RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 001021
(1186 letters)
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 1271 bits (3290), Expect = 0.0
Identities = 524/1151 (45%), Positives = 717/1151 (62%), Gaps = 57/1151 (4%)
Query: 29 WAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYL 88
W V+ AYF+EKGLVRQ LDS+++FI+ +QEIVDE +I+ PG + +I +
Sbjct: 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKT-----EIPGLKIVLGKIRV 56
Query: 89 SKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFI 148
+P + E+DG + P ARLRNLTY+APLY+ + +G E + V I
Sbjct: 57 GEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMIPVE-----NGIEYEPEE----VKI 107
Query: 149 GKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFK 208
G +PIM++S C L S +L E+GE P D GGYFIINGSE+V+++QE ++ N V V K
Sbjct: 108 GDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDK 167
Query: 209 KRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPII 268
+ + A+V S R K G+ I + P + +IP +
Sbjct: 168 GEAGSSITHTAKVISSRAGYRAQ--VTVERR------KDGT----IYVSFPAVPGKIPFV 215
Query: 269 IVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQN-QQVALDYIGKRGATVG 327
I+ RALG D+DI+ + D ++ + L PSLE+A I + ALDYIGKR A +G
Sbjct: 216 ILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASSIAATVEDALDYIGKRVA-IG 271
Query: 328 VTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYG 387
R+ RI+ A++IL K +LPH+GT KKAY+ G + +LL LGRR DD+DHY
Sbjct: 272 QPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYA 331
Query: 388 NKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLA 447
NKRL LAG LL LFR+ F++L +D++ ++K G+ ++L+ ++ IT ++++LA
Sbjct: 332 NKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALA 391
Query: 448 TGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMC 507
TGNW G R GVSQ+L+R Y STLSHLRR+ SP+ R + R LH +QWG +C
Sbjct: 392 TGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRIC 446
Query: 508 PAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVN 567
P ETPEG CGLVKNLALM I+VG + E L E G EE +++++N
Sbjct: 447 PFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506
Query: 568 GCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGV--VRDIRLKELRIYTDYGRCSRPLFIVE 625
G +G H D E L + +R LRR ++ EV V + + E+ + D GR RPL +VE
Sbjct: 507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVE 566
Query: 626 KQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLH 685
+ + + + L++ E + DLV G IEY+D EEEE +++ DL
Sbjct: 567 NGKPKLTREHVEKLKKGELT----FDDLVKMGVIEYLDAEEEENAYVALDPEDLT----- 617
Query: 686 PEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM 745
PE +TH EI P ILG+ ASIIP+P+HNQSPRNTYQ+AM KQ++G+Y N++ R
Sbjct: 618 PE------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRT 671
Query: 746 DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRG 805
DT ++L+YPQ+PLV TRA+E + + PAG NA+VA+ Y+GYN ED++IMN++SI+RG
Sbjct: 672 DTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERG 731
Query: 806 FFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMR-HGSYDKLDDDGLAPPGTRVSGE 864
RS FFR+Y EE+K ++ P+ N G R Y KLD+DG+ P V G
Sbjct: 732 LARSTFFRTYETEERKYPGGQEDKIEIPE-PNVRGYRGEEYYRKLDEDGIVSPEVEVKGG 790
Query: 865 DVIIGKTTPISQDEAQGQASRYT--RRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRV 922
DV+IGKT+P E + S RRD S+++RH E G+VD VL+T + +G + VKVRV
Sbjct: 791 DVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRV 850
Query: 923 RSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIE 982
R +RIP++GDKF+SRHGQKG +GM QEDMP+T +GI PD+I+NPHAIPSRMT+GQL+E
Sbjct: 851 RDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 910
Query: 983 CIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLG 1042
I GKVAA G+ DATPF + + K L K GY+ G E MY+G TG ++ A IF+G
Sbjct: 911 SIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIG 970
Query: 1043 PTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLK 1102
YYQ+L HMV DKIH+R RGPVQILTRQP EGR+R+GGLRFGEMERDC+I HGA+ LK
Sbjct: 971 VVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLK 1030
Query: 1103 ERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMA 1162
ERL D SD ++VCE CG IA + +KN + C +K +I V + YA KLL QELM+
Sbjct: 1031 ERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMS 1090
Query: 1163 MAIAPRMLTKE 1173
M I+PR+ +
Sbjct: 1091 MGISPRLKLGD 1101
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 1077 bits (2789), Expect = 0.0
Identities = 377/1181 (31%), Positives = 553/1181 (46%), Gaps = 159/1181 (13%)
Query: 24 TQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDF 83
D++ I + + LV QLDS++ F +QE+ E I P +N + ++
Sbjct: 10 RIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFRE-----IFPIESYNGNTELEY 64
Query: 84 AEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDF 143
L +P +P+ RLR LTYSAPLYV + V ++ E + Q+
Sbjct: 65 GSYRLGEP---------PKFYPEECRLRGLTYSAPLYVKLRLVV----NETGEEIKEQE- 110
Query: 144 TKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNH 203
V++G +P+M R GGYFIING+E+V+++QE S
Sbjct: 111 --VYMGDIPLMTR------------------------GGYFIINGTERVIVSQEHRSPGV 144
Query: 204 VYVFKKRQP-NKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIR 262
++V KK + +K YVA V S + K Y+R +
Sbjct: 145 IFVEKKDKTGSKVLYVARVIPYRGS----------WLEFEFDPKDNL---YVR---IDRK 188
Query: 263 TEIPIIIVFRALGFVADKDILEHIC----YDFQDTQMMELLRPSLEEA--FVIQNQQVAL 316
+IP+ I+ RALG D++I+E D + E L EEA I + AL
Sbjct: 189 RKIPVTILLRALGLETDEEIIEAFGGDELTDLVPPEGEEALLEIYEEAKGEKITARN-AL 247
Query: 317 DYIGKRGATVGVT--RDKRIKYAKEILQKEMLPHVGTG----DFCETKKAYYFGYIIHRL 370
+ IG R V ++ R K AK +L KE+LPH+G D KA +I L
Sbjct: 248 ELIGSRVFVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYL 307
Query: 371 LLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQ 430
+ LG+ EDD DH GN+RL L G LL LFR+ ++ RDV+ ++K
Sbjct: 308 IELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKAD------KRD 361
Query: 431 FAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGRE 489
+ I + ++L TG +G R+ +SQ +++ S LSH RRL++ + RE
Sbjct: 362 TLVPQDLINAKPIHALITGFFG-------RSQLSQFMDQTNPLSELSHKRRLSALGLSRE 414
Query: 490 GKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPILEFL-EEWGT 547
+ R +H + +G +CP ETPEG GL+K+LAL I G P + L
Sbjct: 415 RAGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVV 474
Query: 548 ENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLK- 606
+ E +S ++V G G +P LV+ L RR EV V +
Sbjct: 475 DEIEYLSADE----EDVYVIGQANGTLDEPGELVEELVECRRGGS--GEVSVADPEGVDY 528
Query: 607 ---ELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYID 663
+ GR P + + ++ Q++ P LV G +EY+D
Sbjct: 529 MDVSPKQVVSVGRSLIPFLEHDDANRALMGSNM---QRQAVPLLRTEAPLVGTG-MEYLD 584
Query: 664 TEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 723
E+ +I+ P TH EI P +ILG+ AS+IP+P+HNQSP N
Sbjct: 585 AEDSGAAVIAK----------RPGV-----VTHVEISPIVILGIEASLIPYPEHNQSPYN 629
Query: 724 TYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAI 783
Y+ A QA GI R DT+ L Y P V T +L G NA+VA
Sbjct: 630 LYKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDTG--------ELALGQNALVAF 681
Query: 784 ACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH 843
++GYN ED++I+++ S++R F S+ Y E + +E P+ S
Sbjct: 682 MPWNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVSEEA---- 737
Query: 844 GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQASRYT-----RRDHSISLRHS 898
LD+DG+ G V G D+++GK TP + E + RD S+ + H
Sbjct: 738 --LRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEKVRDTSLRVPHG 795
Query: 899 ETGMVDQVLLTTNADG----LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMP 954
E G+VD V + T DG + VKV V R PQIGDK + RHG KG V QEDMP
Sbjct: 796 EEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMP 855
Query: 955 WTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALH 1014
+ +G PDII+NP +PSRM IGQ++E +GK AA +G D F ++I + L
Sbjct: 856 FLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGAPEEDIRELLK 915
Query: 1015 KCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAE 1074
+ G+ G E +Y+G TG A IF+G YYQ+L HMVDDKIH+R GP ++T+QP
Sbjct: 916 EAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLG 975
Query: 1075 GRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFE 1134
G+++ GG RFGEME + A+GA++ L+ERL +SD CG I I +E
Sbjct: 976 GKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVKSDDV-------CGRIKI-------YE 1021
Query: 1135 CRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1175
C +I +V IP + K+L +EL ++ I R+ ++
Sbjct: 1022 CIVK--GENIPEVGIPESFKVLLKELRSLGIDVRLELEDGK 1060
>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 = 802 bits (2075), Expect = 0.0
Identities = 251/483 (51%), Positives = 313/483 (64%), Gaps = 15/483 (3%)
Query: 692 DTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYV 751
TH EI PS IL V AS+IPFP+HNQSPRN YQS M KQA+G N Q+RMDT Y+
Sbjct: 393 KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYL 452
Query: 752 LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLF 811
L YPQKPLV T E++ F +LP G NAIVA+ YSGYN ED++I+N+SS+DRGFFRS+
Sbjct: 453 LLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIH 512
Query: 812 FRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKT 871
++ Y E +K K R + + LD+DG+ PG RV D+++GK
Sbjct: 513 YKKYEIELRK----TKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKI 568
Query: 872 TPISQDEA--QGQASRYTRRDHSISLRHSETGMVDQVLLTT---NADGLRFVKVRVRSVR 926
TP + E+ RD S+ E G+VD V + + N G + VKV +R R
Sbjct: 569 TPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKR 628
Query: 927 IPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMG 986
PQIGDKF+SRHGQKG + QEDMP+T +GI PDII+NPH PSRMTIGQL+E ++G
Sbjct: 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLG 688
Query: 987 KVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYY 1046
K A +GK GDATPF ++IS+ L + G G E +Y+G TG L A IF+GP YY
Sbjct: 689 KAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYY 748
Query: 1047 QRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLF 1106
QRLKHMVDDKIH+R GP +LTRQP +GRSR GG RFGEMERD +IAHGA++ L+ERL
Sbjct: 749 QRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLT 808
Query: 1107 DQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIA 1166
+SD VC CG+I ANL CR CK T+I +V IPYA KLLFQEL +M I
Sbjct: 809 IKSDDVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQSMNID 862
Query: 1167 PRM 1169
PR+
Sbjct: 863 PRL 865
Score = 444 bits (1145), Expect = e-139
Identities = 177/491 (36%), Positives = 232/491 (47%), Gaps = 111/491 (22%)
Query: 41 LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGET 100
LV+QQ+DSF+ F+ +QEIV I + + F +IYL KP + E G T
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTD---DDGRLKLKFGDIYLGKPKVEE-GGVT 56
Query: 101 ATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYC 160
L P RLR+LTYSAPLYVD+ V KG E+ +VFIG++PIMLRS C
Sbjct: 57 RKLTPNECRLRDLTYSAPLYVDIRLTVNDKGKIKEQ--------EVFIGEIPIMLRSKLC 108
Query: 161 TLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAE 220
L + ++L +LGECP D GGYFIING+EKV+I QE+ S N + V +K +
Sbjct: 109 NLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE----DSKGKRIYT 164
Query: 221 VRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADK 280
S+ S + V+ + I + R
Sbjct: 165 KTSIPSYSPYRGSWLEVKSDKKK--------DRIYVRIDLKR------------------ 198
Query: 281 DILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEI 340
Q+ AL YIGKR
Sbjct: 199 -------------------------------QEEALKYIGKRF----------------- 210
Query: 341 LQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGG 400
Y+I +L+L LG+ DD DH GNKR+ LAG LL
Sbjct: 211 --------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQN 250
Query: 401 LFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTR 460
LFR ++L R+V+ +QK + KD+ Q I +K ITSG+K LATGNWG R
Sbjct: 251 LFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQR 310
Query: 461 AGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGL 519
+G+SQVL+RL S LSH RR++S + RE K + R LH S WG +CP ETPEG+ CGL
Sbjct: 311 SGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGL 370
Query: 520 VKNLALMVYIT 530
VKNLALM I+
Sbjct: 371 VKNLALMARIS 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 = 745 bits (1925), Expect = 0.0
Identities = 294/613 (47%), Positives = 401/613 (65%), Gaps = 19/613 (3%)
Query: 564 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFI 623
+++NG +G H DPE LV+ +R+LRR ++ EV V E+ I D GR RPL +
Sbjct: 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIV 60
Query: 624 VEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQAR 683
VE + + + + L++ E W DLV +G IEY+D EEEE I++ +L
Sbjct: 61 VENGKPKLTREHVEKLKEGELT----WDDLVKQGVIEYLDAEEEENAYIALDPEELT--- 113
Query: 684 LHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF 743
+TH EI PS ILG+ AS IP+P+HNQSPRNT +AM KQ++G+Y NY+
Sbjct: 114 --------PEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRI 165
Query: 744 RMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 803
R+DT ++L+YPQKPLV TR +E + + PAG N +VA+ Y GYN ED++IMN++SI+
Sbjct: 166 RLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225
Query: 804 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMR-HGSYDKLDDDGLAPPGTRVS 862
RG RS FFR+Y EE++ ++ F P+ + G R +Y LD+DG+ P V
Sbjct: 226 RGLARSTFFRTYEAEERRYPGGQEDRFEIPE-PDVRGYRGEEAYKHLDEDGIVYPEVEVK 284
Query: 863 GEDVIIGKTTP--ISQDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKV 920
G DV+IGKT+P ++ + RRD S+++RH E G+VD+V++T +G + VKV
Sbjct: 285 GGDVLIGKTSPPRFLEELRELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKV 344
Query: 921 RVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQL 980
RVR +RIP++GDKF+SRHGQKG +GM QEDMP+T +GI PD+I+NPHAIPSRMT+GQL
Sbjct: 345 RVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQL 404
Query: 981 IECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 1040
+E I GKVAA G+ D TPF + + K L K G++ G E MY+G TG +L A IF
Sbjct: 405 LEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
Query: 1041 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 1100
+G YYQ+L HMV DKIH+R RGPVQ+LTRQP EGR+R+GGLRFGEMERD +I HGA+
Sbjct: 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAML 524
Query: 1101 LKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQEL 1160
LKERL D+SD Y V+VCE+CG IA + +K + C C DI V + YA KLL EL
Sbjct: 525 LKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDEL 584
Query: 1161 MAMAIAPRMLTKE 1173
++ I+PR+ +
Sbjct: 585 KSLGISPRLELGD 597
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 730 bits (1886), Expect = 0.0
Identities = 287/612 (46%), Positives = 396/612 (64%), Gaps = 21/612 (3%)
Query: 562 TKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPL 621
K++VNG +G H DPE LV+ +R RR +++ EV V E+ I TD GR RPL
Sbjct: 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPL 64
Query: 622 FIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQ 681
+VE L+ + I L+ E + DLV +G IEY+D EEEE I++ DL
Sbjct: 65 IVVENGEPLLTEEHIEKLKNGEL----TFDDLVKQGVIEYLDAEEEENAYIAVYEEDL-- 118
Query: 682 ARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 741
+ +TH EI PSLILG+ A +IP+P+HN SPR T + M KQ++G+ NY
Sbjct: 119 ---------TEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANY 169
Query: 742 QFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSS 801
+ R DT ++L+YPQ PLV T+ E + F + PAG N +VA+ Y GYN ED++IMN++S
Sbjct: 170 KLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKAS 229
Query: 802 IDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMR-HGSYDKLDDDGLAPPGTR 860
I+RG RS FFR+Y EE++ ++ F PD + G R +Y LD+DGL P T
Sbjct: 230 IERGLGRSHFFRTYEGEERRYPGGQEDRFEIPD-KDVRGYRGEEAYRHLDEDGLVNPETE 288
Query: 861 VSGEDVIIGKTTP---ISQDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRF 917
V DV+IGKT+P + + + G + RR+ S+++R E G+VD V+LT +G R
Sbjct: 289 VKEGDVLIGKTSPPRFLEEPDDFGISPE-KRRETSVTMRSGEEGIVDTVILTETEEGSRL 347
Query: 918 VKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTI 977
VKVRVR +RIP++GDKF+SRHGQKG +G+ QEDMP+T G+ PD+I+NPHAIPSRMT+
Sbjct: 348 VKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTV 407
Query: 978 GQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTA 1037
G ++E I GKV + G+ D T F+ +++ +AL K G++ G E MY+G TG ++ A
Sbjct: 408 GHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEA 467
Query: 1038 MIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGA 1097
IF+G YYQ+L HMV +K+H+R RGPVQ+LTRQP EGR+R+GGLRFGEMERD +I HGA
Sbjct: 468 EIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGA 527
Query: 1098 SHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLF 1157
+ LKERL D+SD ++VC CG+IAI + K+N C C +TDI V + YA KLL
Sbjct: 528 AMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLL 587
Query: 1158 QELMAMAIAPRM 1169
EL ++ IAPR+
Sbjct: 588 DELKSLGIAPRL 599
>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 = 541 bits (1397), Expect = 0.0
Identities = 189/379 (49%), Positives = 249/379 (65%), Gaps = 12/379 (3%)
Query: 706 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 765
G+ AS+IPF DHNQSPR TYQ AMGKQA+GIY N R D Y+L YPQKPLV T A+
Sbjct: 1 GIVASLIPFVDHNQSPRITYQCAMGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAV 60
Query: 766 EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKM-GT 824
E F +LP G NA+VA+ Y+GYNQED++I+N+SS+DRG F S+ + Y E +K
Sbjct: 61 EKGGFGELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHIKEYEIEARKTKLG 120
Query: 825 LVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---G 881
++E P + +Y KLD+DG+ G V D+++GK TP + + G
Sbjct: 121 PIEEITRDPPNVSE-----EAYRKLDEDGIVRVGAEVKPGDILVGKITPKGEKLLRAIFG 175
Query: 882 QASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQK 941
+ +R +D S+ ++H E G VD V + N G++ VKV +R R PQ+GDKF+SRHGQK
Sbjct: 176 EKAR-DVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQVGDKFASRHGQK 234
Query: 942 GTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPF 1001
G V QEDMP+T +GI PDII+NPH +PSRMTIGQL+E ++GK AA +GK DATPF
Sbjct: 235 GVVSKILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFIDATPF 294
Query: 1002 TDVT--VDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHS 1059
+ V++I + L + GY G E +Y+G TG A IF+GP YYQ+LKHMVDDKIH+
Sbjct: 295 DGASEDVEDIGELLKEAGYNAYGKEVLYDGRTGEPFKAPIFVGPIYYQKLKHMVDDKIHA 354
Query: 1060 RGRGPVQILTRQPAEGRSR 1078
R GP +LT+QP GRSR
Sbjct: 355 RSTGPYSLLTQQPLGGRSR 373
>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 = 475 bits (1224), Expect = e-158
Identities = 179/410 (43%), Positives = 229/410 (55%), Gaps = 16/410 (3%)
Query: 40 GLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGE 99
GLV QQLDSF+ F+ +QE +DE IE E P +I L+KP + ESDG+
Sbjct: 1 GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDE---EPEFSLKVGQIKLAKPKIKESDGK 57
Query: 100 TATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSY 159
T ++P+ ARLRNLTYS+PLYV V TE + KVFIGK+P+MLRS+
Sbjct: 58 TREIYPREARLRNLTYSSPLYVPAELTVNN--------TEEIEKEKVFIGKIPLMLRSNA 109
Query: 160 CTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVA 219
C L SE +L +LGECP D GGYFI+NGSEKV+I Q + S N YVFKK + Y A
Sbjct: 110 CILNGASESELVKLGECPLDPGGYFIVNGSEKVIINQIQRSPNIYYVFKKDKNGIRIYSA 169
Query: 220 EVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVAD 279
+ S R T ++ +R ++ + L EI + ++ +
Sbjct: 170 SIISNRGRSLRLEITSKGKIYARINSGAKLIMFVLLLALGLNLVEIILNLLVPEVDLEIQ 229
Query: 280 KDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKE 339
DI + D T +P LEE FVIQ Q ALDYIG RG+ G R++RI A
Sbjct: 230 DDIGINDEEDEFLTD-----KPELEEQFVIQTQDEALDYIGGRGSAKGFPRERRILGAVG 284
Query: 340 ILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLG 399
IL +LPH+G + T KA GY+IHRLLL ALGR DD DH GNKRL LAG LL
Sbjct: 285 ILDLNLLPHLGVSENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGELLQ 344
Query: 400 GLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATG 449
FR+L +L RDVR +QKC+ D LQ + +K ITSG++Y L TG
Sbjct: 345 SQFRILLNRLERDVRERIQKCLKKKFDFTLQNLVNSKPITSGIRYFLGTG 394
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 430 bits (1107), Expect = e-139
Identities = 205/529 (38%), Positives = 313/529 (59%), Gaps = 35/529 (6%)
Query: 24 TQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDF 83
ED + AYF+E LVR +DS+++F+ N +Q+I+DE IE + G +
Sbjct: 1 MMEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIET----EIEDGVYVEL 56
Query: 84 AEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDF 143
+I + KP++ E+DG ++P ARLRNLTYSAPLY++++ ++ GEE ++
Sbjct: 57 GKIRVGKPVVKEADGSEREIYPMEARLRNLTYSAPLYLEMS--PVE---GGEE----EEP 107
Query: 144 TKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNH 203
+V+IG++P+M+ S C LY SE++L E+GE P D GGYFI+NGSE+VL+ E ++ N
Sbjct: 108 EEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNK 167
Query: 204 VYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRT 263
+ V K + VA+V S R T + R + G + + P +
Sbjct: 168 ILVEKDERYGDRIEVAKVFSQ-RRGYRALVT-----VERN--RDG----LLEVSFPSVPG 215
Query: 264 EIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRG 323
IP +I+ RALG D++I+E + D + +++ + +LEEA + Q+ AL+YIGKR
Sbjct: 216 SIPFVILMRALGLETDEEIVEAVSDDPE---IVKFMLENLEEA-EVDTQEEALEYIGKRV 271
Query: 324 ATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDR 383
A G T++ RIK A+ ++ + +LPH+G KA+Y G + ALGRR EDD+
Sbjct: 272 AP-GQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDK 330
Query: 384 DHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLK 443
DHY NKRL LAG L+ LFR+ F +L RDV+ +++ ++++++ A+++ +T L+
Sbjct: 331 DHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLE 390
Query: 444 YSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQW 503
+++ATGNW G R GVSQ+L+R Y +TLSHLRR+ SP+ R + R LH +QW
Sbjct: 391 HAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQW 445
Query: 504 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEE 552
G +CP+ETPEG CGLVKN A MV I+ G + E L+E G E
Sbjct: 446 GRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPERG 494
>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 = 197 bits (502), Expect = 8e-58
Identities = 73/200 (36%), Positives = 102/200 (51%), Gaps = 22/200 (11%)
Query: 200 STNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLP 259
+N +YV K+ N S S K G+ + + P
Sbjct: 1 RSNGIYVEKELDKNGIGAT--YTSSLISNR-----------GSWL-KLEIDGKTLIWSRP 46
Query: 260 YIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYI 319
+ +IPI+I +ALG V+D++IL+ +CYDF D QM+ELL+P LEEA I Q+ ALDYI
Sbjct: 47 SKKRKIPIVIFLKALGLVSDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYI 106
Query: 320 GKRGATVGVTRDKRIKYAKEILQK-----EMLPHVGTGDFCETK--KAYYFGYIIHRLLL 372
GK A + + R++ A+EIL + H+G + E + KA Y+I RLL
Sbjct: 107 GKGFA-LRRGEEPRLQRAREILYSRDPKYNLNKHLGLNEPFENERLKAQDILYMIDRLLN 165
Query: 373 CALGRRAEDDRDHYGNKRLD 392
LGRR DD DH GNKR+
Sbjct: 166 LKLGRRKPDDIDHLGNKRVR 185
>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 = 202 bits (516), Expect = 5e-53
Identities = 119/363 (32%), Positives = 189/363 (52%), Gaps = 34/363 (9%)
Query: 772 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE--EKKMGTLVKED 829
+L G N +VA ++GYN ED++++++ + F S+ Y E + K+G E+
Sbjct: 670 ELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG---PEE 726
Query: 830 FGR--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ------- 880
R P+ S + LD++G+ G V D+++GK TP + E
Sbjct: 727 ITRDIPNVSED------ALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLR 780
Query: 881 ---GQASRYTRRDHSISLRHSETGMVDQVLLTTNADG-------LRFVKVRVRSVRIPQI 930
G+ +R R D S+ + G V V + + +G + VKV + R Q+
Sbjct: 781 AIFGEKARDVR-DTSLRVPPGVEGTVIDVKVFSRKEGDELPPGVNKLVKVYIAQKRKIQV 839
Query: 931 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 990
GDK + RHG KG V EDMP+ +G DI++NP +PSRM IGQ++E +G
Sbjct: 840 GDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGK 899
Query: 991 HMGKEGD--ATPFTD-VTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQ 1047
+G++G ATP D + + I + L K G G +Y+G TG + + +G Y
Sbjct: 900 KLGRKGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDNPVTVGYMYML 959
Query: 1048 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFD 1107
+L H+VDDK+H+R GP ++T+QP G+++ GG RFGEME + A+GA++ L+E L
Sbjct: 960 KLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1019
Query: 1108 QSD 1110
+SD
Sbjct: 1020 KSD 1022
Score = 65.5 bits (160), Expect = 2e-10
Identities = 47/156 (30%), Positives = 76/156 (48%), Gaps = 24/156 (15%)
Query: 376 GRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNL---QFA 432
G+ DD DH GN+R+ G LL FR+ ++ R VR + +D + Q
Sbjct: 314 GKGEVDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM-----TTQDTDTLTPQDL 368
Query: 433 IKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--R 488
I AK I++ +K + +SQ +++ + L+H RRL++ P G R
Sbjct: 369 INAKPISAAIKEFFGSSQ------------LSQFMDQTNPLAELTHKRRLSALGPGGLTR 416
Query: 489 EGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 524
E + R +H + +G +CP ETPEG GL+ +L+
Sbjct: 417 ERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS 452
Score = 52.4 bits (126), Expect = 1e-06
Identities = 43/170 (25%), Positives = 70/170 (41%), Gaps = 44/170 (25%)
Query: 32 ISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIE-----IRPESQHNPGQQSDFAEI 86
I E L+ QLDS+D F+Q + +E I P + + ++
Sbjct: 11 IPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNMELEYLSY 70
Query: 87 YLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKV 146
L +P + + R LTYS PL V + R+I K DG + + Q+ V
Sbjct: 71 ELGEPKYD----------VEECKERGLTYSVPLKVKL--RLINKEEDGTKEIKEQE---V 115
Query: 147 FIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQ 196
++G +P+M T+ G FIING+E+V+++Q
Sbjct: 116 YMGDIPLM----------------TDRGT--------FIINGAERVVVSQ 141
Score = 39.7 bits (93), Expect = 0.012
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 659 IEYIDTEEEETTMIS----------MTINDLVQARLHPE--EAYADTYTHCEIHPSLILG 706
+ Y+ +EE+ +I+ + DLV AR E + + ++ P I+
Sbjct: 481 VVYLTADEEDNYVIAQANAPLDENGRFVGDLVPARYRGEISLVSPEQVDYMDVSPKQIVS 540
Query: 707 VCASIIPFPDHNQSPRNTYQSAMGKQA 733
V AS+IPF +H+ + R S M +QA
Sbjct: 541 VAASLIPFLEHDDANRALMGSNMQRQA 567
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 185 bits (471), Expect = 1e-47
Identities = 136/505 (26%), Positives = 225/505 (44%), Gaps = 102/505 (20%)
Query: 699 IHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM------------------------ 734
I P + + S+IPF +HN + R S M +QA+
Sbjct: 512 ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGM 571
Query: 735 -------GI--YVTNYQFRM--DTLAYVLYYPQK-------------PLV---------- 760
GI V+ Y+ + D Y+ YY QK P+V
Sbjct: 572 TIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQ 631
Query: 761 ---TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRD 817
+++ +L G N +VA + GYN ED++++N+ + F S+ Y +
Sbjct: 632 ILADGSDIDN---SELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-E 687
Query: 818 EEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD 877
E + L E+ R N + S LD++G+ G++V D+++GK TP +
Sbjct: 688 IELRQTKLGSEEITR----NIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGES 743
Query: 878 EAQ----------GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRF-------VKV 920
+ G+ ++ + D S+ + + G V +V + + + G ++V
Sbjct: 744 DQLPEGKLLRAIFGEKAKDVK-DTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRV 802
Query: 921 RVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQL 980
+ +R Q+GDK + RHG KG + ++DMP+ +G PDII+NP +PSRM +GQL
Sbjct: 803 FIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQL 862
Query: 981 IECIMGKVAAHMGKEGDATPFTDVTVDNISKAL----HKCGYQMRGFETMYN-------- 1028
EC++G ++ K PF ++ S+ L ++N
Sbjct: 863 FECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMV 922
Query: 1029 ---GHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFG 1085
G TG + + +G Y +L H+VDDKIH+R GP ++T+QP G+++ GG RFG
Sbjct: 923 LRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFG 982
Query: 1086 EMERDCMIAHGASHFLKERLFDQSD 1110
EME + A GA++ LKE L +SD
Sbjct: 983 EMEVWALEAFGAAYTLKELLTIKSD 1007
Score = 75.5 bits (186), Expect = 1e-13
Identities = 87/374 (23%), Positives = 153/374 (40%), Gaps = 60/374 (16%)
Query: 173 LGECP-YDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRP 231
+G P Q G FIING E+V+++Q + + +Y FKK + + +
Sbjct: 96 IGNLPKMTQRGTFIINGLERVIVSQ-IIRSPGIY-FKKEIKKNSNKIYSATLIPNRGS-- 151
Query: 232 PSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQ 291
+++ + I + R + P+II +ALG + D+DI +
Sbjct: 152 ----WIKF-------ELDKNKEIWIRIDKNR-KKPLIIFLKALG-LTDQDIYSRLTKSEF 198
Query: 292 DTQMMELLRPSLEEAFVIQNQQVALDYIGK----RGATVGVTRD---------KRIKYAK 338
++ L+P L + N+++ L+ ATV K K
Sbjct: 199 ----LKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGK 254
Query: 339 EILQKEMLPHVGTGDFCETKKAYY--FGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGP 396
+ + ++ + + Y II +L+ + + DD DH N+R+ G
Sbjct: 255 -VGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGE 313
Query: 397 LLGGLFRMLFRKLTRDVRAYVQKCV-DNGKDVNLQFAIKAKTITSGLKYSLATGNWGQAN 455
LL FR+ ++L R +R + C D+ NL I K + + ++ +
Sbjct: 314 LLQNQFRIGLKRLERILRNRMTICDIDSLSKFNL---INPKPLIALIREFFGSSQ----- 365
Query: 456 AAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREG--KLAKP---RQLHNSQWGMMCPAE 510
+SQ +++ S L+H RR++ +G G K R +H S +G +CP E
Sbjct: 366 -------LSQYMDQTNPLSELTHKRRISI-LGPGGLDKDRISFAVRDIHPSHYGRICPIE 417
Query: 511 TPEGQACGLVKNLA 524
TPEG CGL+ +LA
Sbjct: 418 TPEGPNCGLIGSLA 431
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 167 bits (426), Expect = 5e-42
Identities = 125/361 (34%), Positives = 189/361 (52%), Gaps = 40/361 (11%)
Query: 776 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSY----RDEEKKMGTLVKEDFG 831
G N +VA ++GYN ED++++++ + F S+ Y RD K+G E+
Sbjct: 716 GQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARD--TKLG---PEEIT 770
Query: 832 R--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ--------- 880
R P+ S +R+ LD+ G+ G V D+++GK TP + E
Sbjct: 771 RDIPNVSEEA-LRN-----LDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAI 824
Query: 881 -GQASRYTRRDHSISLRHSETGMV-DQVLLTTNADG-------LRFVKVRVRSVRIPQIG 931
G+ +R +D S+ + H E G V D + T G + VKV + R Q+G
Sbjct: 825 FGEKAR-DVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVG 883
Query: 932 DKFSSRHGQKGTVGMTYTQEDMPWTVEGITP-DIIVNPHAIPSRMTIGQLIECIMGKVAA 990
DK + RHG KG V EDMP+ +G TP DI++NP +PSRM IGQ++E +G A
Sbjct: 884 DKMAGRHGNKGVVSRILPVEDMPYLEDG-TPVDIVLNPLGVPSRMNIGQILETHLGWAAK 942
Query: 991 HMGKEGDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRL 1049
+G + ATP F + I + L + G G T+Y+G TG + +G Y +L
Sbjct: 943 GLGIKF-ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKL 1001
Query: 1050 KHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQS 1109
H+VDDKIH+R GP ++T+QP G+++ GG RFGEME + A+GA++ L+E L +S
Sbjct: 1002 HHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1061
Query: 1110 D 1110
D
Sbjct: 1062 D 1062
Score = 59.7 bits (146), Expect = 9e-09
Identities = 76/315 (24%), Positives = 125/315 (39%), Gaps = 85/315 (26%)
Query: 45 QLDSFDEFIQNT-------MQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESD 97
QLDSFD F+Q ++E+ I P N +F L +P
Sbjct: 31 QLDSFDWFLQLDVPPEDEGLEEVFRS-----IFPIEDFNGNLSLEFVSYELGEPKYDV-- 83
Query: 98 GETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRS 157
+ + R LTYSAPL V + R+I K + E+ E Q+ V++G +P+M
Sbjct: 84 --------EECKERGLTYSAPLRVKL--RLINK--ETGEIKE-QE---VYMGDIPLM--- 124
Query: 158 SYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFK----KRQPN 213
TE G FIING+E+V+++Q S VY F K
Sbjct: 125 -------------TE--------NGTFIINGTERVIVSQLHRSPG-VY-FDHDKDKTSSG 161
Query: 214 KYAYVAEV---R-SMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIII 269
K Y A + R S E + P ++VR + R R ++P+ +
Sbjct: 162 KLLYSARIIPYRGSWLEFEFDPKDILYVR-IDR-------------------RRKLPVTV 201
Query: 270 VFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVT 329
+ RALG+ +D++IL+ + + +E+ L + ++ A +T
Sbjct: 202 LLRALGY-SDEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEIT 260
Query: 330 RDKRIKYAKEILQKE 344
+ Y + L+K+
Sbjct: 261 EELDGPYIRNTLEKD 275
Score = 49.3 bits (119), Expect = 1e-05
Identities = 52/158 (32%), Positives = 77/158 (48%), Gaps = 28/158 (17%)
Query: 376 GRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAY--VQKCVDNGKDVNLQFAI 433
G+ DD DH GN+R+ G LL FR+ ++ R VR +Q +D +L I
Sbjct: 359 GKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQD-LDTLTPQDL---I 414
Query: 434 KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVL---NRLTYASTLSHLRRLNS--PIG- 487
AK + + +K + Q +SQ + N L S L+H RRL++ P G
Sbjct: 415 NAKPVVAAIKEFFGSS---Q---------LSQFMDQTNPL---SELTHKRRLSALGPGGL 459
Query: 488 -REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 524
RE + R +H + +G +CP ETPEG GL+ +LA
Sbjct: 460 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLA 497
>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 = 132 bits (335), Expect = 1e-36
Identities = 36/93 (38%), Positives = 48/93 (51%), Gaps = 15/93 (16%)
Query: 1080 GGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCK 1139
GG RFGEME + A+GA++ L+ERL +SD VC CG A CK
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVCGRCGAYAA-----------ICK 45
Query: 1140 NKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 1172
KT I IP + KLL QEL ++ + R+ +
Sbjct: 46 GKTIIEPGDIPESFKLLLQELRSLGLDIRLFLE 78
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 136 bits (346), Expect = 2e-32
Identities = 105/372 (28%), Positives = 170/372 (45%), Gaps = 41/372 (11%)
Query: 772 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG 831
+L G N +VA + GYN ED+V++++ + + S R Y + + + + E
Sbjct: 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERIT 706
Query: 832 RP-DRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------- 880
+ +R+ LD +G+ G+ V D+++GK TP +E+
Sbjct: 707 KEIPHLEAHLLRN-----LDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRA 761
Query: 881 ---GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLR----FVKVRVRSVRIPQIGDK 933
Q S T ++ + L G V V G + V + R Q+GDK
Sbjct: 762 IFGIQVS--TSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDK 819
Query: 934 FSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMG 993
+ RHG KG + ++DMP+ +G D+++NP +PSRM +GQ+ EC++G +
Sbjct: 820 VAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLN 879
Query: 994 KEGDATPFTDVTVDNISKA-----LHKCGYQMRG---FETMY-------NGHTGRRLTAM 1038
+ PF + S+ L++ Q FE Y +G TG
Sbjct: 880 RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQP 939
Query: 1039 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAS 1098
+ +G Y +L H VDDKIH+R GP ++T+QP GRS+ GG R GEME + G +
Sbjct: 940 VTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVA 999
Query: 1099 HFLKERLFDQSD 1110
+ L+E L +SD
Sbjct: 1000 YILQEMLTYKSD 1011
Score = 53.0 bits (128), Expect = 1e-06
Identities = 40/153 (26%), Positives = 65/153 (42%), Gaps = 26/153 (16%)
Query: 381 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITS 440
DD DH NKR+ LL F + +L VR + + Q + + +T+
Sbjct: 304 DDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTT 363
Query: 441 GLK-----YSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIGREGKLA 493
+ + L SQ L++ + + H R+L+S P G G+ A
Sbjct: 364 TYESFFGSHPL-----------------SQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTA 406
Query: 494 --KPRQLHNSQWGMMCPAETPEGQACGLVKNLA 524
+ R +H S +G +CP +T EG GL+ +LA
Sbjct: 407 SFRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
Score = 46.4 bits (111), Expect = 1e-04
Identities = 68/260 (26%), Positives = 99/260 (38%), Gaps = 84/260 (32%)
Query: 40 GLVRQQLDSFDEFI-QNTMQEIVD----ESADIEIRPESQHNPGQQSDFAEIY-LSKPMM 93
G + Q + F FI Q +E+ E D EI + F E Y L +P++
Sbjct: 14 GFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQL---------FVETYQLVEPLI 64
Query: 94 TESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPI 153
E D A +LTYS+ LYV +I K + + Q+ T VFIG +P+
Sbjct: 65 KERD----------AVYESLTYSSELYVPA--GLIWK-----KSRDMQEQT-VFIGNIPL 106
Query: 154 MLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPN 213
M NS G FIING +V+I Q R P
Sbjct: 107 M----------NSL--------------GTFIINGIYRVVINQ-----------ILRSPG 131
Query: 214 KYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYI-RATLPYIRT----EIPII 268
Y Y RS + V + S GG I R + R +I I+
Sbjct: 132 IY-Y----RSELDHNGIS-----VYTGTIISDWGGRLELEIDRKARIWARVSRKQKISIL 181
Query: 269 IVFRALGFVADKDILEHICY 288
++ A+G ++IL+++CY
Sbjct: 182 VLLSAMGL-NLREILDNVCY 200
>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 = 110 bits (277), Expect = 3e-29
Identities = 37/62 (59%), Positives = 47/62 (75%)
Query: 564 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFI 623
++VNG VG HR+PE LV+TLR LRR+ ++ EV VVR+IR +E+RI TD GR RPL I
Sbjct: 1 VYVNGKLVGTHRNPEELVETLRELRRKGKISPEVSVVRNIRQREIRINTDAGRICRPLII 60
Query: 624 VE 625
VE
Sbjct: 61 VE 62
>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 = 104 bits (261), Expect = 6e-27
Identities = 33/68 (48%), Positives = 43/68 (63%), Gaps = 2/68 (2%)
Query: 465 QVLNRLTYASTLSHLRRLN--SPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKN 522
QVL++ + S LSH RR+N + +E K + R LH SQ+G +CP ETPEG CGLV +
Sbjct: 1 QVLDQTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNS 60
Query: 523 LALMVYIT 530
LAL I
Sbjct: 61 LALYARIN 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 = 78.0 bits (193), Expect = 6e-18
Identities = 26/52 (50%), Positives = 32/52 (61%), Gaps = 6/52 (11%)
Query: 650 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHP 701
+ DL+ +G IEY+D EEEET MI+M+ DL E T THCEIHP
Sbjct: 1 FVDLLKEGVIEYLDAEEEETAMIAMSPEDL------RLEDITKTTTHCEIHP 46
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 86.1 bits (213), Expect = 9e-17
Identities = 43/114 (37%), Positives = 65/114 (57%), Gaps = 1/114 (0%)
Query: 998 ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDK 1056
A P F ++ + K M G +Y+G TG ++ + +G Y +L H+VD+K
Sbjct: 1215 AIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEK 1274
Query: 1057 IHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSD 1110
+H+R GP ++T QP G++ GG RFGEME + A+GA+H LKE L +SD
Sbjct: 1275 VHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
Score = 74.2 bits (182), Expect = 4e-13
Identities = 33/81 (40%), Positives = 50/81 (61%)
Query: 915 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 974
++ VK+ + + R ++GDK + RHG KG V DMP+T +G DI++NP +PSR
Sbjct: 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSR 1134
Query: 975 MTIGQLIECIMGKVAAHMGKE 995
M IGQ++E +G V GK+
Sbjct: 1135 MNIGQILEMHLGLVGKEFGKQ 1155
Score = 63.4 bits (154), Expect = 7e-10
Identities = 52/155 (33%), Positives = 76/155 (49%), Gaps = 30/155 (19%)
Query: 381 DDRDHYGNKRLDLAGPLLG-----GLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKA 435
DDRDH GN+R+ G LL GL +M +K +D + D+ +L + +
Sbjct: 455 DDRDHLGNRRIRAVGELLANELHSGLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNS 509
Query: 436 KTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAK- 494
K ITS + G GQ +SQ +++ S ++H RRL S +G EG L K
Sbjct: 510 KMITSTI-MEFFMG--GQ---------LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKD 555
Query: 495 -----PRQLHNSQWGMMCPAETPEGQACGLVKNLA 524
R +H + +G +CP ETPEGQ GL+ L+
Sbjct: 556 RVGFEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
Score = 40.7 bits (95), Expect = 0.007
Identities = 28/104 (26%), Positives = 51/104 (49%), Gaps = 9/104 (8%)
Query: 772 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRS--LFFRSYRDEEKKMGTLVKED 829
+L G N VA ++GYN ED++++++ F S ++ + E K G E+
Sbjct: 803 ELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGV---EE 859
Query: 830 FGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 873
F + ++ + LD+ G+ GT VS +++GKT+P
Sbjct: 860 FTA----DIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSP 899
Score = 37.6 bits (87), Expect = 0.052
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 676 INDLVQARLHPEEAYADT--YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQA 733
+ DL++ R+ E + T ++ S+++GV AS+IPF +H+ + R + M +QA
Sbjct: 644 LGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQA 703
Query: 734 M 734
+
Sbjct: 704 V 704
Score = 34.5 bits (79), Expect = 0.50
Identities = 41/190 (21%), Positives = 74/190 (38%), Gaps = 59/190 (31%)
Query: 106 KAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTK--VFIGKVPIML-RSSYCTL 162
+ A R +TYS PL + V + +K E +D + +FI ++P+M R+S
Sbjct: 83 REAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMTERTS---- 138
Query: 163 YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQP----NKYAYV 218
FIING E+V++ Q S +FK+ + NK Y
Sbjct: 139 ---------------------FIINGVERVVVNQLHRSPG--VIFKEEESSTSLNKLIYT 175
Query: 219 AEV----RSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 274
++ S + ++ R+ R ++P+ I+FRA+
Sbjct: 176 GQIIPDRGSWLYFEYDSKDVLYARINK--------------------RRKVPVTILFRAM 215
Query: 275 GFVADKDILE 284
+ +DI++
Sbjct: 216 DY-QKQDIIK 224
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 82.0 bits (202), Expect = 1e-15
Identities = 40/104 (38%), Positives = 61/104 (58%)
Query: 1007 DNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQ 1066
+ I+K G G +Y+G +G + + +G Y +L H+VD KIH+R GP
Sbjct: 1283 EQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYS 1342
Query: 1067 ILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSD 1110
++T+QP G+S GG RFGEME + A+GA++ L+E L +SD
Sbjct: 1343 LVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
Score = 65.8 bits (160), Expect = 2e-10
Identities = 31/78 (39%), Positives = 45/78 (57%)
Query: 918 VKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTI 977
VKV + Q GDK + RHG KG + EDMP+ +G DII+NP +PSRM +
Sbjct: 1071 VKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNV 1130
Query: 978 GQLIECIMGKVAAHMGKE 995
GQ++E +G +G++
Sbjct: 1131 GQILETHVGWACKKLGEK 1148
Score = 62.3 bits (151), Expect = 1e-09
Identities = 56/195 (28%), Positives = 91/195 (46%), Gaps = 21/195 (10%)
Query: 366 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGK 425
I+ +++L G+ + DD DH GN+R+ G + FR KL R A V +
Sbjct: 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLER---AVVDSMSTSSL 505
Query: 426 D-VNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS 484
D V+ I K +T+ L+ + +SQ +++ S ++H RRL++
Sbjct: 506 DKVSPSDFINPKVLTNVLRDFFNSSQ------------LSQFMDQTNPLSEITHKRRLSA 553
Query: 485 --PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPIL 539
P G RE + R +H + +G +CP ETPEGQ GL+ +LA+ I G P
Sbjct: 554 LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYR 613
Query: 540 EFLEEWGTENFEEIS 554
+ + T+ E +S
Sbjct: 614 KVVNRVVTDQIEYLS 628
Score = 43.8 bits (103), Expect = 7e-04
Identities = 30/104 (28%), Positives = 49/104 (47%), Gaps = 9/104 (8%)
Query: 772 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 829
+L G N +VA + GYN EDS+I++ + + F S+ + + +G+ E
Sbjct: 813 ELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGS---EK 869
Query: 830 FGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 873
R G+ + LDD G+ GTRV +++GK TP
Sbjct: 870 ITRA----IPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTP 909
Score = 31.1 bits (70), Expect = 5.0
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 691 ADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 734
+D ++ ++ P ++ V AS+IPF +++ + R S M +QA+
Sbjct: 668 SDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAV 711
>gnl|CDD|133123 cd06592, GH31_glucosidase_KIAA1161, KIAA1161 is an uncharacterized
Homo sapiens protein with a glycosyl hydrolase family 31
(GH31) domain that is homologous to the Escherichia coli
YihQ glucosidase. Orthologs of KIA1161 are found in
eukaryotes and prokaryotes. In bacteria, YihQ (along
with YihO) is important for bacterial O-antigen capsule
assembly and translocation. Enzymes of the GH31 family
possess a wide range of different hydrolytic activities
including alpha-glucosidase (glucoamylase and
sucrase-isomaltase), alpha-xylosidase,
6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein.
Length = 303
Score = 33.3 bits (77), Expect = 0.65
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 12/63 (19%)
Query: 214 KYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRA 273
++ + EVR+ SQ P +FVRM+ + S+ GG +G +++ IP +
Sbjct: 195 EFGDLIEVRAGWRSQGLP---LFVRMMDKDSSWGGDNG---------LKSLIPTALTMGL 242
Query: 274 LGF 276
LG+
Sbjct: 243 LGY 245
>gnl|CDD|117964 pfam09424, YqeY, Yqey-like protein. The function of this domain
found in the YqeY protein is uncertain.
Length = 143
Score = 32.2 bits (74), Expect = 0.69
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 7/58 (12%)
Query: 13 QQEEEDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVD-ESADIEI 69
+QEE DE E++ E+ V++ V+Q+ +S ++F + Q++ + E A+I I
Sbjct: 31 KQEEVDERIELSDEEVLTVLA------KEVKQRRESIEQFEKAGRQDLAEKEKAEIAI 82
>gnl|CDD|133872 PHA00380, PHA00380, tail protein.
Length = 599
Score = 31.4 bits (71), Expect = 3.2
Identities = 24/118 (20%), Positives = 40/118 (33%), Gaps = 8/118 (6%)
Query: 36 FEEKGLVRQQLDSFD---EFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPM 92
F+ +VR+ + + + NT+ E +D + + P + F I M
Sbjct: 123 FQPSYIVREHQTEWQSNGKPVVNTIDEGLDYGTEYDTVYVEHFKPYEDLMFLVIISKSEM 182
Query: 93 MTESDGETATLFPKAARLRNL-----TYSAPLYVDVTKRVIKKGHDGEEVTETQDFTK 145
T +GE +A Y P Y D T G + E + +D K
Sbjct: 183 HTTEEGEQFKAGQISASFNGAPQPLVYYLHPFYRDGTGPKPVIGVNHFERSPVEDVLK 240
>gnl|CDD|212088 cd11519, SLC5sbd_SMCT1, Na(+)/monocarboxylate cotransporter SMCT1
and related proteins; solute-binding domain. SMCT1 is a
high-affinity transporter of various monocarboxylates
including lactate and pyruvate, short-chain fatty acids,
ketone bodies, nicotinate and its structural analogs,
pyroglutamate, benzoate and its derivatives, and iodide.
Human SMCT1 (hSMCT1, also called AIT) is encoded by the
tumor suppressor gene SLC5A8. Its expression is under
the control of the C/EBP transcription factor. Its
tumor-suppressive role is related to uptake of butyrate,
propionate, and pyruvate, these latter are inhibitors of
histone deacetylases. SMCT1 is expressed in the colon,
small intestine, kidney, thyroid gland, retina, and
brain. SMCT1 may contribute to the intestinal/colonic
and oral absorption of monocarboxylate drugs. SMCT1 also
mediates iodide transport from thyrocyte into the
colloid lumen in thyroid gland and through transporting
l-lactate and ketone bodies helps maintain the energy
status and the function of neurons. In the kidney its
expression is limited to the S3 segment of the proximal
convoluted tubule (in contrast to the low-affinity
monocarboxylate transporter SMCT2, belonging to a
different family, which is expressed along the entire
length of the tubule). In the retina, SMCT1 and SMCT2
may play a differential role in monocarboxylate
transport in a cell type-specific manner, SMCT1 is
expressed predominantly in retinal neurons and in
retinal pigmented epithelial (RPE) cells. This subgroup
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 541
Score = 31.3 bits (71), Expect = 3.9
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 504 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYP 537
G++ P G GLV A+ +++ +G+ YP
Sbjct: 425 GILFPFANSIGALVGLVSGFAISLWVGIGAQIYP 458
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.1 bits (70), Expect = 5.0
Identities = 11/25 (44%), Positives = 20/25 (80%)
Query: 3 EDDYDYEEQHQQEEEDEEEEITQED 27
E++ + EE+ ++EEE+EEEE +E+
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEEE 888
Score = 30.7 bits (69), Expect = 5.9
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 3 EDDYDYEEQHQQEEEDEEEEITQ 25
E++ + EE+ ++EEE+EEEE +
Sbjct: 870 EEEEEEEEEEEEEEEEEEEENEE 892
Score = 30.3 bits (68), Expect = 7.0
Identities = 10/25 (40%), Positives = 19/25 (76%)
Query: 3 EDDYDYEEQHQQEEEDEEEEITQED 27
E++ + EE+ ++EEE+EEEE + +
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEENE 891
Score = 30.3 bits (68), Expect = 8.0
Identities = 11/25 (44%), Positives = 20/25 (80%)
Query: 3 EDDYDYEEQHQQEEEDEEEEITQED 27
E++ + EE+ ++EEE+EEEE +E+
Sbjct: 866 EEEEEEEEEEEEEEEEEEEEEEEEN 890
Score = 30.3 bits (68), Expect = 9.0
Identities = 11/24 (45%), Positives = 19/24 (79%)
Query: 3 EDDYDYEEQHQQEEEDEEEEITQE 26
E++ + EE+ ++EEE+EEEE +E
Sbjct: 869 EEEEEEEEEEEEEEEEEEEEENEE 892
>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355). This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 180 and
214 amino acids in length.
Length = 125
Score = 29.1 bits (66), Expect = 5.0
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 16/78 (20%)
Query: 3 EDDYDYEEQHQQEE-EDEEEEITQEDAWAVISAYFEEKGL---------------VRQQL 46
E+ +YE + ++E E+ E E+ + + A EKGL + +
Sbjct: 44 EEKAEYELEKLEKELEELEAELARRELKAEAKKMLSEKGLPVELLDLVVGEDAEETKANV 103
Query: 47 DSFDEFIQNTMQEIVDES 64
+F + ++ V E
Sbjct: 104 KAFKKLFDKAVEAGVKER 121
>gnl|CDD|212074 cd11505, SLC5sbd_SMCT, Na(+)/monocarboxylate cotransporters SMCT1
and 2 and related proteins; solute-binding domain.
SMCT1 is a high-affinity transporter of various
monocarboxylates including lactate and pyruvate,
short-chain fatty acids, ketone bodies, nicotinate and
its structural analogs, pyroglutamate, benzoate and its
derivatives, and iodide. Human SMCT1 (hSMCT1, also
called AIT) is encoded by the tumor suppressor gene
SLC5A8. SMCT1 is expressed in the colon, small
intestine, kidney, thyroid gland, retina, and brain.
SMCT1 may contribute to the intestinal/colonic and oral
absorption of monocarboxylate drugs. It also mediates
iodide transport from thyrocyte into the colloid lumen
in thyroid gland and, through transporting L-lactate and
ketone bodies, helps maintain the energy status and the
function of neurons. SMCT2 is a low-affinity transporter
for short-chain fatty acids, lactate, pyruvate, and
nicotinate. hSMCT2 is encoded by the SLC5A12 gene. SMCT2
is expressed in the kidney, small intestine, skeletal
muscle, and retina. In the kidney, SMCT2 may initiate
lactate absorption in the early parts of the tubule,
SMCT1 in the latter parts of the tubule. In the retina,
SMCT1 and SMCT2 may play a differential role in
monocarboxylate transport in a cell type-specific
manner. This subgroup belongs to the solute carrier 5
(SLC5) transporter family.
Length = 536
Score = 30.5 bits (69), Expect = 6.0
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 504 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYP 537
G++ P +G GL+ A+ +++ +G+ YP
Sbjct: 425 GILFPFANSKGALSGLLTGFAISLWVGIGAQIYP 458
>gnl|CDD|222925 PHA02743, PHA02743, Viral ankyrin protein; Provisional.
Length = 166
Score = 29.4 bits (66), Expect = 7.2
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 285 HICYDFQDTQMMELLR 300
HI Y +D +MME+LR
Sbjct: 133 HIAYKMRDRRMMEILR 148
>gnl|CDD|237613 PRK14109, PRK14109, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 1007
Score = 30.2 bits (69), Expect = 9.2
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 575 RDPEMLVKTLR-RLRRRVDVNTEVGVVRDIRLKEL-RI 610
R E L + L R D V R +R +EL RI
Sbjct: 638 RSREALARELLAAASRHDDPERAVAAARALRRRELLRI 675
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
0.320 0.136 0.401
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 61,480,797
Number of extensions: 6224023
Number of successful extensions: 5823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5715
Number of HSP's successfully gapped: 65
Length of query: 1186
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1078
Effective length of database: 6,147,370
Effective search space: 6626864860
Effective search space used: 6626864860
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 (28.8 bits)