RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046825
(1208 letters)
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 466 bits (1201), Expect = e-147
Identities = 251/733 (34%), Positives = 351/733 (47%), Gaps = 164/733 (22%)
Query: 341 WMNLQQSVNVLFD----GKNAAGQRDMASG-----ICQLLEKKEGLFRQKLMGKRVNYAC 391
W LQ V FD G A R SG + Q L+ KEG FR L GKRVN++
Sbjct: 268 WELLQYHVTTYFDNEIPGIPPARHR---SGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 324
Query: 392 RSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKL 451
R+VISPDP L++NE+G+P A LT PERVT WN+ +LR+ ++NG E HPGA Y+ +
Sbjct: 325 RTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGAN-YVIR- 382
Query: 452 STMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEF------EGKMVYRHLQDGDVVLV 505
P +++++ D + E G +V RHL DGD+VL
Sbjct: 383 -----PDGRRIKL-----------------TDKNKEELAEKLEPGWIVERHLIDGDIVLF 420
Query: 506 NRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYN 565
NRQP+LH+ SIMAH VRVL G KT R++ A C YNADFDGDEMN+H PQ E +RAEA
Sbjct: 421 NRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARI 479
Query: 566 IVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSF 625
++ + P G P+ IQDHI A LLT+K T ++E LL ++G+
Sbjct: 480 LMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGID------- 532
Query: 626 TGKPGQRVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLP 685
E+ PAI +P WTGKQ+ + LP
Sbjct: 533 ---------------ELPEPEPAIENGKPYWTGKQIFSLF------------------LP 559
Query: 686 QDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEK 745
+D N K K + + KE
Sbjct: 560 KDL------------------------NLEFKAKICSGCDECK--------------KED 581
Query: 746 ELSEEKLLIYKNDLVRGVIDKAQFADYG--LVHTVQELYGSNTAGTLLSALSRLFTVFLQ 803
+ ++I L+ GVIDK ++ + + YG A L +++RL F+
Sbjct: 582 CEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIM 641
Query: 804 MHGFTCGVDDLLILKDKERERKNHLHGSE-------EIGKRVHLEAL---ELEDGAEIDP 853
+ GFT G+DD I ++ + E + +E E + LE L LE+ E
Sbjct: 642 LRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLE--- 698
Query: 854 IKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMT 913
+K+ + KA G+ A Y + + +VI M
Sbjct: 699 MKIMQVLGKARDEAGEIAEKYLGL---------DNPAVI-------------------MA 730
Query: 914 TSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTG 973
+GA+GS +N Q+++ +GQQ + G+R+ R +TLP F P D A GF+ + +G
Sbjct: 731 RTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSG 790
Query: 974 LRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFC 1033
L P E++FH M GREGLVDTAV+TS+SGY+QR LI L+ LK+ YD +VRD G+IVQF
Sbjct: 791 LTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFK 850
Query: 1034 YGEDGVDVHQTSF 1046
YGEDGVD ++
Sbjct: 851 YGEDGVDPMKSDH 863
Score = 69.5 bits (171), Expect = 8e-12
Identities = 29/66 (43%), Positives = 39/66 (59%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRK 60
CKTCG R CPGHFGHI+L PV + L+Y LL+ C C K + E+E+ + K
Sbjct: 61 CKTCGGRAGECPGHFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEK 120
Query: 61 LELIIK 66
LE + +
Sbjct: 121 LERLKE 126
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 449 bits (1157), Expect = e-141
Identities = 268/828 (32%), Positives = 387/828 (46%), Gaps = 166/828 (20%)
Query: 242 LLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPS--- 298
L PS++++ +EK+ + + EL K A L V+ VPP+ R PS
Sbjct: 173 LTPSEIRERLEKIPDEDAELLGINP--------KVARPEWMVLTVLPVPPVTVR-PSITL 223
Query: 299 -KGGDSVMEHPQTVLLSKVLQANIYLANAYV-NQPDNAKVIVARWMNLQQSVNVLFD--- 353
G S E T L +++ N L P +I W LQ V FD
Sbjct: 224 ETGERS--EDDLTHKLVDIIRINQRLKENIEAGAPQL--IIEDLWELLQYHVATYFDNEL 279
Query: 354 -GKNAAGQRD--MASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPP 410
G A R + Q L+ KEG FR L GKRVN++ R+VISPDP +++NE+G+P
Sbjct: 280 PGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPE 339
Query: 411 YFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKL 470
A LT PERVTPWN+ +LR+ ++NG + PGA + + P ++++I K
Sbjct: 340 QIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIR-------PDGRRIKIRDENKE 392
Query: 471 DTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTL 530
+ ++ G +V RHL DGD+VL NRQP+LH+ S+M H V+VL G KT
Sbjct: 393 EL-----------AERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPG-KTF 440
Query: 531 RMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHI 590
R++ A C YNADFDGDEMN+H PQ E +RAEA ++ + P G P+ I D+I
Sbjct: 441 RLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYI 500
Query: 591 VSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIW 650
A LLT K T ++E +L +G + G P + PAI
Sbjct: 501 SGAYLLTHKSTLFTKEEVQTILGVAG--------YFGDPPE---------------PAIE 537
Query: 651 KPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLS 710
KP+ WTGKQ+ +A LP+D
Sbjct: 538 KPKEYWTGKQIFSAF------------------LPEDL---------------------- 557
Query: 711 KTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA 770
N + K KE+ + ++I L++GVIDK
Sbjct: 558 --NFEGRAKICSSDAC---------------KKEECPHDAYVVIKNGKLLKGVIDKKAIG 600
Query: 771 DY--GLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHL 828
++H + YG A L +++RLF F+ + GFT G+DD+ I K+ + E + +
Sbjct: 601 AEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELI 660
Query: 829 HGSE-------EIGKRVHLEAL---ELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMK 878
+E E + LE L +E+ E +K+ + KA G+ A Y D
Sbjct: 661 EKAEKRVDNLIERYRNGELEPLPGRTVEETLE---MKIMEVLGKARDEAGEVAEKYLDP- 716
Query: 879 MTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEG 938
+ +VI M +GA+GS +N Q+++ +GQQ + G
Sbjct: 717 --------ENHAVI-------------------MARTGARGSLLNITQMAAMVGQQSVRG 749
Query: 939 KRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTS 998
R+ R +TLP F D +A GF+ F GL P EY+FH GREGLVDTAV+TS
Sbjct: 750 GRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTS 809
Query: 999 RSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSF 1046
+SGY+QR LI L+ L + YD +VRD G+++QF YGEDGVD ++
Sbjct: 810 QSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDH 857
Score = 59.0 bits (143), Expect = 1e-08
Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRK 60
CKTCG + CPGHFGHI+L PV + +Y +L+ C C + E+E+ + K
Sbjct: 56 CKTCGGKVGECPGHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTEEEIEQYLEK 115
Query: 61 L 61
+
Sbjct: 116 I 116
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 437 bits (1125), Expect = e-132
Identities = 287/998 (28%), Positives = 448/998 (44%), Gaps = 190/998 (19%)
Query: 242 LLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPS--- 298
LLP +++DI EK+ +++ EL F KKA L LVPP+ R PS
Sbjct: 186 LLPIEIRDIFEKIIDDDLELIGFDP--------KKARPEWAVLQAFLVPPLTAR-PSIIL 236
Query: 299 -KGGDSVMEHPQTVLLSKVLQANIYLANAY-VNQPDNAKVIVARWMNLQQSVNVLFDGKN 356
G S E T +L +++AN L + P ++ +LQ + FD
Sbjct: 237 ETGERS--EDDLTHILVDIIKANQKLKESKDAGAP--PLIVEDEVDHLQYHTSTFFDNAT 292
Query: 357 AA-------GQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIP 409
A G + Q L+ KEG FR L+GKRV+++ R+VISPDP + ++E+G+P
Sbjct: 293 AGIPQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVP 352
Query: 410 PYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRK 469
A++LT PE V N+ K+++ +ING + PGA +R K+R+
Sbjct: 353 EAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANA-------IRKGDGTKIRLDF--- 402
Query: 470 LDTSRGAIVQPGKDSDNEFE-----GKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVL 524
+ GKD+ E G +V RHL DGD+V+ NRQP+LHK SI+AH V+VL
Sbjct: 403 -------LEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVL 455
Query: 525 KGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRS 584
G T R+H A C YNADFDGDEMN+H PQ E +RAEA ++ + + P G P+
Sbjct: 456 PG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIG 514
Query: 585 LIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLP 644
+QD I +A L+TK D +++E + +G++ +P +
Sbjct: 515 ALQDFITAAYLITKDDALFDKNEASNIAMLAGITDP-----LPEPAIKT----------- 558
Query: 645 LLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKN 704
K P WTGKQ+ + LP+DF
Sbjct: 559 ------KDGPAWTGKQLFSLF------------------LPKDF---------------- 578
Query: 705 DKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVI 764
K K+G+ K+ L + +LI + +L+ GVI
Sbjct: 579 ---NFEGIAKWSAGKAGEAKD------------------PSCLGDGYVLIKEGELISGVI 617
Query: 765 DKAQFADY-----GLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKD 819
D L+ + + YG A L+ + + + +GF+ G DL+I +
Sbjct: 618 DDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDE 677
Query: 820 KERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKM 879
++E ++ + G ++ + + + +I K K E+ + M+ +A A ++
Sbjct: 678 AKQEIEDDIQGMKDEVSDL---IDQRKITRKITIYKGKEELLRGMK-EEEALEADIVNEL 733
Query: 880 TSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQE---- 935
+K + S N+ + N +M +GA+GS N QI+ LGQQ+
Sbjct: 734 DKARDK--AGSSANDCID-------ADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTR 784
Query: 936 ----LEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLV 991
L G R+ + L F D P A GF+ + + GL E++FH M GREGL+
Sbjct: 785 IGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLI 844
Query: 992 DTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFD 1051
D A +T SGY QR L LE +++ YD +VRD G I+QF +GEDG+D + F+
Sbjct: 845 DKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDHGEAFN 904
Query: 1052 ------ALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDA 1105
+RG+G +++ E + K+ + +A+ LP
Sbjct: 905 LERIIEKQKIEDRGKGASKDEI--------------EELAKEYTKTFNAN------LPKL 944
Query: 1106 LKDNAEKFADKFLSNEMAKQDFLKLVKHKFVL----SLAQPGEPVGLLASQSVGEPSTQM 1161
L D + K+D L+ + + + +PG+ +G++++QS+ EP TQM
Sbjct: 945 LADA--------IHGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQM 996
Query: 1162 TLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVI 1199
TL TFH AG M+VT G+ R E L A TP +
Sbjct: 997 TLRTFHAAGIKAMDVTHGLERFIE-LVDARAKPSTPTM 1033
Score = 46.6 bits (110), Expect = 9e-05
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKA--SRREVEKCV 58
C TCG CPGHFGHI+L PV + + + LL C C K V K +
Sbjct: 61 CLTCGNLAANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLI 120
Query: 59 RK 60
+
Sbjct: 121 EE 122
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 395 bits (1017), Expect = e-122
Identities = 188/807 (23%), Positives = 287/807 (35%), Gaps = 181/807 (22%)
Query: 242 LLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPS--K 299
L P+ VK ++++L + L + L V+ VPP R PS
Sbjct: 156 LSPTKVKKLLKRLKVVDAFL---------LSGNRP---EWMILTVLPVPPPDLR-PSIQL 202
Query: 300 GGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAG 359
G E L +V+ N L ++ LQ++V+ LFD N
Sbjct: 203 DGGRFAESDLNDLYRRVINRNNRLKRLLELAAPI--IVRNEKRMLQEAVDALFD--NRRP 258
Query: 360 QRDMAS----GICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALR 415
+ + Q L+ K+G FRQ L+GKRV+Y+ RSVIS P L +N+ G+P AL
Sbjct: 259 RAVTGGRPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALE 318
Query: 416 LTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRG 475
L P VT N+ LR + R+L
Sbjct: 319 LFKPFVVTELNIEGLRTGAK--YAKRM-----------------------VERRLP---- 349
Query: 476 AIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYA 535
E V R + DGD VL+NR PTLH+ SIM VL K +R+H
Sbjct: 350 -------------EVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPL 396
Query: 536 NCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAAL 595
C YNADFDGDEM VH P + AEA ++ + P G P+ + IQD + L
Sbjct: 397 VCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYL 456
Query: 596 LTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLPAIWKPEPL 655
LT D L ++ ++E AI K L
Sbjct: 457 LTIVDAKLPSTPVGEIYLKD-------------------EYADDREK---AEAIAKKIEL 494
Query: 656 WTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKM 715
TGK +++ + + + T
Sbjct: 495 TTGKVIVSTIS-----------------------------------PDLAELSIIVTT-- 517
Query: 716 HKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKN-DLVRGVIDKAQFADYGL 774
D + + K + + ++ + IY+ + D
Sbjct: 518 --DGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKALVKLLD--- 572
Query: 775 VHTVQELYGSNTAGTLLSALSRLFTVFLQM-HGFTCGVDDLLILKDKERERKNHLHGSEE 833
+L + ++ GF G+ I + E E+ + E
Sbjct: 573 ---------------------KLKNLGIKGIGGFGIGIGRKDI--EAEDEKDEIV---IE 606
Query: 834 IGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVIN 893
V L+ + + ++ + + +E ++ L +
Sbjct: 607 AEGSV-LKLILQYEEGDLTRTERNNIVEI------------IEVLGIEALRNAIIEEIKI 653
Query: 894 ELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSF 953
L +GL + G G+++N QI +GQQ + G+++ + +F
Sbjct: 654 TLEEQGL-------DFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVL----ARAAF 702
Query: 954 HPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLEC 1013
A G FL GL EY+ H + GR GLVDTA+KT+ SGYL R L+ +
Sbjct: 703 EVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQD 762
Query: 1014 LKISYDYSVRDADGSIVQFCYGEDGVD 1040
L + D V D G ++QF YGEDG D
Sbjct: 763 LIVQEDDCVTDGIGVVIQFEYGEDGED 789
Score = 64.6 bits (158), Expect = 2e-10
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 3 TCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREV 54
TCG+ + +CPG FGHI+L PV + F + +LL C C V
Sbjct: 56 TCGKYKRICPGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCERVLYFEAYV 107
Score = 51.9 bits (125), Expect = 2e-06
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 1138 SLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAG--RGEMNVTLGIPRLQEILTIA-SKDI 1194
+A G A+++ G TQM + T H G + T+G P L LTI +K
Sbjct: 409 EMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYL---LTIVDAKLP 465
Query: 1195 KTPVIT 1200
TPV
Sbjct: 466 STPVGE 471
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 333 bits (856), Expect = e-105
Identities = 124/318 (38%), Positives = 169/318 (53%), Gaps = 32/318 (10%)
Query: 282 FFLGVVLVPPIKFRLPSKGGDS-VMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVAR 340
L V+ VPP R + E T LL +++ N L + +I
Sbjct: 3 MILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLEL-GAPSIIIRNE 61
Query: 341 WMNLQQSVNVLFDGKNAAGQRDMASG-----ICQLLEKKEGLFRQKLMGKRVNYACRSVI 395
LQ++V+ L D + + SG + Q L+ KEG FRQ L+GKRV+++ RSVI
Sbjct: 62 KRLLQEAVDTLIDN-EGLPRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVI 120
Query: 396 SPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMR 455
+PDP L +NE+G+P AL LT+PE VTP N+ KLR + NG GA + + T
Sbjct: 121 TPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNG---PNGAKYIIRGKKTN- 176
Query: 456 LPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPS 515
L KK +I+ + G +V RH+ DGDVVL NRQPTLH+ S
Sbjct: 177 LKLAKKSKIAN-------------------HLKIGDIVERHVIDGDVVLFNRQPTLHRMS 217
Query: 516 IMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVR 575
I AH VRVL+G KT+R++ CS YNADFDGDEMN+H PQ +RAEA ++ N +
Sbjct: 218 IQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILS 276
Query: 576 PSNGDPLRSLIQDHIVSA 593
P NG P+ IQD ++
Sbjct: 277 PKNGKPIIGPIQDMLLGL 294
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, 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). This
domain, domain 2, contains the active site. The
invariant motif -NADFDGD- binds the active site
magnesium ion.
Length = 165
Score = 234 bits (598), Expect = 4e-71
Identities = 86/187 (45%), Positives = 114/187 (60%), Gaps = 23/187 (12%)
Query: 384 GKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPG 443
GKRV+++ RSVI+PDP L ++E+G+P AL LT PE VT N+ KLR + NG + PG
Sbjct: 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPG 60
Query: 444 ATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNE-FEGKMVYRHLQDGDV 502
A + K + + K K E + G +V RH+ DGDV
Sbjct: 61 AKYIKR---------IKGAKRDLEYK------------KRIAIELWYGDIVLRHVIDGDV 99
Query: 503 VLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAE 562
VL+NRQPTLH+ SIMAH RVL+G KT+R++ + CS YNADFDGDEMN+H PQ E +RAE
Sbjct: 100 VLLNRQPTLHRMSIMAHRPRVLEG-KTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAE 158
Query: 563 AYNIVNA 569
A ++
Sbjct: 159 ARELMLV 165
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, 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). This domain, domain 5,
represents the discontinuous cleft domain that is
required to from the central cleft or channel where the
DNA is bound.
Length = 447
Score = 241 bits (617), Expect = 7e-70
Identities = 98/231 (42%), Positives = 130/231 (56%), Gaps = 23/231 (9%)
Query: 973 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQF 1032
GL PQE++FH M GREGL+DTAVKT+ +GYLQR L+K LE L + YD +VR++ G IVQF
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQF 60
Query: 1033 CYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCD-KGSHTFVMGRNQEMIYKKCSGQ 1091
YGEDG+D + G+GR + D K F + N ++
Sbjct: 61 LYGEDGLD-------------PLKIEGQGRFTIEDSDLKLEKKFKIDLNDVLLLLSEFSL 107
Query: 1092 LDASNAYIMELPDALKDNAEKFA--DKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLL 1149
+ L+ E + N A FL + K+ SL +PGE VG++
Sbjct: 108 STLLFEIL------LRSGIESKRVRSELTCNSKAGVCFLCYGRDKYRRSLVEPGEAVGII 161
Query: 1150 ASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVIT 1200
A+QS+GEP TQMTLNTFH AG NVTLG+PRL+EI+ +K+ K PVIT
Sbjct: 162 AAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEII-NVAKNNKKPVIT 211
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA
polymerase I (RNAP I), C-terminal domain. RNA polymerase
I (RNAP I) is a multi-subunit protein complex responsible
for the synthesis of rRNA precursor. It consists of at
least 14 different subunits, and the largest one is
homologous to subunit Rpb1 of yeast RNAP II and subunit
beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in
yeast. Structure studies suggest that different RNAP
complexes share a similar crab-claw-shape structure. The
C-terminal domain of Rpb1, the largest subunit of RNAP
II, makes up part of the foot and jaw structures of RNAP
II. The similarity between this domain and the C-terminal
domain of Rpb1, its counterpart in RNAP II, suggests a
similar functional and structural role.
Length = 309
Score = 158 bits (402), Expect = 9e-43
Identities = 56/75 (74%), Positives = 65/75 (86%)
Query: 1134 KFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKD 1193
K++ SL +PGE VGLLA+QS+GEPSTQMTLNTFH AGRGEMNVTLGIPRL+EIL ASK+
Sbjct: 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKN 60
Query: 1194 IKTPVITCPLLVGKT 1208
IKTP +T PL GK+
Sbjct: 61 IKTPSMTLPLKNGKS 75
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA
polymerase II (RNAP II), C-terminal domain. RNA
polymerase II (RNAP II) is a large multi-subunit complex
responsible for the synthesis of mRNA. RNAP II consists
of a 10-subunit core enzyme and a peripheral heterodimer
of two subunits. The largest core subunit (Rpb1) of yeast
RNAP II is the best characterized member of this family.
Structure studies suggest that RNAP complexes from
different organisms share a crab-claw-shape structure. In
yeast, Rpb1 and Rpb2, the largest and the second largest
subunits, each makes up one clamp, one jaw, and part of
the cleft. Rpb1 interacts with Rpb2 to form the DNA entry
and RNA exit channels in addition to the catalytic center
of RNA synthesis. The C-terminal domain of Rpb1 makes up
part of the foot and jaw structures.
Length = 410
Score = 119 bits (301), Expect = 1e-28
Identities = 44/76 (57%), Positives = 57/76 (75%), Gaps = 1/76 (1%)
Query: 1128 LKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIL 1187
L ++ +F SL PGE VG +A+QS+GEP+TQMTLNTFH AG NVTLG+PRL+EI+
Sbjct: 12 LGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII 71
Query: 1188 TIASKDIKTPVITCPL 1203
+A K+IKTP +T L
Sbjct: 72 NVA-KNIKTPSLTVYL 86
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA
polymerase III (RNAP III), C-terminal domain. Eukaryotic
RNA polymerase III (RNAP III) is a large multi-subunit
complex responsible for the synthesis of tRNAs, 5SrRNA,
Alu-RNA, U6 snRNA, among others. Rpc1 is also known as
C160 in yeast. Structure studies suggest that different
RNA polymerase complexes share a similar crab-claw-shape
structure. The C-terminal domain of Rpb1, the largest
subunit of RNAP II, makes up part of the foot and jaw
structures of RNAP II. The similarity between this domain
and the C-terminal domain of Rpb1, its counterpart in
RNAP II, suggests a similar functional and structural
role.
Length = 300
Score = 113 bits (285), Expect = 2e-27
Identities = 39/71 (54%), Positives = 53/71 (74%), Gaps = 1/71 (1%)
Query: 1134 KFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKD 1193
K++ + +PG VG +A+QS+GEP TQMTL TFH AG MN+TLG+PR++EI+ ASK+
Sbjct: 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIIN-ASKN 59
Query: 1194 IKTPVITCPLL 1204
I TP+IT L
Sbjct: 60 ISTPIITAKLE 70
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 114 bits (287), Expect = 5e-27
Identities = 49/105 (46%), Positives = 73/105 (69%), Gaps = 3/105 (2%)
Query: 1100 MELPDALKDN-AEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPS 1158
+ELP LK+ EK ++ L+ E ++ ++ V +++ SL +PGE VG++A+QS+GEP
Sbjct: 16 LELPQKLKEELREKLEERKLTEEEVEE-IIEEVVREYLRSLVEPGEAVGVVAAQSIGEPG 74
Query: 1159 TQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPL 1203
TQMT+ TFH AG E+NVTLG+PRL EI+ A K+ TP++T L
Sbjct: 75 TQMTMRTFHYAGVAEINVTLGLPRLIEIVD-ARKEPSTPMMTIYL 118
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 117 bits (294), Expect = 2e-26
Identities = 81/261 (31%), Positives = 124/261 (47%), Gaps = 50/261 (19%)
Query: 344 LQQSVNVLFD----GK--NAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+ LFD GK R + S + +L+ K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 281 LQEAVDALFDNGRRGKPVVGKNNRPLKS-LSDMLKGKQGRFRQNLLGKRVDYSGRSVIVV 339
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLP 457
P L + + G+P AL L P II A +
Sbjct: 340 GPELKMYQCGLPKKMALELFKP-------------FIIKRLIDRELAAN----------- 375
Query: 458 PNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIM 517
I +K+ I Q D E ++ +++ V+L NR PTLH+ I
Sbjct: 376 ------IKSAKKM------IEQ----EDPEVWD-VLEDVIKEHPVLL-NRAPTLHRLGIQ 417
Query: 518 AHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPS 577
A +++G K +R+H C+ +NADFDGD+M VH P ++AEA ++ A+N + P
Sbjct: 418 AFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPK 476
Query: 578 NGDPLRSLIQDHIVSAALLTK 598
+G P+ + QD ++ LT
Sbjct: 477 DGKPIVTPSQDMVLGLYYLTT 497
Score = 92.4 bits (230), Expect = 1e-18
Identities = 79/307 (25%), Positives = 135/307 (43%), Gaps = 54/307 (17%)
Query: 890 SVINELLSEGLLK-----PTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRM 944
S + +++ ++K N I +M SGA+G+ F+Q++ G + L K
Sbjct: 656 SETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARGNISQFRQLA---GMRGLMAK----- 707
Query: 945 VSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQ 1004
SG + P I F GL EY+ R+GL DTA+KT+ SGYL
Sbjct: 708 PSGDIIEL-------P-----IKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLT 755
Query: 1005 RCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGR-G 1063
R L+ ++ D VR+ D C E+G++V + ++R GR
Sbjct: 756 RRLVD------VAQDVVVREED------CGTEEGIEVEAIVEGKDEIIESLKDRIVGRYS 803
Query: 1064 RNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEK-FADKFLSNEM 1122
D + + N +I ++ + +++ S +++ L +E K ++
Sbjct: 804 AEDVYDPDTGKLIAEAN-TLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDL 862
Query: 1123 AKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAG--RGEMNVTLGI 1180
A L + GE VG++A+QS+GEP TQ+T+ TFH G ++T G+
Sbjct: 863 AT------------GKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGL 910
Query: 1181 PRLQEIL 1187
PR++E+
Sbjct: 911 PRVKELF 917
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein
[Transcription, DNA-dependent RNA polymerase].
Length = 367
Score = 106 bits (267), Expect = 1e-24
Identities = 45/101 (44%), Positives = 65/101 (64%), Gaps = 2/101 (1%)
Query: 1101 ELPDALKDN-AEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPST 1159
LP+ L E + +S++ + +K V+ +++ SL PGE VG++A+QS+GEP T
Sbjct: 1 VLPEKLLKELEETVKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGT 60
Query: 1160 QMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVIT 1200
QMT+ TFH AG E+NVTLG+PRL EI+ A K TP +T
Sbjct: 61 QMTMRTFHYAGVAELNVTLGLPRLIEIVD-ARKTPSTPSMT 100
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a
large multi-subunit complex responsible for the synthesis
of all RNAs in the cell. The relative positioning of the
RNAP core is highly conserved between archaeal RNAP and
the three classes of eukaryotic RNAPs. In archaea, the
largest subunit is split into two polypeptides, A' and
A'', which are encoded by separate genes in an operon.
Sequence alignments reveal that the archaeal A'' subunit
corresponds to the C-terminal one-third of the RNAPII
largest subunit (Rpb1). In subunit A'', several loops in
the jaw domain are shorter. The RNAPII Rpb1 interacts
with the second-largest subunit (Rpb2) to form the DNA
entry and RNA exit channels in addition to the catalytic
center of RNA synthesis.
Length = 363
Score = 105 bits (265), Expect = 2e-24
Identities = 45/98 (45%), Positives = 64/98 (65%), Gaps = 1/98 (1%)
Query: 1106 LKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNT 1165
LK+ E+ + ++ +K V +++ SL +PGE VG++A+QS+GEP TQMTL T
Sbjct: 3 LKEKLEEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRT 62
Query: 1166 FHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPL 1203
FH AG E+NVTLG+PRL EI+ A K+ TP +T L
Sbjct: 63 FHYAGVAEINVTLGLPRLIEIVD-ARKEPSTPTMTIYL 99
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 110 bits (277), Expect = 2e-24
Identities = 83/269 (30%), Positives = 128/269 (47%), Gaps = 57/269 (21%)
Query: 344 LQQSVNVLFD----GK--NAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+ LFD G+ G R + S + +L+ K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 377 LQEAVDSLFDNGRRGRPVTGPGNRPLKS-LADMLKGKQGRFRQNLLGKRVDYSGRSVIVV 435
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLP 457
P+L +++ G+P AL L P + +L +
Sbjct: 436 GPHLKLHQCGLPSAMALELFKP--------------------------FVMKRLVELEYA 469
Query: 458 PNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPTLHKP 514
N K K RGA V+ L++ VL+NR PTLH+
Sbjct: 470 ANIK-----AAKRAVDRGASY--------------VWDVLEEVIQDHPVLLNRAPTLHRL 510
Query: 515 SIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYV 574
I A +++G K +++H C+ +NADFDGD+M VH P ++AEA ++ ++N
Sbjct: 511 GIQAFEPVLVEG-KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIK 569
Query: 575 RPSNGDPLRSLIQDHIVSAALLT-KKDTF 602
P++G PL QD I+ LT ++D F
Sbjct: 570 SPAHGRPLTVPTQDMIIGVYYLTTERDGF 598
Score = 68.4 bits (167), Expect = 2e-11
Identities = 77/353 (21%), Positives = 126/353 (35%), Gaps = 89/353 (25%)
Query: 857 KSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVI----NELLSEGLLKP-TGKNWISL 911
K EI A ++ S+ +H I E + E +L N I +
Sbjct: 731 KPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYM 790
Query: 912 MTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDR-- 969
M SGA+G+ +Q++ G M K G IID
Sbjct: 791 MADSGARGNIKQIRQLAGMRGL----------MADMK---------------GEIIDLPI 825
Query: 970 ---FLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCL--------IKNLECLK--- 1015
F GL EY+ R+GLVDTA++T+ SGYL R L ++ +C
Sbjct: 826 KANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEG 885
Query: 1016 ISYDY--SVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSH 1073
++Y D D +++ C ED D + +S D + + + +
Sbjct: 886 VTYPLVKPKGDVDTNLIGRCLLEDVCDPNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIR 945
Query: 1074 TFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKH 1133
T + + + +KC G D + + + A+ +A Q
Sbjct: 946 TLMTCHAEYGVCQKCYG-WDLATRRPVNIGTAV-------------GIIAAQ-------- 983
Query: 1134 KFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEI 1186
S+ +PG TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 984 ----SIGEPG---------------TQLTMRTFHSGGVAGDDITQGLPRVAEL 1017
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 105 bits (264), Expect = 4e-23
Identities = 73/253 (28%), Positives = 115/253 (45%), Gaps = 52/253 (20%)
Query: 343 NLQQSVNVLFDGKNAAGQRDMASG-------ICQLLEKKEGLFRQKLMGKRVNYACRSVI 395
LQ++V+ L D N + M G ++E KEG FR+ L+GKRV+Y+ RSVI
Sbjct: 327 LLQEAVDALLD--NGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVI 384
Query: 396 SPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMR 455
P L++++ G+P A+ L P +R I
Sbjct: 385 VVGPSLSLHQCGLPREIAIELFQP--------FVIRGLIRQH------------------ 418
Query: 456 LPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPS 515
L N + S R+ + IV + + + G VL+NR PTLH+
Sbjct: 419 LASNIRAAKSKIRE----KEPIVWE------------ILQEVMQGHPVLLNRAPTLHRLG 462
Query: 516 IMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVR 575
I A +++G + + +H C +NADFDGD+M VH P ++AEA ++ ++ +
Sbjct: 463 IQAFQPILVEG-RAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLS 521
Query: 576 PSNGDPLRSLIQD 588
P+ GDP+ QD
Sbjct: 522 PAIGDPISVPSQD 534
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit.
The RNA polymerase gamma subunit, encoded by the rpoC1
gene, is found in cyanobacteria and corresponds to the
N-terminal region the beta' subunit, encoded by rpoC, in
other bacteria. The equivalent subunit in plastids and
chloroplasts is designated beta', while the product of
the rpoC2 gene is designated beta''.
Length = 619
Score = 105 bits (262), Expect = 5e-23
Identities = 74/259 (28%), Positives = 120/259 (46%), Gaps = 48/259 (18%)
Query: 344 LQQSVNVLFD----GKNAAGQRDMA-SGICQLLEKKEGLFRQKLMGKRVNYACRSVISPD 398
LQ++V+ L D G+ G + + ++E K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 300 LQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVG 359
Query: 399 PYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPP 458
P L +++ G+P A+ L P H L + +
Sbjct: 360 PKLKMHQCGLPKEMAIEL-----------------------FQPFVIHRLIRQGIVN--- 393
Query: 459 NKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMA 518
I +KL +Q D E V + + G V++NR PTLH+ I A
Sbjct: 394 ----NIKAAKKL-------IQRADD-----EIWSVLQEVITGHPVMLNRAPTLHRLGIQA 437
Query: 519 HVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSN 578
++ G + +++H C +NADFDGD+M VH P ++ EA ++ A+N + P+
Sbjct: 438 FEPILVDG-RAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPAT 496
Query: 579 GDPLRSLIQDHIVSAALLT 597
G+P+ + QD ++ LT
Sbjct: 497 GEPIVTPSQDMVLGCYYLT 515
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 103 bits (259), Expect = 1e-22
Identities = 79/264 (29%), Positives = 129/264 (48%), Gaps = 58/264 (21%)
Query: 344 LQQSVNVLFD----GKNAAG--QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+ L D G+ G R + S + ++E K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 307 LQEAVDALIDNGRRGRTVVGANNRPLKS-LSDIIEGKQGRFRQNLLGKRVDYSGRSVIVV 365
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKL-RDSIINGAEIHPGATHYLDKLSTMRL 456
P L +++ G+P A+ L P+ + +L R I+N
Sbjct: 366 GPKLKMHQCGLPKEMAIEL-----FQPFVIHRLIRQGIVNN------------------- 401
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQ---DGDVVLVNRQPTLHK 513
I +KL +Q V++ L+ +G VL+NR PTLH+
Sbjct: 402 -------IKAAKKL-------IQRADPE--------VWQVLEEVIEGHPVLLNRAPTLHR 439
Query: 514 PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQY 573
I A +++G + +++H C +NADFDGD+M VH P ++AEA ++ A+N
Sbjct: 440 LGIQAFEPILVEG-RAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNI 498
Query: 574 VRPSNGDPLRSLIQDHIVSAALLT 597
+ P+ G+P+ + QD ++ LT
Sbjct: 499 LSPATGEPIVTPSQDMVLGCYYLT 522
>gnl|CDD|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, 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). This
domain, domain 4, represents the funnel domain. The
funnel contain the binding site for some elongation
factors.
Length = 108
Score = 92.8 bits (231), Expect = 2e-22
Identities = 36/92 (39%), Positives = 49/92 (53%), Gaps = 5/92 (5%)
Query: 875 FDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQ 934
F+ + + LNK + S+ L N I +M SGAKGS +N QI+ GQQ
Sbjct: 22 FEALINNILNKARD--PAGNIASKSLDP---NNSIYMMADSGAKGSIINISQIAGCRGQQ 76
Query: 935 ELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFI 966
+EGKR+P SG+TLP F D P + GF+
Sbjct: 77 NVEGKRIPFGFSGRTLPHFKKDDEGPESRGFV 108
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 103 bits (259), Expect = 4e-22
Identities = 84/281 (29%), Positives = 128/281 (45%), Gaps = 53/281 (18%)
Query: 344 LQQSVNVLFDGK------NAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+ LFD N AG I +L+ K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 1731 LQEAVDSLFDNSRRNALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVV 1790
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLP 457
P L +N+ G+P AL L P KL +
Sbjct: 1791 GPTLKLNQCGLPKRMALELFKP--------------------------FVYSKLKMYGMA 1824
Query: 458 PNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIM 517
P I KL + V M+ +++ V+L NR PTLH+ I
Sbjct: 1825 PT----IKFASKLIRAEKPEVW-----------DMLEEVIKEHPVLL-NRAPTLHRLGIQ 1868
Query: 518 AHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPS 577
A +++G K +++H C+ +NADFDGD+M VH P ++ EA ++ + N + PS
Sbjct: 1869 AFEPILIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPS 1927
Query: 578 NGDPLRSLIQDHIVSAALLT----KKDTFLNRDEFCQLLYS 614
NG P+ +D ++ LT K+D + FC++ +S
Sbjct: 1928 NGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHS 1968
Score = 46.9 bits (111), Expect = 9e-05
Identities = 37/120 (30%), Positives = 57/120 (47%), Gaps = 21/120 (17%)
Query: 907 NWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFI 966
N + +M SGA+GS +Q++ G + L K SG+ + + P I
Sbjct: 2141 NSVYMMVNSGARGSTSQMKQLA---GMRGLMTKP-----SGEIIET-------P-----I 2180
Query: 967 IDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIK-NLECLKISYDYSVRDA 1025
I F GL EY+ R+GL DTA+KT+ SGYL R L+ + C+ +D ++
Sbjct: 2181 ISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNG 2240
Score = 46.5 bits (110), Expect = 9e-05
Identities = 18/28 (64%), Positives = 24/28 (85%)
Query: 1143 GEPVGLLASQSVGEPSTQMTLNTFHLAG 1170
GE VG++A+QSVGEP TQ+T+ TFH+ G
Sbjct: 2333 GEAVGVIAAQSVGEPGTQLTMRTFHIGG 2360
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 103 bits (258), Expect = 5e-22
Identities = 83/261 (31%), Positives = 128/261 (49%), Gaps = 64/261 (24%)
Query: 344 LQQSVNVLFD-GKNA-----AGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+VLFD G++ A +R + S + ++++ K+G FRQ L+GKRV+++ RSVI
Sbjct: 1688 LQEAVDVLFDNGRSTNAVKGANKRPLKS-LSEIIKGKQGRFRQNLLGKRVDFSGRSVIVV 1746
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLS----T 453
P L ++E G+P AL L P H L KL
Sbjct: 1747 GPNLKMDECGLPKNMALELFKP--------------------------HLLSKLEERGYA 1780
Query: 454 MRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPT 510
L K+M I +K NE V+ LQ+ G VL+NR PT
Sbjct: 1781 TTLKQAKRM---IEQK---------------SNE-----VWECLQEITEGYPVLLNRAPT 1817
Query: 511 LHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNAN 570
LHK SI A +++ G K +++H CS +NADFDGD+M VH P + + AE ++ ++
Sbjct: 1818 LHKQSIQAFHPKLIDG-KAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSS 1876
Query: 571 NQYVRPSNGDPLRSLIQDHIV 591
+ P++G + QD ++
Sbjct: 1877 MNILLPASGKAVAIPSQDMVL 1897
Score = 74.6 bits (183), Expect = 3e-13
Identities = 75/271 (27%), Positives = 117/271 (43%), Gaps = 54/271 (19%)
Query: 905 GKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGG 964
G N I +M SGA+GS +Q+S+ G L K ++ P
Sbjct: 2083 GFNSIYMMADSGARGSAAQIRQLSAMRG---LMTKPDGSIIE------------TP---- 2123
Query: 965 FIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRD 1024
II F GL EY+ R+GL DTA+KT+ +GYL R LI + +K+
Sbjct: 2124 -IISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKV-------- 2174
Query: 1025 ADGSIVQFCYGEDGVDVHQTSFISKF-DALAARERGRGRGRNKFCDKGSHTFVMGR---- 1079
+ C +G+++ + S+ + L R GR + D ++ ++
Sbjct: 2175 ----VSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLED-VIDPITNEILLYADTLI 2229
Query: 1080 NQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSL 1139
++E K + + + P K A K AK L L + K +
Sbjct: 2230 DEEGAKKVVEAGI---KSITIRTPVTCK--APK-------GVCAKCYGLNLGEGK----M 2273
Query: 1140 AQPGEPVGLLASQSVGEPSTQMTLNTFHLAG 1170
+ PGE VG++A+QS+GEP TQ+TL TFH+ G
Sbjct: 2274 SYPGEAVGVVAAQSIGEPGTQLTLRTFHVGG 2304
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase
(RNAP), C-terminal domain. RNA polymerase (RNAP) is a
large multi-subunit complex responsible for the synthesis
of RNA. It is the principal enzyme of the transcription
process, and is the final target in many regulatory
pathways that control gene expression in all living
cells. At least three distinct RNAP complexes are found
in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for
the synthesis of ribosomal RNA precursor, mRNA precursor,
and 5S and tRNA, respectively. A single distinct RNAP
complex is found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. Structure
studies revealed that prokaryotic and eukaryotic RNAPs
share a conserved crab-claw-shape structure. The largest
and the second largest subunits each make up one clamp,
one jaw, and part of the cleft. The largest RNAP subunit
(Rpb1) interacts with the second-largest RNAP subunit
(Rpb2) to form the DNA entry and RNA exit channels in
addition to the catalytic center of RNA synthesis. The
region covered by this domain makes up part of the foot
and jaw structures. In archaea, some photosynthetic
organisms, and some organelles, this domain exists as a
separate subunit, while it forms the C-terminal region of
the RNAP largest subunit in eukaryotes and bacteria.
Length = 158
Score = 93.3 bits (232), Expect = 6e-22
Identities = 35/49 (71%), Positives = 40/49 (81%)
Query: 1143 GEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIAS 1191
GE VG+LA+QS+GEP TQMTL TFH AG MNVTLG+PRL+EIL AS
Sbjct: 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAAS 49
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 91.4 bits (227), Expect = 7e-19
Identities = 42/112 (37%), Positives = 65/112 (58%), Gaps = 7/112 (6%)
Query: 1092 LDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKH---KFVLSLAQPGEPVGL 1148
+D LP ++ E+ A E++ ++ ++++ ++ + P E VG+
Sbjct: 131 IDDVKKLGFRLPPSV---IEEIAKAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGI 187
Query: 1149 LASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVIT 1200
+A+QS+GEP TQMT+ TFH AG EMNVTLG+PRL EI+ A K TP +T
Sbjct: 188 VAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVD-ARKKPSTPTMT 238
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, 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). This
domain, domain 3, represents the pore domain. The 3' end
of RNA is positioned close to this domain. The pore
delimited by this domain is thought to act as a channel
through which nucleotides enter the active site and/or
where the 3' end of the RNA may be extruded during
back-tracking.
Length = 158
Score = 83.4 bits (207), Expect = 2e-18
Identities = 56/244 (22%), Positives = 81/244 (33%), Gaps = 87/244 (35%)
Query: 572 QYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQ 631
+ P NG P+ QD ++ LLT++DTF +R+E QLL V
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYGIVL------------- 47
Query: 632 RVLISRSEQEVLPLLPAIWKP-EPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFK 690
PAI KP +PLWTGKQ + + LP +
Sbjct: 48 -------------PHPAILKPIKPLWTGKQTFSRL------------------LPNEINP 76
Query: 691 TRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEE 750
+ +ND L G+ V K KS
Sbjct: 77 KGKPKTNEETLCENDSYVLINN--------GELISGVIDK------KLGGKSLGS----- 117
Query: 751 KLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCG 810
LI+ +I + +YG TV+ L L +L +L GF+ G
Sbjct: 118 --LIH-------II----YKEYGPEETVK----------FLDRLQKLGFRYLTKSGFSIG 154
Query: 811 VDDL 814
+DD+
Sbjct: 155 IDDI 158
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 78.7 bits (194), Expect = 2e-14
Identities = 67/217 (30%), Positives = 94/217 (43%), Gaps = 41/217 (18%)
Query: 964 GFIID-----RFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISY 1018
G IID F GL EY R+GLVDTA++T+ SGYL R L+ +S
Sbjct: 151 GEIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLV------DVSQ 204
Query: 1019 DYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAARERGRGRGRNKFCDKGSHTFVMG 1078
D VR+ D C E + V + K +L R GR + V+
Sbjct: 205 DVIVREED------CGTERSIVVRAMTEGDKKISLGDRLLGRLVAED----------VLH 248
Query: 1079 RNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLS 1138
E+I K + +D A + A E L+ E A+ + + + S
Sbjct: 249 PEGEVIVPK-NTAIDPDLA--KTIETAGIS--EVVVRSPLTCEAARS----VCRKCYGWS 299
Query: 1139 LAQP-----GEPVGLLASQSVGEPSTQMTLNTFHLAG 1170
LA GE VG++A+QS+GEP TQ+T+ TFH G
Sbjct: 300 LAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGG 336
>gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial
DNA-dependent RNA polymerase (RNAP), C-terminal domain.
Bacterial RNA polymerase (RNAP) is a large multi-subunit
complex responsible for the synthesis of all RNAs in the
cell. This family also includes the eukaryotic
plastid-encoded RNAP beta" subunit. Structure studies
suggest that RNAP complexes from different organisms
share a crab-claw-shape structure with two pincers
defining a central cleft. Beta' and beta, the largest and
the second largest subunits of bacterial RNAP, each makes
up one pincer and part of the base of the cleft. The
C-terminal domain includes a G loop that forms part of
the floor of the downstream DNA-binding cavity. The
position of the G loop may determine the switch of the
bridge helix between flipped-out and normal alpha-helical
conformations.
Length = 204
Score = 61.0 bits (149), Expect = 2e-10
Identities = 22/45 (48%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 1143 GEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIL 1187
GE VG++A+QS+GEP TQ+T+ TFH G ++T G+PR++E+
Sbjct: 6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELF 49
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 62.4 bits (153), Expect = 1e-09
Identities = 34/87 (39%), Positives = 51/87 (58%), Gaps = 15/87 (17%)
Query: 503 VLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAE 562
VL+NR PTLH+ I A +++G K +++H C+ +NADFDGD+M VH P ++AE
Sbjct: 411 VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAE 469
Query: 563 A-------YNIVNANNQYVRPSNGDPL 582
A NI++ P+NG P+
Sbjct: 470 ARVLMLSSNNILS-------PANGKPI 489
Score = 57.0 bits (139), Expect = 6e-08
Identities = 23/48 (47%), Positives = 35/48 (72%), Gaps = 3/48 (6%)
Query: 1139 LAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEI 1186
L GE VG++A+QS+GEP TQ+T+ TFH G +++T G+PR+ E+
Sbjct: 875 LVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGG---VDITGGLPRVAEL 919
Score = 55.1 bits (134), Expect = 2e-07
Identities = 34/85 (40%), Positives = 46/85 (54%), Gaps = 19/85 (22%)
Query: 344 LQQSVNVLFD----GKNAAGQ--R------DMASGICQLLEKKEGLFRQKLMGKRVNYAC 391
LQ++V+ LFD G+ G R DM G K+G FRQ L+GKRV+Y+
Sbjct: 289 LQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKG-------KQGRFRQNLLGKRVDYSG 341
Query: 392 RSVISPDPYLAVNEIGIPPYFALRL 416
RSVI P L +++ G+P AL L
Sbjct: 342 RSVIVVGPELKLHQCGLPKKMALEL 366
Score = 43.9 bits (105), Expect = 5e-04
Identities = 35/123 (28%), Positives = 53/123 (43%), Gaps = 33/123 (26%)
Query: 892 INELLSEGLLK-----PTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKR----VP 942
+ +++ ++K N I +M SGA+GS +Q++ G R P
Sbjct: 667 ATDEVAKAMMKNLSKDQESFNPIYMMADSGARGSASQIRQLA---------GMRGLMAKP 717
Query: 943 RMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGY 1002
SG+ + + P I F GL EY+ R+GL DTA+KT+ SGY
Sbjct: 718 ---SGEIIET-------P-----IKSNFREGLTVLEYFISTHGARKGLADTALKTADSGY 762
Query: 1003 LQR 1005
L R
Sbjct: 763 LTR 765
>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1. 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, domain 1, represents the clamp domain, which a
mobile domain involved in positioning the DNA,
maintenance of the transcription bubble and positioning
of the nascent RNA strand.
Length = 330
Score = 58.9 bits (143), Expect = 6e-09
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRRE 53
C+TCG CPGHFGHI+L PV++ F + ++L+ +C C +
Sbjct: 57 CETCGVEVTECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESV 109
Score = 39.6 bits (93), Expect = 0.008
Identities = 32/113 (28%), Positives = 45/113 (39%), Gaps = 22/113 (19%)
Query: 284 LGVVLVPPIKFRLPS------KGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVI 337
L V+ VPP R PS + + + T L +++ N L + A
Sbjct: 226 LTVLPVPPPCIR-PSVQLDGGRFAEDDL----THKLRDIIKRNNRLKKM---LEEGAPSH 277
Query: 338 VAR--WMNLQQSVNVLFD----GKNAAGQRDMAS--GICQLLEKKEGLFRQKL 382
+ R LQ+ V LFD G+ A Q+ I Q L+ KEG FR L
Sbjct: 278 IIREEKRLLQEHVATLFDNDIPGQPPALQKSGRPLKSISQRLKGKEGRFRGNL 330
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 51.4 bits (123), Expect = 3e-06
Identities = 25/66 (37%), Positives = 43/66 (65%), Gaps = 3/66 (4%)
Query: 1100 MELPDALKDNA-EKFA-DKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEP 1157
++LP +LKD EK + ++ EM ++ + V ++ +L +P E VG++A+QS+GEP
Sbjct: 13 LDLPRSLKDELFEKLSKRDGVTEEMV-EEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEP 71
Query: 1158 STQMTL 1163
TQM+L
Sbjct: 72 GTQMSL 77
Score = 49.9 bits (119), Expect = 8e-06
Identities = 23/45 (51%), Positives = 31/45 (68%), Gaps = 1/45 (2%)
Query: 1159 TQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVITCPL 1203
T T+ TFH AG E+NVTLG+PR+ EI+ A K+ TP++T L
Sbjct: 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVD-ARKEPSTPIMTVHL 584
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 49.6 bits (119), Expect = 1e-05
Identities = 18/28 (64%), Positives = 22/28 (78%)
Query: 1143 GEPVGLLASQSVGEPSTQMTLNTFHLAG 1170
GE VG++A QS+GEP TQ+TL TFH G
Sbjct: 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGG 342
Score = 45.3 bits (108), Expect = 2e-04
Identities = 23/50 (46%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 964 GFIIDR-----FLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLI 1008
G IID F GL EY C R+G+VDTAV+T+ +GYL R L+
Sbjct: 158 GQIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 49.2 bits (118), Expect = 1e-05
Identities = 17/28 (60%), Positives = 23/28 (82%)
Query: 1143 GEPVGLLASQSVGEPSTQMTLNTFHLAG 1170
GE VG++A+QS+GEP TQ+T+ TFH G
Sbjct: 311 GEAVGIIAAQSIGEPGTQLTMRTFHTGG 338
Score = 44.6 bits (106), Expect = 3e-04
Identities = 28/68 (41%), Positives = 35/68 (51%), Gaps = 11/68 (16%)
Query: 964 GFIID-----RFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISY 1018
G IID F GL EY R+GLVDTA++T+ SGYL R L+ +S
Sbjct: 152 GEIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLV------DVSQ 205
Query: 1019 DYSVRDAD 1026
D VR+ D
Sbjct: 206 DVIVREED 213
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 36.6 bits (85), Expect = 0.034
Identities = 15/52 (28%), Positives = 21/52 (40%)
Query: 700 DRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEK 751
+ K K K K KDK KK+ K E++ +K + K SE
Sbjct: 82 QKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYSETL 133
Score = 29.7 bits (67), Expect = 7.1
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 696 DKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELS 748
K+ +KK DK K K + DKS KK E K E+K + KS + LS
Sbjct: 87 KKKKSKKKKDKDK-DKKDDKKDDKSEKKDE----KEAEDKLEDLTKSYSETLS 134
>gnl|CDD|219901 pfam08555, DUF1754, Eukaryotic family of unknown function
(DUF1754). This is a eukaryotic protein family of
unknown function.
Length = 90
Score = 32.0 bits (73), Expect = 0.30
Identities = 19/60 (31%), Positives = 28/60 (46%)
Query: 703 KNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRG 762
K K + K K K K+ K+EVV K EEK + ++ KE E E+ I + +
Sbjct: 13 KGKKIDVKKKKKKKKKKNKSKEEVVTEKEEEEKSSAESDLKEGEEDEDNEKIEQEEDGMN 72
>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 90 amino acids in length.
There are two completely conserved L residues that may
be functionally important.
Length = 70
Score = 30.4 bits (69), Expect = 0.78
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 709 LSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKL 752
+K ++ ++ +++E K E KE EKNKS E+ L+E +L
Sbjct: 23 KAKKKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESEL 66
>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62.
Length = 217
Score = 32.5 bits (74), Expect = 0.91
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 16/85 (18%)
Query: 686 QDFFKT-RFNADKQSDRKK--NDKGKLSKTNKMH-KDKSGKK---------KEVVEGKPG 732
QDFF+ R +S++ K DKG NK++ +DK+ +K E V+
Sbjct: 4 QDFFRAKRVVRALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHS 63
Query: 733 EEKEAEKNKSKEKELSEEKLLIYKN 757
+EK+ EK K K+K++ L +
Sbjct: 64 QEKKEEKKKPKKKKV---PLQVNPA 85
>gnl|CDD|205400 pfam13219, DUF4027, Protein of unknown function (DUF4027). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 40 amino acids in length.
There is a conserved CLGGF sequence motif.
Length = 36
Score = 29.0 bits (65), Expect = 1.1
Identities = 15/34 (44%), Positives = 17/34 (50%)
Query: 607 EFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQ 640
EF L YS GVS LG F VLI ++Q
Sbjct: 3 EFQNLSYSQGVSLICLGGFALSVTLAVLIKMAQQ 36
>gnl|CDD|218472 pfam05158, RNA_pol_Rpc34, RNA polymerase Rpc34 subunit. Subunit
specific to RNA Pol III, the tRNA specific polymerase.
The C34 subunit of yeast RNA Pol III is part of a
subcomplex of three subunits which have no counterpart
in the other two nuclear RNA polymerases. This subunit
interacts with TFIIIB70 and is therefore participates in
Pol III recruitment.
Length = 312
Score = 32.7 bits (75), Expect = 1.2
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 849 AEIDPIK-LKSEIEKAMRGGGDAAVAYFDM--KMTSQLNKHTSSSVINELLSEGLLKPTG 905
A ++ L + +A + + L+ + S IN LL +GLL
Sbjct: 2 ASAGKLQELAKRLYEACLKAPGPNLFSQQDLQALVPGLSLNLLMSAINILLDQGLLVLLK 61
Query: 906 KN 907
+N
Sbjct: 62 QN 63
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 32.2 bits (73), Expect = 2.1
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 695 ADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKL 752
++ + KK K K + K K K +E E +P +EKE EK K E+ E+
Sbjct: 110 KEQVKEEKKKKKEKPKEEPKDRKPK----EEAKEKRPPKEKEKEKEKKVEEPRDREEE 163
Score = 32.2 bits (73), Expect = 2.1
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 702 KKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEK 751
K KG +KT + K+ KE + K ++E +K K K KE +++
Sbjct: 82 KGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDR 131
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 31.6 bits (71), Expect = 3.3
Identities = 17/42 (40%), Positives = 22/42 (52%)
Query: 710 SKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEK 751
SK K ++ K K E K EE+E EK K KE+E E+
Sbjct: 575 SKLAKKREEAVEKAKREAEQKAREEREREKEKEKERERERER 616
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 31.3 bits (70), Expect = 4.2
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 697 KQSDRKKNDKGKLSKTNKMHKD--KSGKKKEVVEGKPGEEK---EAEKNKSKEKELSEE 750
K + KK + ++ + + +K E E K E K +A K K++EK+ ++E
Sbjct: 1337 KAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADE 1395
>gnl|CDD|233136 TIGR00805, oat, sodium-independent organic anion transporter. The
Organo Anion Transporter (OAT) Family (TC
2.A.60)Proteins of the OAT family catalyze the
Na+-independent facilitated transport of organic anions
such as bromosulfobromophthalein and prostaglandins as
well as conjugated and unconjugated bile acids
(taurocholate and cholate, respectively). These
transporters have been characterized in mammals, but
homologues are present in C. elegans and A. thaliana.
Some of the mammalian proteins exhibit a high degree of
tissue specificity. For example, the rat OAT is found at
high levels in liver and kidney and at lower levels in
other tissues. These proteins possess 10-12 putative
a-helical transmembrane spanners. They may catalyze
electrogenic anion uniport or anion exchange.
Length = 633
Score = 30.8 bits (70), Expect = 5.4
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 12/49 (24%)
Query: 263 SFISDMQQQGFGKKAGHSIFFLGVVLVPPI------------KFRLPSK 299
+F+ + +G + + F +GVV VP KF+L K
Sbjct: 351 TFLPKYLENQYGISSAEANFLIGVVNVPAAGLGYLIGGFIMKKFKLNVK 399
>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family. This
family includes the HABP4 family of hyaluronan-binding
proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1.
HABP4 has been observed to bind hyaluronan (a
glucosaminoglycan), but it is not known whether this is
its primary role in vivo. It has also been observed to
bind RNA, but with a lower affinity than that for
hyaluronan. PAI-1 mRNA-binding protein specifically
binds the mRNA of type-1 plasminogen activator inhibitor
(PAI-1), and is thought to be involved in regulation of
mRNA stability. However, in both cases, the sequence
motifs predicted to be important for ligand binding are
not conserved throughout the family, so it is not known
whether members of this family share a common function.
Length = 106
Score = 28.9 bits (65), Expect = 5.7
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 712 TNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSE-EKLLIYKN 757
++K ++E + EE+E E+ + KE L E EK L K
Sbjct: 46 EKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKEMTLEEYEKALQEKR 92
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 30.9 bits (70), Expect = 5.8
Identities = 23/94 (24%), Positives = 30/94 (31%), Gaps = 27/94 (28%)
Query: 781 LYGSNTAG--TLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEE--IGK 836
+ G N AG T+ A+ L GF R + LH E +G
Sbjct: 1 IVGPNEAGKSTIRRAIKSLL------FGF------------PLRTPYDFLHPREGLRVGG 42
Query: 837 RVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDA 870
LE DG E+ +LK GD
Sbjct: 43 -----LLENRDGGELAFERLKKRAASLYDPDGDP 71
>gnl|CDD|236916 PRK11492, hyfE, hydrogenase 4 membrane subunit; Provisional.
Length = 216
Score = 29.9 bits (68), Expect = 6.6
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 282 FFLGVVLVPPIKFRLPSKGGDSVMEHPQ-TVLLSKVLQANIYLANAYVNQP 331
F V+LVP I K GD++ E P +S +L A I L A+V QP
Sbjct: 65 FITKVLLVPLIMTYAARKLGDNIEEEPVFGPAMSILLAALIVLLCAFVVQP 115
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 30.7 bits (69), Expect = 6.6
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 12/59 (20%)
Query: 703 KNDKGKLSKTN-----KMHKDKSGKKKE-----VVEGKPGEEKEAEKNKSKEKELSEEK 751
K+D G+L K N K++ S K+K+ +E + E ++ N EK+L+EEK
Sbjct: 447 KSDLGQLKKENDMLQTKLNSMVSAKQKDKQSMQSMEKRLKSEADSRVNA--EKQLAEEK 503
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 30.6 bits (69), Expect = 6.8
Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 17/99 (17%)
Query: 702 KKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKE---------KELSEEKL 752
K KL K ++K + KKK+V+ K K NK K +ELS L
Sbjct: 118 PKPKTEKLKKKITVNKSTNKKKKKVLSSKDELIKYD-NNKPKSISIHSPLTIQELST-LL 175
Query: 753 LIYKNDLVRGVIDKA------QFADYGLVHTVQELYGSN 785
I + ++++ + K Q D ++ V + +G N
Sbjct: 176 CIPETEIIKSLFLKGISVTVNQIIDISIISQVADDFGIN 214
>gnl|CDD|214936 smart00956, RQC, This DNA-binding domain is found in the RecQ
helicase among others and has a helix-turn-helix
structure. The RQC domain, found only in RecQ family
enzymes, is a high affinity G4 DNA binding domain.
Length = 92
Score = 28.2 bits (64), Expect = 6.9
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 883 LNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAK 918
L+K +I +L++EG L+ G + L T A+
Sbjct: 54 LSKKEWRRLIRQLIAEGYLREDGGRYPYLKLTEKAR 89
>gnl|CDD|206063 pfam13892, DBINO, DNA-binding domain. DBINO is a DNA-binding
domain found on global transcription activator SNF2L1
proteins and chromatin re-modelling proteins.
Length = 140
Score = 29.2 bits (66), Expect = 7.4
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 22/85 (25%)
Query: 689 FKTRFNADKQSDRKK-------NDKGKLSKTNKMHKD---KSGK------------KKEV 726
K + + ++ S+ KK + +T K+ KD ++ + +KE
Sbjct: 26 IKQQNHQNRLSNAKKTAQLCAREARRWQLRTQKIMKDTQLRAKRLMREMLLFWKKNEKEE 85
Query: 727 VEGKPGEEKEAEKNKSKEKELSEEK 751
E + EKEA + KE+EL E K
Sbjct: 86 RELRKRAEKEALEQAKKEEELREAK 110
>gnl|CDD|225954 COG3420, NosD, Nitrous oxidase accessory protein [Inorganic ion
transport and metabolism].
Length = 408
Score = 29.8 bits (67), Expect = 8.8
Identities = 27/116 (23%), Positives = 41/116 (35%), Gaps = 11/116 (9%)
Query: 141 GNCKAKNPRISKPTFGWIHMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAP 200
GN A N K F + + IR N GC +G + G E ++ +S +
Sbjct: 254 GNRVAGNVS-GKCVFIY----NANYNKIRGNSFEGCAIGIHLTAGSEGNEIIGNSFIGNR 308
Query: 201 ETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKD-LFSGPLLPSDVKDIIEKLW 255
+ GT D +AR F D + P P+D D + +W
Sbjct: 309 VQVKYVGT--RELDWSARGQGNYWSDNL-AFDLDGDGIGDSPYRPNDGIDRL--IW 359
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
0.318 0.135 0.401
Gapped
Lambda K H
0.267 0.0849 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 61,315,540
Number of extensions: 6106833
Number of successful extensions: 5578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5482
Number of HSP's successfully gapped: 108
Length of query: 1208
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1100
Effective length of database: 6,147,370
Effective search space: 6762107000
Effective search space used: 6762107000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 65 (28.6 bits)