), Gaps = 87/396 (21%)
Query: 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSS 829
EL G+N +VA GYN ED+++++ + ++ S HIR Y E+Q S
Sbjct: 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-------EIQTHVTSQ 700
Query: 830 DDMVNFGKIQSKIGRVDS-----LDDDGFPFIGANLQSGDIVIGKYADSGADHS------ 878
+I +I +++ LD +G +G+ +++GDI++GK A+ S
Sbjct: 701 ----GPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEG 756
Query: 879 --------IKLKHTE----------RGMVQKVVLSSNDDGKNFSV----VSLRQVRSPCL 916
I++ ++ RG V V G +++ V + Q R +
Sbjct: 757 RLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQV 816
Query: 917 GDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIA 976
GDK + HG KG++ + +++ P+ G D+V+NP PSR GQ+ E LG +A
Sbjct: 817 GDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLG--LA 874
Query: 977 ALGKGICSGLKRY--ATPFATPSVDAITEQ----------LHRAGFSK-----W------ 1013
L R+ PF D EQ L+ A SK W
Sbjct: 875 G------DLLNRHYRIAPF-----DERYEQEASRKLVFSELYEA--SKQTANPWVFEPEY 921
Query: 1014 -GTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFG 1072
G RL+DGRTG+ + IG + +LIH +DK+ R++GP +T+QP+ R + G
Sbjct: 922 PGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQG 981
Query: 1073 GIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHI 1108
G + GEME L G A L E L SD HI
Sbjct: 982 GQRVGEMEVWALEGFGVAYILQEMLTYKSD----HI 1013
Score = 48.0 bits (115), Expect = 3e-05
Identities = 43/158 (27%), Positives = 65/158 (41%), Gaps = 36/158 (22%)
Query: 379 DNRDDFRNKRLELAGELLERELK---VHIAHA-RKRMAKALQRDLYGDRTVRPIEYYLDA 434
D+ D +NKR+ +LL+ + + +A R + A++R L P L
Sbjct: 304 DDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKL------IPTPQNLVT 357
Query: 435 SI-LTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQVQYTGKVG 493
S LT F SHP + L + NPL +V R+ + G G
Sbjct: 358 STPLTTTYESFFG----SHPLSQF---------LDQTNPLTEIVHGRK----LSSLGPGG 400
Query: 494 --------DARYPHPSHWGKICFLSTPDGENCGLVKNL 523
R HPSH+G+IC + T +G N GL+ +L
Sbjct: 401 LTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSL 438
Score = 31.0 bits (71), Expect = 5.3
Identities = 51/264 (19%), Positives = 87/264 (32%), Gaps = 93/264 (35%)
Query: 38 GLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPS 97
G Q + FI GL + F D + E E++ + L +P
Sbjct: 14 GFNQIQFEGFCRFIDQGLTEELSKFP-----KIEDTDQ--EIEFQLFVETY---QLVEPL 63
Query: 98 FFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVL 157
R A +++TYSS + V ++ + R +Q++
Sbjct: 64 I-----------KERDAVYESLTYSSELYVPAGL-IWKKSRD------------MQEQT- 98
Query: 158 SDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLW 217
+ IG IP+M + G FII G +V + Q
Sbjct: 99 ------VFIGNIPLM------------------NSLGTFIINGIYRVVINQ--------- 125
Query: 218 VSNSMGWTVAYKSENKRNRLIVRLVDM-------SKFE-DIKG------GEKVLSVYFLS 263
+ S G + Y+SE N + V + + E D K K
Sbjct: 126 ILRSPG--IYYRSELDHNGISVYTGTIISDWGGRLELEIDRKARIWARVSRK-------- 175
Query: 264 TEIPIWILFFALGVSSDKEIVNLI 287
+I I +L A+G + +EI++ +
Sbjct: 176 QKISILVLLSAMG-LNLREILDNV 198
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 107 bits (268), Expect = 3e-23
Identities = 77/239 (32%), Positives = 106/239 (44%), Gaps = 52/239 (21%)
Query: 916 LGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGI 975
+GDK + HG KG++ + + P+T G DIV+NP PSR GQ+LE LG
Sbjct: 1090 VGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVG 1149
Query: 976 AALGKGICSGLKR-----------------------------------------YA---- 990
GK I S L+ YA
Sbjct: 1150 KEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWS 1209
Query: 991 --TPFATPSVDAIT-EQLHR----AGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIH 1043
A P + I+ E+ ++ A + G LYDGRTGE +R + +G + +L H
Sbjct: 1210 KGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHH 1269
Query: 1044 MSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSD 1102
+ ++KV R+TGP +T QPV + FGG +FGEME L A+GAA L E L SD
Sbjct: 1270 LVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
Score = 61.5 bits (149), Expect = 3e-09
Identities = 45/163 (27%), Positives = 77/163 (47%), Gaps = 18/163 (11%)
Query: 365 VKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRT 424
VK L++ + + K D+RD N+R+ GELL EL + +K + L +
Sbjct: 441 VKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDS 500
Query: 425 VRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQ 484
+ P + +++ ++T+ + F G S +T NPL + RR
Sbjct: 501 LMPHDL-VNSKMITSTIMEFFMGGQLSQFMDQT-------------NPLSEVTHKRRLSA 546
Query: 485 QVQ---YTGKVG-DARYPHPSHWGKICFLSTPDGENCGLVKNL 523
+ +VG +AR HP+H+G+IC + TP+G+N GL+ L
Sbjct: 547 LGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTL 589
Score = 40.3 bits (94), Expect = 0.008
Identities = 33/108 (30%), Positives = 55/108 (50%), Gaps = 8/108 (7%)
Query: 768 RPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVK-R 826
R EL G+N VA GYN ED++V++ + +F S HI Y+ EVD +E++
Sbjct: 801 RGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHI--YEKEVDARELKHGVE 858
Query: 827 RSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSG 874
+ D+ + K + LD+ G +G + +G I++GK + G
Sbjct: 859 EFTADIPD-----VKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKG 901
Score = 34.5 bits (79), Expect = 0.45
Identities = 41/174 (23%), Positives = 66/174 (37%), Gaps = 61/174 (35%)
Query: 43 QINSYNEFI------KNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKP 96
Q +SY+ F+ ++G++K F S + P D + E YA FG K
Sbjct: 31 QRDSYDSFLYSKDGKESGIEKVFKS-----IFPIQDEHNRITLE--YAGCEFG-----KS 78
Query: 97 SFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKF--KTGREQYIQK 154
+ R A + +TYS +K+KV+ ++ + + +K K +EQ
Sbjct: 79 KYTV-----------REAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ---- 123
Query: 155 EVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQ 208
+I I IP+M + FII G E+V V Q
Sbjct: 124 --------SIFIREIPLMTERT------------------SFIINGVERVVVNQ 151
>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 = 76.9 bits (190), Expect = 2e-17
Identities = 26/63 (41%), Positives = 40/63 (63%)
Query: 563 VFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLV 622
V+V+G +G ++ V LR RR+ ++ +V + R+ Q E+RI DAGRI RPL++
Sbjct: 1 VYVNGKLVGTHRNPEELVETLRELRRKGKISPEVSVVRNIRQREIRINTDAGRICRPLII 60
Query: 623 VEN 625
VEN
Sbjct: 61 VEN 63
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 77.7 bits (191), Expect = 3e-14
Identities = 42/118 (35%), Positives = 60/118 (50%)
Query: 985 GLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHM 1044
G+ A F P + I + AG G LYDG +GE + +G + +L H+
Sbjct: 1269 GIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHL 1328
Query: 1045 SEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSD 1102
+ K+ R+ GP +T+QP+ + FGG +FGEME L A+GAA L E L SD
Sbjct: 1329 VDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
Score = 53.1 bits (127), Expect = 9e-07
Identities = 39/171 (22%), Positives = 77/171 (45%), Gaps = 30/171 (17%)
Query: 364 MVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDR 423
+V+ ++ G+ D+ D N+R+ GE +E + + + + + ++
Sbjct: 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLD-- 506
Query: 424 TVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRR-- 481
V P ++ ++ +LTN L F++ S +T NPL + RR
Sbjct: 507 KVSPSDF-INPKVLTNVLRDFFNSSQLSQFMDQT-------------NPLSEITHKRRLS 552
Query: 482 -------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGV 525
TR++ + + R HP+H+G+IC + TP+G+N GL+ +L +
Sbjct: 553 ALGPGGLTRERAGF-----EVRDVHPTHYGRICPIETPEGQNIGLINSLAI 598
Score = 52.3 bits (125), Expect = 2e-06
Identities = 25/66 (37%), Positives = 36/66 (54%)
Query: 917 GDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIA 976
GDK + HG KGV+ + E+ P+ G DI++NP PSR GQ+LE +G
Sbjct: 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACK 1143
Query: 977 ALGKGI 982
LG+ +
Sbjct: 1144 KLGEKV 1149
Score = 42.7 bits (100), Expect = 0.001
Identities = 37/140 (26%), Positives = 61/140 (43%), Gaps = 19/140 (13%)
Query: 736 SHQLFYPQRPLFRTMISDCLGKPGY-GHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLV 794
+H Q+PL + D + + + EL GQN +VA GYN EDS++
Sbjct: 780 NHNTCINQKPLVC--VGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSII 837
Query: 795 MNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDS-----LD 849
++ +++ +F S HI ++ V + + + KI I V+ LD
Sbjct: 838 ISSEVVKKDLFTSIHIEEFECVVHDTPLGSE-----------KITRAIPGVNEENLYHLD 886
Query: 850 DDGFPFIGANLQSGDIVIGK 869
D G IG + G I++GK
Sbjct: 887 DSGIVKIGTRVGPGYILVGK 906
>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 = 70.4 bits (173), Expect = 1e-13
Identities = 40/156 (25%), Positives = 63/156 (40%), Gaps = 17/156 (10%)
Query: 248 EDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDA 307
+I G + S +IPI I ALG+ SD+EI++ + + D +L +L + +A
Sbjct: 34 LEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDPQMLELLKPELEEA 93
Query: 308 DNKCDEFRKGRNALKYVDKLIKGTTFPPGESTEEC-----------MNT--YLFPSLHGT 354
+N + AL Y+ K +N L
Sbjct: 94 ENIYTQ----EEALDYIGKGFALRRGEEPRLQRAREILYSRDPKYNLNKHLGLNEPFENE 149
Query: 355 KQKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLE 390
+ KA+ + YM+ LL GRRK D+ D NKR+
Sbjct: 150 RLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 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 = 60.7 bits (148), Expect = 1e-11
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 469 RANPLQTLVDLRRTRQQVQY--TGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVT 526
+ N L L RR + K + R HPS +G+IC + TP+G NCGLV +L +
Sbjct: 5 QTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNSLALY 64
Query: 527 GLVS 530
++
Sbjct: 65 ARIN 68
>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 = 49.1 bits (118), Expect = 1e-07
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 639 FQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELD 686
F LL G+IE + EEEE A + L + K THCE+
Sbjct: 1 FVDLLKEGVIEYLDAEEEETAMIAMSPEDLRLEDITK---TTTHCEIH 45
>gnl|CDD|233723 TIGR02094, more_P_ylases, alpha-glucan phosphorylases. This family
consists of known phosphorylases, and homologs believed
to share the function of using inorganic phosphate to
cleave an alpha 1,4 linkage between the terminal glucose
residue and the rest of the polymer (maltodextrin,
glycogen, etc.). The name of the glucose storage polymer
substrate, and therefore the name of this enzyme,
depends on the chain lengths and branching patterns. A
number of the members of this family have been shown to
operate on small maltodextrins, as may be obtained by
utilization of exogenous sources. This family represents
a distinct clade from the related family modeled by
TIGR02093/pfam00343.
Length = 601
Score = 33.8 bits (78), Expect = 0.63
Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 18/91 (19%)
Query: 394 ELLERELKVH---IAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAW 450
EL E LK+ I + R+R+ + R + + +LD +LT G +R F+T
Sbjct: 344 ELWEVHLKLKARLIDYIRRRLRERWLRRGADAAILMATDRFLDPDVLTIGFARRFAT--- 400
Query: 451 SHPFKRT-------ERISGIVANLGRANPLQ 474
+KR ER++ I+ N R P+Q
Sbjct: 401 ---YKRADLIFRDLERLARILNNPER--PVQ 426
>gnl|CDD|215067 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
iron-sulfur subunit.
Length = 276
Score = 33.2 bits (76), Expect = 0.64
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 359 RFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKA 414
+FLG LL AY R D+RD++ +RL E L+ E K++ H + + A
Sbjct: 208 KFLGPAA--LLHAY--RWISDSRDEYTKERL----EALDDEFKLYRCHTIRNCSNA 255
>gnl|CDD|223073 PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like
protein; Provisional.
Length = 865
Score = 33.7 bits (78), Expect = 0.78
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 917 GDKFSSMHGQKGVLGFLESQENFP-FTIQ-GIVPDIVINPHAFPSRQT 962
G K +HGQKGV L E+ + + G I ++P ++ SRQT
Sbjct: 711 GLKICGIHGQKGV---LNGSEDLTEWMAEDGTHAQICLSPISYLSRQT 755
>gnl|CDD|219334 pfam07210, DUF1416, Protein of unknown function (DUF1416). This
family consists of several hypothetical bacterial
proteins of around 100 residues in length. Members of
this family appear to be Actinomycete specific. The
function of this family is unknown.
Length = 86
Score = 30.5 bits (69), Expect = 0.95
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 1118 VIQ-RVVGGGRKVRGPYCRICDSGDDIVKANVPYGA 1152
VIQ V G+ V G Y R+ DS + A V A
Sbjct: 10 VIQGVVRRDGQPVGGAYVRLLDSSGEFT-AEVVTSA 44
>gnl|CDD|240121 cd04817, PA_VapT_like, PA_VapT_like: Protease-associated domain
containing proteins like VapT from Vibrio metschnikovii
strain RH530. This group contains various PA
domain-containing proteins similar to V. metschnikovii
VapT, including the serine alkaline protease SapSh from
the psychotroph Shewanella strain Ac10 and the Apa1
protease from the psychrotroph Pseudoalteromonas Sp.
As-11. VapT is a sodium dodecyl sulfate (SDS) resistant
extracellular alkaline serine protease showing high
activity over a broad pH range and temperature. SapSh
has a high level of protease activity at low
temperatures. Apa1 is also cold-adapted. The
significance of the PA domain to these proteins has not
been ascertained. It may be a protein-protein
interaction domain. At peptidase active sites, the PA
domain may participate in substrate binding and/or
promoting conformational changes, which influence the
stability and accessibility of the site to substrate.
Length = 139
Score = 30.5 bits (69), Expect = 2.1
Identities = 15/64 (23%), Positives = 16/64 (25%), Gaps = 10/64 (15%)
Query: 847 SLDDDGFPFIGAN--------LQSGDIVIGKYADSGADHSIKLKHTERGMVQKVVLSSND 898
L G + L G Y G I L ERG K V D
Sbjct: 19 RLIASGTSYASMPVTGSATGSLYYCGTSGGSYICGGMAGKICL--IERGGNSKSVYPEID 76
Query: 899 DGKN 902
K
Sbjct: 77 KVKA 80
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 840
Score = 31.7 bits (72), Expect = 2.7
Identities = 13/44 (29%), Positives = 19/44 (43%)
Query: 1056 PVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFT 1099
P H RQ + + +R+ + E E L A G L + LF
Sbjct: 471 PAHYRRRQTLKNAERYITPELKEKEDKVLEAEGKILALEKELFE 514
>gnl|CDD|173783 cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI: The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to Escherichia coli DNA topoisomerase I. Type
IA DNA topoisomerases remove (relax) negative supercoils
in the DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). For topoisomerases the conserved glutamate is
believed to act as a general base in strand joining and,
as a general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 123
Score = 29.8 bits (68), Expect = 2.8
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 620 LLVVENMGKIKSLE---GKNYTFQALLDHGIIEL 650
L++VE+ K K+++ GK Y A + H I +L
Sbjct: 3 LVIVESPAKAKTIKKYLGKEYEVLASVGH-IRDL 35
>gnl|CDD|139876 PRK13814, pyrB, aspartate carbamoyltransferase catalytic subunit;
Provisional.
Length = 310
Score = 31.2 bits (70), Expect = 3.2
Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 18/78 (23%)
Query: 461 SGIVANLGRAN---PLQTLVDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENC 517
SG+V N G N P Q L+DL +Q H HW K+C D +
Sbjct: 124 SGVVINAGDGNHQHPSQALIDLMTIKQ--------------HKPHWNKLCVTIIGDIRHS 169
Query: 518 GLVKNLGVTGLVSTSILE 535
+ +L + GLV+ + E
Sbjct: 170 RVANSL-MDGLVTMGVPE 186
>gnl|CDD|223436 COG0359, RplI, Ribosomal protein L9 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 30.3 bits (69), Expect = 3.4
Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 14/87 (16%)
Query: 757 KPGYGHNHILPRPELYNGQNAIVAVNVHLG-YNQEDSLVMNRASLER-GMFRSEHIRSYK 814
K GY N ++P+ A+ A +L RA LE+ + K
Sbjct: 22 KDGYARNFLIPK------GLAVPATKGNLKLLEAR------RAKLEKKAAEELAEAEALK 69
Query: 815 AEVDNKEMQVKRRSSDDMVNFGKIQSK 841
+++ K +++ ++ +D FG + SK
Sbjct: 70 EKLEGKTVEIAVKAGEDGKLFGSVTSK 96
>gnl|CDD|223112 COG0034, PurF, Glutamine phosphoribosylpyrophosphate amidotransferase
[Nucleotide transport and metabolism].
Length = 470
Score = 30.3 bits (69), Expect = 6.3
Identities = 24/106 (22%), Positives = 38/106 (35%), Gaps = 21/106 (19%)
Query: 1063 QPVADRKRFGGIKFGEMERDCLIAHGA----AANLHERLF-------TLSDS-YQMHICR 1110
QP GGI +AH A L L T SDS +H+
Sbjct: 92 QPFYVNSPGGGIA---------LAHNGNLVNAEELRRELEEEGAIFNTTSDSEVLLHLLA 142
Query: 1111 KCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLC 1156
+ + ++ + V R+V+G Y + D ++ P G + L
Sbjct: 143 RELDEDDIFEAVKEVLRRVKGAYALVALIKDGLIAVRDPNGIRPLV 188
>gnl|CDD|130194 TIGR01124, ilvA_2Cterm, threonine ammonia-lyase, biosynthetic, long
form. This model describes a form of threonine
ammonia-lyase, a pyridoxal-phosphate dependent enzyme,
with two copies of the threonine dehydratase C-terminal
domain (pfam00585). Members with known function
participate in isoleucine biosynthesis and are inhibited
by isoleucine. Alternate name: threonine deaminase,
threonine dehydratase. Forms scoring between the trusted
and noise cutoff tend to branch with this subgroup of
threonine ammonia-lyase phylogenetically but have only a
single copy of the C-terminal domain [Amino acid
biosynthesis, Pyruvate family].
Length = 499
Score = 30.1 bits (68), Expect = 7.8
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 693 LSCGIIPFANHDHARRVLYQSQKHSSQA-IGFPTTNPSIRVD 733
+ G+I + +HA+ V + + + +A I P T P I+VD
Sbjct: 64 KARGVIAASAGNHAQGVAFSAARLGLKALIVMPETTPDIKVD 105
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 0.418
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 60,524,583
Number of extensions: 6114690
Number of successful extensions: 4809
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4695
Number of HSP's successfully gapped: 65
Length of query: 1173
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1065
Effective length of database: 6,147,370
Effective search space: 6546949050
Effective search space used: 6546949050
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 (21.9 bits)
S2: 65 (28.9 bits)