RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 003180
(842 letters)
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 1024 bits (2651), Expect = 0.0
Identities = 402/833 (48%), Positives = 540/833 (64%), Gaps = 26/833 (3%)
Query: 2 LPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRML 61
LPH+GT KKAY+ G + +LL LGRR DD+DHY NKRL LAG LL LFR+
Sbjct: 290 LPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVA 349
Query: 62 FRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQ 121
F++L +D++ ++K G+ ++L+ ++ IT ++++LATGNW G R GVSQ
Sbjct: 350 FKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV-----GGRTGVSQ 404
Query: 122 VLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLAL 181
+L+R Y STLSHLRR+ SP+ R + R LH +QWG +CP ETPEG CGLVKNLAL
Sbjct: 405 LLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLAL 464
Query: 182 MVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLR 241
M I+VG + E L E G EE +++++NG +G H D E L + +R
Sbjct: 465 MAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIR 524
Query: 242 RLRRRVDVNTEVGV--VRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRE 299
LRR ++ EV V + + E+ + D GR RPL +VE + + + + L++ E
Sbjct: 525 ELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE 584
Query: 300 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSL 359
+ DLV G IEY+D EEEE +++ DL PE +TH EI P
Sbjct: 585 LT----FDDLVKMGVIEYLDAEEEENAYVALDPEDLT-----PE------HTHLEIWPPA 629
Query: 360 ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTR 419
ILG+ ASIIP+P+HNQSPRNTYQ+AM KQ++G+Y N++ R DT ++L+YPQ+PLV TR
Sbjct: 630 ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTR 689
Query: 420 AMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 479
A+E + + PAG NA+VA+ Y+GYN ED++IMN++SI+RG RS FFR+Y EE+K
Sbjct: 690 ALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYP 749
Query: 480 TLVKEDFGRPDRSNTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQ 538
++ P+ N G R Y KLD+DG+ P V G DV+IGKT+P E +
Sbjct: 750 GGQEDKIEIPE-PNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEE 808
Query: 539 ASRYT--RRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQ 596
S RRD S+++RH E G+VD VL+T + +G + VKVRVR +RIP++GDKF+SRHGQ
Sbjct: 809 LSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQ 868
Query: 597 KGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATP 656
KG +GM QEDMP+T +GI PD+I+NPHAIPSRMT+GQL+E I GKVAA G+ DATP
Sbjct: 869 KGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATP 928
Query: 657 FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSR 716
F + + K L K GY+ G E MY+G TG ++ A IF+G YYQ+L HMV DKIH+R
Sbjct: 929 FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHAR 988
Query: 717 GRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHC 776
RGPVQILTRQP EGR+R+GGLRFGEMERDC+I HGA+ LKERL D SD ++VCE C
Sbjct: 989 ARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELC 1048
Query: 777 GLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 829
G IA + +KN + C +K +I V + YA KLL QELM+M I+PR+ +
Sbjct: 1049 GHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGD 1101
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 888 bits (2298), Expect = 0.0
Identities = 284/851 (33%), Positives = 412/851 (48%), Gaps = 88/851 (10%)
Query: 1 MLPHVGTG----DFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGG 56
+LPH+G D KA +I L+ LG+ EDD DH GN+RL L G LL
Sbjct: 278 LLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLEN 337
Query: 57 LFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTR 116
LFR+ ++ RDV+ ++K + I + ++L TG +G R
Sbjct: 338 LFRVGLSRMERDVKERLEKAD------KRDTLVPQDLINAKPIHALITGFFG-------R 384
Query: 117 AGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGL 175
+ +SQ +++ S LSH RRL++ + RE + R +H + +G +CP ETPEG GL
Sbjct: 385 SQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVRDVHPTHYGRICPIETPEGPNIGL 444
Query: 176 VKNLALMVYIT-VGSAAYPILEFL-EEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDP 233
+K+LAL I G P + L + E +S ++V G G +P
Sbjct: 445 IKSLALYARINEYGFLETPYRKVLDGSLVVDEIEYLSADE----EDVYVIGQANGTLDEP 500
Query: 234 EMLVKTLRRLRRRVDVNTEVGVVRDIRLK----ELRIYTDYGRCSRPLFIVEKQRLLIKK 289
LV+ L RR EV V + + GR P + +
Sbjct: 501 GELVEELVECRRGGS--GEVSVADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMG 558
Query: 290 RDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADT 349
++ Q++ P LV G +EY+D E+ +I+ P
Sbjct: 559 SNM---QRQAVPLLRTEAPLVGTG-MEYLDAEDSGAAVIAK----------RPGV----- 599
Query: 350 YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLY 409
TH EI P +ILG+ AS+IP+P+HNQSP N Y+ A QA GI R DT+ L
Sbjct: 600 VTHVEISPIVILGIEASLIPYPEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLV 659
Query: 410 YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFR 469
Y P V T +L G NA+VA ++GYN ED++I+++ S++R F S+
Sbjct: 660 YADGPSVDTG--------ELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFTSIHIE 711
Query: 470 SYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 529
Y E + +E P+ S LD+DG+ G V G D+++GK TP
Sbjct: 712 EYETEARDTKLGPEEIRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTP 765
Query: 530 ISQDEAQGQASRYT-----RRDHSISLRHSETGMVDQVLLTTNADG----LRFVKVRVRS 580
+ E + RD S+ + H E G+VD V + T DG + VKV V
Sbjct: 766 KGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQ 825
Query: 581 VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 640
R PQIGDK + RHG KG V QEDMP+ +G PDII+NP +PSRM IGQ++E
Sbjct: 826 KRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETH 885
Query: 641 MGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPT 700
+GK AA +G D F ++I + L + G+ G E +Y+G TG A IF+G
Sbjct: 886 LGKAAALLGIPVDTPVFDGAPEEDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVM 945
Query: 701 YYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKER 760
YYQ+L HMVDDKIH+R GP ++T+QP G+++ GG RFGEME + A+GA++ L+ER
Sbjct: 946 YYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 1005
Query: 761 LFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMA 820
L +SD CG I I +EC +I +V IP + K+L +EL ++
Sbjct: 1006 LTVKSDDV-------CGRIKI-------YECIVK--GENIPEVGIPESFKVLLKELRSLG 1049
Query: 821 IAPRMLTKEDT 831
I R+ ++
Sbjct: 1050 IDVRLELEDGK 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: 348 DTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYV 407
TH EI PS IL V AS+IPFP+HNQSPRN YQS M KQA+G N Q+RMDT Y+
Sbjct: 393 KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYL 452
Query: 408 LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLF 467
L YPQKPLV T E++ F +LP G NAIVA+ YSGYN ED++I+N+SS+DRGFFRS+
Sbjct: 453 LLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIH 512
Query: 468 FRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKT 527
++ Y E +K K R + + LD+DG+ PG RV D+++GK
Sbjct: 513 YKKYEIELRK----TKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKI 568
Query: 528 TPISQDEA--QGQASRYTRRDHSISLRHSETGMVDQVLLTT---NADGLRFVKVRVRSVR 582
TP + E+ RD S+ E G+VD V + + N G + VKV +R R
Sbjct: 569 TPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKR 628
Query: 583 IPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMG 642
PQIGDKF+SRHGQKG + QEDMP+T +GI PDII+NPH PSRMTIGQL+E ++G
Sbjct: 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLG 688
Query: 643 KVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYY 702
K A +GK GDATPF ++IS+ L + G G E +Y+G TG L A IF+GP YY
Sbjct: 689 KAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYY 748
Query: 703 QRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLF 762
QRLKHMVDDKIH+R GP +LTRQP +GRSR GG RFGEMERD +IAHGA++ L+ERL
Sbjct: 749 QRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLT 808
Query: 763 DQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIA 822
+SD VC CG+I ANL CR CK T+I +V IPYA KLLFQEL +M I
Sbjct: 809 IKSDDVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQSMNID 862
Query: 823 PRM 825
PR+
Sbjct: 863 PRL 865
Score = 254 bits (652), Expect = 2e-72
Identities = 87/174 (50%), Positives = 112/174 (64%), Gaps = 1/174 (0%)
Query: 14 KKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYV 73
K+ Y+I +L+L LG+ DD DH GNKR+ LAG LL LFR ++L R+V+ +
Sbjct: 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKL 267
Query: 74 QKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLS 133
QK + KD+ Q I +K ITSG+K LATGNWG R+G+SQVL+RL S LS
Sbjct: 268 QKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELS 327
Query: 134 HLRRLNS-PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT 186
H RR++S + RE K + R LH S WG +CP ETPEG+ CGLVKNLALM I+
Sbjct: 328 HKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 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 = 748 bits (1933), Expect = 0.0
Identities = 294/613 (47%), Positives = 401/613 (65%), Gaps = 19/613 (3%)
Query: 220 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFI 279
+++NG +G H DPE LV+ +R+LRR ++ EV V E+ I D GR RPL +
Sbjct: 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIV 60
Query: 280 VEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQAR 339
VE + + + + L++ E W DLV +G IEY+D EEEE I++ +L
Sbjct: 61 VENGKPKLTREHVEKLKEGELT----WDDLVKQGVIEYLDAEEEENAYIALDPEELT--- 113
Query: 340 LHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF 399
+TH EI PS ILG+ AS IP+P+HNQSPRNT +AM KQ++G+Y NY+
Sbjct: 114 --------PEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRI 165
Query: 400 RMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 459
R+DT ++L+YPQKPLV TR +E + + PAG N +VA+ Y GYN ED++IMN++SI+
Sbjct: 166 RLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225
Query: 460 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMR-HGSYDKLDDDGLAPPGTRVS 518
RG RS FFR+Y EE++ ++ F P+ + G R +Y LD+DG+ P V
Sbjct: 226 RGLARSTFFRTYEAEERRYPGGQEDRFEIPE-PDVRGYRGEEAYKHLDEDGIVYPEVEVK 284
Query: 519 GEDVIIGKTTP--ISQDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKV 576
G DV+IGKT+P ++ + RRD S+++RH E G+VD+V++T +G + VKV
Sbjct: 285 GGDVLIGKTSPPRFLEELRELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKV 344
Query: 577 RVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQL 636
RVR +RIP++GDKF+SRHGQKG +GM QEDMP+T +GI PD+I+NPHAIPSRMT+GQL
Sbjct: 345 RVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQL 404
Query: 637 IECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 696
+E I GKVAA G+ D TPF + + K L K G++ G E MY+G TG +L A IF
Sbjct: 405 LEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
Query: 697 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 756
+G YYQ+L HMV DKIH+R RGPVQ+LTRQP EGR+R+GGLRFGEMERD +I HGA+
Sbjct: 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAML 524
Query: 757 LKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQEL 816
LKERL D+SD Y V+VCE+CG IA + +K + C C DI V + YA KLL EL
Sbjct: 525 LKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDEL 584
Query: 817 MAMAIAPRMLTKE 829
++ I+PR+ +
Sbjct: 585 KSLGISPRLELGD 597
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 733 bits (1895), Expect = 0.0
Identities = 287/612 (46%), Positives = 396/612 (64%), Gaps = 21/612 (3%)
Query: 218 TKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPL 277
K++VNG +G H DPE LV+ +R RR +++ EV V E+ I TD GR RPL
Sbjct: 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPL 64
Query: 278 FIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQ 337
+VE L+ + I L+ E + DLV +G IEY+D EEEE I++ DL
Sbjct: 65 IVVENGEPLLTEEHIEKLKNGEL----TFDDLVKQGVIEYLDAEEEENAYIAVYEEDL-- 118
Query: 338 ARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 397
+ +TH EI PSLILG+ A +IP+P+HN SPR T + M KQ++G+ NY
Sbjct: 119 ---------TEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANY 169
Query: 398 QFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSS 457
+ R DT ++L+YPQ PLV T+ E + F + PAG N +VA+ Y GYN ED++IMN++S
Sbjct: 170 KLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKAS 229
Query: 458 IDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMR-HGSYDKLDDDGLAPPGTR 516
I+RG RS FFR+Y EE++ ++ F PD + G R +Y LD+DGL P T
Sbjct: 230 IERGLGRSHFFRTYEGEERRYPGGQEDRFEIPD-KDVRGYRGEEAYRHLDEDGLVNPETE 288
Query: 517 VSGEDVIIGKTTP---ISQDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRF 573
V DV+IGKT+P + + + G + RR+ S+++R E G+VD V+LT +G R
Sbjct: 289 VKEGDVLIGKTSPPRFLEEPDDFGISPE-KRRETSVTMRSGEEGIVDTVILTETEEGSRL 347
Query: 574 VKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTI 633
VKVRVR +RIP++GDKF+SRHGQKG +G+ QEDMP+T G+ PD+I+NPHAIPSRMT+
Sbjct: 348 VKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTV 407
Query: 634 GQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTA 693
G ++E I GKV + G+ D T F+ +++ +AL K G++ G E MY+G TG ++ A
Sbjct: 408 GHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEA 467
Query: 694 MIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGA 753
IF+G YYQ+L HMV +K+H+R RGPVQ+LTRQP EGR+R+GGLRFGEMERD +I HGA
Sbjct: 468 EIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGA 527
Query: 754 SHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLF 813
+ LKERL D+SD ++VC CG+IAI + K+N C C +TDI V + YA KLL
Sbjct: 528 AMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLL 587
Query: 814 QELMAMAIAPRM 825
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: 362 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 421
G+ AS+IPF DHNQSPR TYQ AMGKQA+GIY N R D Y+L YPQKPLV T A+
Sbjct: 1 GIVASLIPFVDHNQSPRITYQCAMGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAV 60
Query: 422 EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKM-GT 480
E F +LP G NA+VA+ Y+GYNQED++I+N+SS+DRG F S+ + Y E +K
Sbjct: 61 EKGGFGELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHIKEYEIEARKTKLG 120
Query: 481 LVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---G 537
++E P + +Y KLD+DG+ G V D+++GK TP + + G
Sbjct: 121 PIEEITRDPPNVSE-----EAYRKLDEDGIVRVGAEVKPGDILVGKITPKGEKLLRAIFG 175
Query: 538 QASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQK 597
+ +R +D S+ ++H E G VD V + N G++ VKV +R R PQ+GDKF+SRHGQK
Sbjct: 176 EKAR-DVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQVGDKFASRHGQK 234
Query: 598 GTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPF 657
G V QEDMP+T +GI PDII+NPH +PSRMTIGQL+E ++GK AA +GK DATPF
Sbjct: 235 GVVSKILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFIDATPF 294
Query: 658 TDVT--VDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHS 715
+ V++I + L + GY G E +Y+G TG A IF+GP YYQ+LKHMVDDKIH+
Sbjct: 295 DGASEDVEDIGELLKEAGYNAYGKEVLYDGRTGEPFKAPIFVGPIYYQKLKHMVDDKIHA 354
Query: 716 RGRGPVQILTRQPAEGRSR 734
R GP +LT+QP GRSR
Sbjct: 355 RSTGPYSLLTQQPLGGRSR 373
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 206 bits (527), Expect = 3e-58
Identities = 91/208 (43%), Positives = 129/208 (62%), Gaps = 5/208 (2%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
+LPH+G KA+Y G + ALGRR EDD+DHY NKRL LAG L+ LFR+
Sbjct: 292 LLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRV 351
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 120
F +L RDV+ +++ ++++++ A+++ +T L++++ATGNW G R GVS
Sbjct: 352 AFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW-----VGGRTGVS 406
Query: 121 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
Q+L+R Y +TLSHLRR+ SP+ R + R LH +QWG +CP+ETPEG CGLVKN A
Sbjct: 407 QLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFA 466
Query: 181 LMVYITVGSAAYPILEFLEEWGTENFEE 208
MV I+ G + E L+E G E
Sbjct: 467 QMVEISTGEDEEEVKEILKELGVEPERG 494
>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 = 204 bits (520), Expect = 2e-54
Identities = 119/363 (32%), Positives = 189/363 (52%), Gaps = 34/363 (9%)
Query: 428 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE--EKKMGTLVKED 485
+L G N +VA ++GYN ED++++++ + F S+ Y E + K+G E+
Sbjct: 670 ELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG---PEE 726
Query: 486 FGR--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ------- 536
R P+ S + LD++G+ G V D+++GK TP + E
Sbjct: 727 ITRDIPNVSED------ALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLR 780
Query: 537 ---GQASRYTRRDHSISLRHSETGMVDQVLLTTNADG-------LRFVKVRVRSVRIPQI 586
G+ +R R D S+ + G V V + + +G + VKV + R Q+
Sbjct: 781 AIFGEKARDVR-DTSLRVPPGVEGTVIDVKVFSRKEGDELPPGVNKLVKVYIAQKRKIQV 839
Query: 587 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 646
GDK + RHG KG V EDMP+ +G DI++NP +PSRM IGQ++E +G
Sbjct: 840 GDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGK 899
Query: 647 HMGKEGD--ATPFTD-VTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQ 703
+G++G ATP D + + I + L K G G +Y+G TG + + +G Y
Sbjct: 900 KLGRKGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDNPVTVGYMYML 959
Query: 704 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFD 763
+L H+VDDK+H+R GP ++T+QP G+++ GG RFGEME + A+GA++ L+E L
Sbjct: 960 KLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1019
Query: 764 QSD 766
+SD
Sbjct: 1020 KSD 1022
Score = 65.9 bits (161), Expect = 6e-11
Identities = 47/156 (30%), Positives = 76/156 (48%), Gaps = 24/156 (15%)
Query: 32 GRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNL---QFA 88
G+ DD DH GN+R+ G LL FR+ ++ R VR + +D + Q
Sbjct: 314 GKGEVDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM-----TTQDTDTLTPQDL 368
Query: 89 IKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--R 144
I AK I++ +K + +SQ +++ + L+H RRL++ P G R
Sbjct: 369 INAKPISAAIKEFFGSSQ------------LSQFMDQTNPLAELTHKRRLSALGPGGLTR 416
Query: 145 EGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
E + R +H + +G +CP ETPEG GL+ +L+
Sbjct: 417 ERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS 452
Score = 39.7 bits (93), Expect = 0.007
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 315 IEYIDTEEEETTMIS----------MTINDLVQARLHPE--EAYADTYTHCEIHPSLILG 362
+ Y+ +EE+ +I+ + DLV AR E + + ++ P I+
Sbjct: 481 VVYLTADEEDNYVIAQANAPLDENGRFVGDLVPARYRGEISLVSPEQVDYMDVSPKQIVS 540
Query: 363 VCASIIPFPDHNQSPRNTYQSAMGKQA 389
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 = 187 bits (478), Expect = 4e-49
Identities = 137/505 (27%), Positives = 227/505 (44%), Gaps = 102/505 (20%)
Query: 355 IHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM------------------------ 390
I P + + S+IPF +HN + R S M +QA+
Sbjct: 512 ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGM 571
Query: 391 -------GI--YVTNYQFRM--DTLAYVLYYPQK-------------PLV---------- 416
GI V+ Y+ + D Y+ YY QK P+V
Sbjct: 572 TIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQ 631
Query: 417 ---TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRD 473
+++ +L G N +VA + GYN ED++++N+ + F S+ Y +
Sbjct: 632 ILADGSDIDN---SELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-E 687
Query: 474 EEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD 533
E + L E+ R N + S LD++G+ G++V D+++GK TP +
Sbjct: 688 IELRQTKLGSEEITR----NIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGES 743
Query: 534 EAQ----------GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRF-------VKV 576
+ G+ ++ + D S+ + + G V +V + + + G ++V
Sbjct: 744 DQLPEGKLLRAIFGEKAKDVK-DTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRV 802
Query: 577 RVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQL 636
+ +R Q+GDK + RHG KG + ++DMP+ +G PDII+NP +PSRM +GQL
Sbjct: 803 FIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQL 862
Query: 637 IECIMGKVAAHMGKEGDATPFTDVTVDNISKAL-HKCGYQ---MRGFETMYN-------- 684
EC++G ++ K PF ++ S+ L + Q ++N
Sbjct: 863 FECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMV 922
Query: 685 ---GHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFG 741
G TG + + +G Y +L H+VDDKIH+R GP ++T+QP G+++ GG RFG
Sbjct: 923 LRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFG 982
Query: 742 EMERDCMIAHGASHFLKERLFDQSD 766
EME + A GA++ LKE L +SD
Sbjct: 983 EMEVWALEAFGAAYTLKELLTIKSD 1007
Score = 69.3 bits (170), Expect = 7e-12
Identities = 49/165 (29%), Positives = 79/165 (47%), Gaps = 22/165 (13%)
Query: 22 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCV-DNG 80
II +L+ + + DD DH N+R+ G LL FR+ ++L R +R + C D+
Sbjct: 283 IIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSL 342
Query: 81 KDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS 140
NL I K + + ++ + +SQ +++ S L+H RR++
Sbjct: 343 SKFNL---INPKPLIALIREFFGSSQ------------LSQYMDQTNPLSELTHKRRISI 387
Query: 141 PIGREG--KLAKP---RQLHNSQWGMMCPAETPEGQACGLVKNLA 180
+G G K R +H S +G +CP ETPEG CGL+ +LA
Sbjct: 388 -LGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 168 bits (429), Expect = 6e-43
Identities = 125/361 (34%), Positives = 189/361 (52%), Gaps = 40/361 (11%)
Query: 432 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSY----RDEEKKMGTLVKEDFG 487
G N +VA ++GYN ED++++++ + F S+ Y RD K+G E+
Sbjct: 716 GQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARD--TKLG---PEEIT 770
Query: 488 R--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ--------- 536
R P+ S +R+ LD+ G+ G V D+++GK TP + E
Sbjct: 771 RDIPNVSEEA-LRN-----LDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAI 824
Query: 537 -GQASRYTRRDHSISLRHSETGMV-DQVLLTTNADG-------LRFVKVRVRSVRIPQIG 587
G+ +R +D S+ + H E G V D + T G + VKV + R Q+G
Sbjct: 825 FGEKAR-DVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVG 883
Query: 588 DKFSSRHGQKGTVGMTYTQEDMPWTVEGITP-DIIVNPHAIPSRMTIGQLIECIMGKVAA 646
DK + RHG KG V EDMP+ +G TP DI++NP +PSRM IGQ++E +G A
Sbjct: 884 DKMAGRHGNKGVVSRILPVEDMPYLEDG-TPVDIVLNPLGVPSRMNIGQILETHLGWAAK 942
Query: 647 HMGKEGDATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRL 705
+G + ATP F + I + L + G G T+Y+G TG + +G Y +L
Sbjct: 943 GLGIKF-ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKL 1001
Query: 706 KHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQS 765
H+VDDKIH+R GP ++T+QP G+++ GG RFGEME + A+GA++ L+E L +S
Sbjct: 1002 HHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1061
Query: 766 D 766
D
Sbjct: 1062 D 1062
Score = 49.7 bits (120), Expect = 6e-06
Identities = 52/158 (32%), Positives = 77/158 (48%), Gaps = 28/158 (17%)
Query: 32 GRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAY--VQKCVDNGKDVNLQFAI 89
G+ DD DH GN+R+ G LL FR+ ++ R VR +Q +D +L I
Sbjct: 359 GKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQD-LDTLTPQDL---I 414
Query: 90 KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVL---NRLTYASTLSHLRRLNS--PIG- 143
AK + + +K + Q +SQ + N L S L+H RRL++ P G
Sbjct: 415 NAKPVVAAIKEFFGSS---Q---------LSQFMDQTNPL---SELTHKRRLSALGPGGL 459
Query: 144 -REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
RE + R +H + +G +CP ETPEG GL+ +LA
Sbjct: 460 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLA 497
>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 = 159 bits (405), Expect = 1e-42
Identities = 56/105 (53%), Positives = 68/105 (64%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
+LPH+G + T KA GY+IHRLLL ALGR DD DH GNKRL LAG LL FR+
Sbjct: 290 LLPHLGVSENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGELLQSQFRI 349
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATG 105
L +L RDVR +QKC+ D LQ + +K ITSG++Y L TG
Sbjct: 350 LLNRLERDVRERIQKCLKKKFDFTLQNLVNSKPITSGIRYFLGTG 394
>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 = 6e-37
Identities = 36/93 (38%), Positives = 48/93 (51%), Gaps = 15/93 (16%)
Query: 736 GGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCK 795
GG RFGEME + A+GA++ L+ERL +SD VC CG A CK
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVCGRCGAYAA-----------ICK 45
Query: 796 NKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 828
KT I IP + KLL QEL ++ + R+ +
Sbjct: 46 GKTIIEPGDIPESFKLLLQELRSLGLDIRLFLE 78
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 137 bits (347), Expect = 5e-33
Identities = 105/372 (28%), Positives = 170/372 (45%), Gaps = 41/372 (11%)
Query: 428 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFG 487
+L G N +VA + GYN ED+V++++ + + S R Y + + + + E
Sbjct: 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERIT 706
Query: 488 RP-DRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ---------- 536
+ +R+ LD +G+ G+ V D+++GK TP +E+
Sbjct: 707 KEIPHLEAHLLRN-----LDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRA 761
Query: 537 ---GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLR----FVKVRVRSVRIPQIGDK 589
Q S T ++ + L G V V G + V + R Q+GDK
Sbjct: 762 IFGIQVS--TSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDK 819
Query: 590 FSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMG 649
+ RHG KG + ++DMP+ +G D+++NP +PSRM +GQ+ EC++G +
Sbjct: 820 VAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLN 879
Query: 650 KEGDATPFTDVTVDNISKA-----LHKCGYQMRG---FETMY-------NGHTGRRLTAM 694
+ PF + S+ L++ Q FE Y +G TG
Sbjct: 880 RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQP 939
Query: 695 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAS 754
+ +G Y +L H VDDKIH+R GP ++T+QP GRS+ GG R GEME + G +
Sbjct: 940 VTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVA 999
Query: 755 HFLKERLFDQSD 766
+ L+E L +SD
Sbjct: 1000 YILQEMLTYKSD 1011
Score = 53.0 bits (128), Expect = 6e-07
Identities = 40/153 (26%), Positives = 65/153 (42%), Gaps = 26/153 (16%)
Query: 37 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITS 96
DD DH NKR+ LL F + +L VR + + Q + + +T+
Sbjct: 304 DDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTT 363
Query: 97 GLK-----YSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIGREGKLA 149
+ + L SQ L++ + + H R+L+S P G G+ A
Sbjct: 364 TYESFFGSHPL-----------------SQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTA 406
Query: 150 --KPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
+ R +H S +G +CP +T EG GL+ +LA
Sbjct: 407 SFRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
>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 = 109 bits (275), Expect = 5e-29
Identities = 37/62 (59%), Positives = 47/62 (75%)
Query: 220 IFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFI 279
++VNG VG HR+PE LV+TLR LRR+ ++ EV VVR+IR +E+RI TD GR RPL I
Sbjct: 1 VYVNGKLVGTHRNPEELVETLRELRRKGKISPEVSVVRNIRQREIRINTDAGRICRPLII 60
Query: 280 VE 281
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 = 103 bits (258), Expect = 1e-26
Identities = 33/68 (48%), Positives = 43/68 (63%), Gaps = 2/68 (2%)
Query: 121 QVLNRLTYASTLSHLRRLN--SPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKN 178
QVL++ + S LSH RR+N + +E K + R LH SQ+G +CP ETPEG CGLV +
Sbjct: 1 QVLDQTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNS 60
Query: 179 LALMVYIT 186
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 = 80.3 bits (199), Expect = 7e-19
Identities = 26/52 (50%), Positives = 32/52 (61%), Gaps = 6/52 (11%)
Query: 306 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHP 357
+ 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 = 86.9 bits (215), Expect = 3e-17
Identities = 43/114 (37%), Positives = 65/114 (57%), Gaps = 1/114 (0%)
Query: 654 ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDK 712
A P F ++ + K M G +Y+G TG ++ + +G Y +L H+VD+K
Sbjct: 1215 AIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEK 1274
Query: 713 IHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSD 766
+H+R GP ++T QP G++ GG RFGEME + A+GA+H LKE L +SD
Sbjct: 1275 VHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
Score = 75.0 bits (184), Expect = 2e-13
Identities = 33/81 (40%), Positives = 50/81 (61%)
Query: 571 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 630
++ VK+ + + R ++GDK + RHG KG V DMP+T +G DI++NP +PSR
Sbjct: 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSR 1134
Query: 631 MTIGQLIECIMGKVAAHMGKE 651
M IGQ++E +G V GK+
Sbjct: 1135 MNIGQILEMHLGLVGKEFGKQ 1155
Score = 64.6 bits (157), Expect = 2e-10
Identities = 52/155 (33%), Positives = 76/155 (49%), Gaps = 30/155 (19%)
Query: 37 DDRDHYGNKRLDLAGPLLG-----GLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKA 91
DDRDH GN+R+ G LL GL +M +K +D + D+ +L + +
Sbjct: 455 DDRDHLGNRRIRAVGELLANELHSGLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNS 509
Query: 92 KTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAK- 150
K ITS + G GQ +SQ +++ S ++H RRL S +G EG L K
Sbjct: 510 KMITSTI-MEFFMG--GQ---------LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKD 555
Query: 151 -----PRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
R +H + +G +CP ETPEGQ GL+ L+
Sbjct: 556 RVGFEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
Score = 41.1 bits (96), Expect = 0.003
Identities = 28/104 (26%), Positives = 51/104 (49%), Gaps = 9/104 (8%)
Query: 428 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRS--LFFRSYRDEEKKMGTLVKED 485
+L G N VA ++GYN ED++++++ F S ++ + E K G E+
Sbjct: 803 ELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGV---EE 859
Query: 486 FGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 529
F + ++ + LD+ G+ GT VS +++GKT+P
Sbjct: 860 FTA----DIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSP 899
Score = 38.0 bits (88), Expect = 0.027
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 332 INDLVQARLHPEEAYADT--YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQA 389
+ DL++ R+ E + T ++ S+++GV AS+IPF +H+ + R + M +QA
Sbjct: 644 LGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQA 703
Query: 390 M 390
+
Sbjct: 704 V 704
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 82.7 bits (204), Expect = 6e-16
Identities = 40/104 (38%), Positives = 61/104 (58%)
Query: 663 DNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQ 722
+ I+K G G +Y+G +G + + +G Y +L H+VD KIH+R GP
Sbjct: 1283 EQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYS 1342
Query: 723 ILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSD 766
++T+QP G+S GG RFGEME + A+GA++ L+E L +SD
Sbjct: 1343 LVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
Score = 66.2 bits (161), Expect = 7e-11
Identities = 31/78 (39%), Positives = 45/78 (57%)
Query: 574 VKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTI 633
VKV + Q GDK + RHG KG + EDMP+ +G DII+NP +PSRM +
Sbjct: 1071 VKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNV 1130
Query: 634 GQLIECIMGKVAAHMGKE 651
GQ++E +G +G++
Sbjct: 1131 GQILETHVGWACKKLGEK 1148
Score = 63.1 bits (153), Expect = 6e-10
Identities = 56/195 (28%), Positives = 91/195 (46%), Gaps = 21/195 (10%)
Query: 22 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGK 81
I+ +++L G+ + DD DH GN+R+ G + FR KL R A V +
Sbjct: 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLER---AVVDSMSTSSL 505
Query: 82 D-VNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS 140
D V+ I K +T+ L+ + +SQ +++ S ++H RRL++
Sbjct: 506 DKVSPSDFINPKVLTNVLRDFFNSSQ------------LSQFMDQTNPLSEITHKRRLSA 553
Query: 141 --PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSAAYPIL 195
P G RE + R +H + +G +CP ETPEGQ GL+ +LA+ I G P
Sbjct: 554 LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYR 613
Query: 196 EFLEEWGTENFEEIS 210
+ + T+ E +S
Sbjct: 614 KVVNRVVTDQIEYLS 628
Score = 44.2 bits (104), Expect = 3e-04
Identities = 30/104 (28%), Positives = 49/104 (47%), Gaps = 9/104 (8%)
Query: 428 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 485
+L G N +VA + GYN EDS+I++ + + F S+ + + +G+ E
Sbjct: 813 ELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGS---EK 869
Query: 486 FGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 529
R G+ + LDD G+ GTRV +++GK TP
Sbjct: 870 ITRA----IPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTP 909
Score = 31.1 bits (70), Expect = 3.0
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 347 ADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 390
+D ++ ++ P ++ V AS+IPF +++ + R S M +QA+
Sbjct: 668 SDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAV 711
>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 = 73.5 bits (181), Expect = 6e-15
Identities = 22/50 (44%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 1 MLPHVGTGDFCETK--KAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLD 48
+ H+G + E + KA Y+I RLL LGRR DD DH GNKR+
Sbjct: 136 LNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
>gnl|CDD|212817 cd11884, SH3_MYO15, Src Homology 3 domain of Myosin XV. This
subfamily is composed of proteins with similarity to
Myosin XVa. Myosin XVa is an unconventional myosin that
is critical for the normal growth of mechanosensory
stereocilia of inner ear hair cells. Mutations in the
myosin XVa gene are associated with nonsyndromic hearing
loss. Myosin XVa contains a unique N-terminal extension
followed by a motor domain, light chain-binding IQ
motifs, and a tail consisting of a pair of MyTH4-FERM
tandems separated by a SH3 domain, and a PDZ domain. SH3
domains bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP motifs;
they play a role in the regulation of enzymes by
intramolecular interactions, changing the subcellular
localization of signal pathway components and mediate
multiprotein complex assemblies.
Length = 56
Score = 28.4 bits (64), Expect = 1.9
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 270 YGRCSRPLFIVEKQRLL-IKKRDIIALQQRESPEDGGW 306
Y R +I Q LL K D+I L +E P D GW
Sbjct: 1 YVVAVRA-YITRDQTLLSFHKGDVIKLLPKEGPLDPGW 37
>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 = 30.9 bits (70), Expect = 3.0
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 160 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYP 193
G++ P G GLV A+ +++ +G+ YP
Sbjct: 425 GILFPFANSIGALVGLVSGFAISLWVGIGAQIYP 458
>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 = 4.7
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 160 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYP 193
G++ P +G GL+ A+ +++ +G+ YP
Sbjct: 425 GILFPFANSKGALSGLLTGFAISLWVGIGAQIYP 458
>gnl|CDD|187771 cd09640, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily
protein Cas7. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas7 is a RAMP superfamily protein; Subunit of the
Cascade complex; also known as CT1132 family.
Length = 258
Score = 29.5 bits (66), Expect = 6.5
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 244 RRRVDVNTEVGVVRDIRLKELRIYTDY-GRCSRPLFIVEKQRLLIKKRDIIALQQRESPE 302
R D T GVV D+R+K R +Y + +F+ K+R+ K R Q + +
Sbjct: 27 MPRTDAETGYGVVSDVRIK--RKVRNYLQDMGKSIFVQTKERIEDKFRSEKRFSQHFTAK 84
Query: 303 DG 304
G
Sbjct: 85 TG 86
>gnl|CDD|181495 PRK08596, PRK08596, acetylornithine deacetylase; Validated.
Length = 421
Score = 30.0 bits (68), Expect = 6.5
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 594 HGQKGTVGMTYTQEDMPWTVEGITPDIIVNP------HAIPSRMTIGQLIE 638
+ + M+ T D W E P +I P H++ ++ I QLIE
Sbjct: 353 LSKNAILDMSTTVTDGGWFAEFGIPAVIYGPGTLEEAHSVNEKVEIEQLIE 403
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 29.9 bits (68), Expect = 6.9
Identities = 15/84 (17%), Positives = 26/84 (30%), Gaps = 24/84 (28%)
Query: 204 ENFEEISPAVIPQATKIFVNGCWV----GIHRDPEMLVKTLRRLR--------------- 244
+ KI + + G+ E + K L+RL
Sbjct: 251 SVVIVGGDEKLTPPRKIELRLERINRLLGLELSAEEIEKILKRLGFKVEVKGDGLTVTVP 310
Query: 245 -RRVDVNTEVGVVRDIRLKELRIY 267
RVD+ E ++ ++ RIY
Sbjct: 311 SYRVDILIEADLIEEV----ARIY 330
>gnl|CDD|237613 PRK14109, PRK14109, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 1007
Score = 29.8 bits (68), Expect = 8.0
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 231 RDPEMLVKTLR-RLRRRVDVNTEVGVVRDIRLKEL-RI 266
R E L + L R D V R +R +EL RI
Sbjct: 638 RSREALARELLAAASRHDDPERAVAAARALRRRELLRI 675
>gnl|CDD|214611 smart00313, PXA, Domain associated with PX domains. unpubl.
observations.
Length = 176
Score = 28.5 bits (64), Expect = 9.1
Identities = 32/184 (17%), Positives = 60/184 (32%), Gaps = 31/184 (16%)
Query: 207 EEISPAVIPQATKIFVNGCWVGIHRDPEMLVK-------TLRRLRRRVDVNTEVGVVRDI 259
E + +I + + +V G + G+ DP L + LR+L RR+ ++
Sbjct: 6 EPLQL-LISKIIRDYVQGWYKGVSEDPSFLREIEQTLEYILRQLYRRLSRQDSAHLIL-- 62
Query: 260 RLKELRIYTDYG-RCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYI 318
I + + L V + I LQ E+ H +
Sbjct: 63 ----YEILKNLISTITNALEAVLRFASPQIPSTEIDLQYAET----AIHKAL-------- 106
Query: 319 DTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPR 378
+ E T + L++ L PE++ + H + ++ I+P H P
Sbjct: 107 SSPSNELTYRRQLVEMLLK-FLLPEDS-LCSRLHRCLLREVL--AMQVILPLITHLSDPD 162
Query: 379 NTYQ 382
Sbjct: 163 TINL 166
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
0.322 0.137 0.414
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 43,615,133
Number of extensions: 4381759
Number of successful extensions: 3300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3240
Number of HSP's successfully gapped: 51
Length of query: 842
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 737
Effective length of database: 6,280,432
Effective search space: 4628678384
Effective search space used: 4628678384
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: 63 (28.2 bits)