RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 000829
(1265 letters)
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 758 bits (1959), Expect = 0.0
Identities = 325/814 (39%), Positives = 480/814 (58%), Gaps = 71/814 (8%)
Query: 5 KMEALRK-----TDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVT 59
K+E L++ DL+K + K+ A+K + CP CG I + K T
Sbjct: 120 KLERLKEWGSLADDLIKEVKKE----AAKRMVCPHCGEKQ---------YKIKFE--KPT 164
Query: 60 ESLQEFASAITHTKESKAAVNVATYILNPVNVLFLFKRMTDTDCEVLYL---SERPEKLI 116
+E L P ++ +++ D D E+L + RPE ++
Sbjct: 165 TFYEER--------------KEGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWMV 210
Query: 117 ITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSA---FKSLAG 173
+T + VPP+ +RPS+ ++ Q +E+D+T +L II+ N L+ E +EA + + L
Sbjct: 211 LTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLK-ENIEAGAPQLIIEDL-- 267
Query: 174 WETLQVEVAQYINSDVRGVPFSMQVA-----RPLSGFVQRLKGKQGRFRGNLSGKRVEYT 228
WE LQ V Y ++++ G+P A RPL QRLKGK+GRFRGNLSGKRV ++
Sbjct: 268 WELLQYHVTTYFDNEIPGIP----PARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFS 323
Query: 229 GRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYP 288
RTVISPDPNL I EV +P +A+ LT PERV++ NIE+LR+ + NGP+K+PGA + P
Sbjct: 324 ARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRP 383
Query: 289 DGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRT 348
DG L K + +LA +L+ G IV+RHL DGD+VLFNRQPSLHRMSIM HR R++P +T
Sbjct: 384 DGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKT 443
Query: 349 LRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDF 408
R N +VC PYNADFDGDEMN+HVPQTEEAR EA +LM VQ ++ +P+ G ++ QD
Sbjct: 444 FRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDH 503
Query: 409 LTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPH 468
++ ++L+TRK T + + + G+D + P PAI WTGKQ+FS+ + P
Sbjct: 504 ISGAYLLTRKSTLFTKEEALDLLRAA--GIDELPEPEPAIENGKPYWTGKQIFSLFL-PK 560
Query: 469 ANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGN 528
+L ++ K E+ C +D +V +N +L+ G + K +G
Sbjct: 561 -------DLNLEFKAKICSGCDECKKED------CEHDAYVVIKNGKLLEGVIDKKAIGA 607
Query: 529 GNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLI 588
+ + ++++YG ++ + +L+ R+I GF+ GIDD +E ++ ++I
Sbjct: 608 E-QGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEII 666
Query: 589 SENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWRNSP 648
E + I+ Y G+L+ PG +TLE I +L + R++AG+ L N
Sbjct: 667 EEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPA 726
Query: 649 LIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANS 708
+IM++ G++GS +N++QM ACVGQQSV G R G+ DR+LPHF A+GFV +S
Sbjct: 727 VIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSS 786
Query: 709 FYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCI 768
+ SGL+ TEFFFH MGGREGLVDTAV+T+ +GYM RRLI AL+DL ++YD +VR+ G I
Sbjct: 787 YKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNI 846
Query: 769 VQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVKA 802
VQF YG+DG+DP M+ G+P++ DR++ +V
Sbjct: 847 VQFKYGEDGVDP--MKSDHGKPVDVDRIIERVLG 878
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 726 bits (1876), Expect = 0.0
Identities = 397/1198 (33%), Positives = 617/1198 (51%), Gaps = 116/1198 (9%)
Query: 86 LNPVNVLFLFKRMTDTDCEVLYL---SERPEKLIITNIAVPPIAIRPSVIMDGSQSNEND 142
L P+ + +F+++ D D E++ RPE ++ VPP+ RPS+I++ + +E+D
Sbjct: 186 LLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDD 245
Query: 143 ITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQ--VAR 200
+T L II+ N L++ + LQ + + ++ G+P + R
Sbjct: 246 LTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKGSGR 305
Query: 201 PLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERV 260
PL QRLKGK+GRFRGNL GKRV+++ RTVISPDP + I EV +P +A LT PE V
Sbjct: 306 PLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIV 365
Query: 261 SDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-----YGKFRNQLAVE-LKSGCIVD 314
+++NIEK+++ + NGPD++PGA IR DGT L GK + A E L+ G IV+
Sbjct: 366 NENNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVE 425
Query: 315 RHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQ 374
RHL DGD+V+FNRQPSLH++SI+ HR +++P T R + +VC PYNADFDGDEMN+HVPQ
Sbjct: 426 RHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQ 485
Query: 375 TEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYM 434
E+AR EA+ LMGV++NL +P+ G ++ + QDF+T+++LIT+ D +D+ S +
Sbjct: 486 IEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLA 545
Query: 435 GDGMDRVDLPTPAI-LKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEG 493
G LP PAI K WTGKQLFS+ + N + + +
Sbjct: 546 GITD---PLPEPAIKTKDGPAWTGKQLFSLFLPKDFNFEGIAKWSAGKAGEAK------- 595
Query: 494 DEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKD--GLYSVLLRDYGAHATSGCM 551
+ C DG+V + ELISG + +G ++ L + +DYG +
Sbjct: 596 ------DPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFL 649
Query: 552 NRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEY--------N 603
N++ ++ + I ++GFS G D+ E + I + + I +
Sbjct: 650 NKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIY 709
Query: 604 EGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINI 663
+GK +L G + LEA I + L++ R+ AG + + N+ IM++ G++GS N+
Sbjct: 710 KGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANL 769
Query: 664 SQMVACVGQQSV--------GGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSA 715
+Q+ +GQQ G R G+ DR+L HF P A GFV N++ GL+A
Sbjct: 770 AQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNA 829
Query: 716 TEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGD 775
EFFFH MGGREGL+D A +T D+GY RRL ALED+ ++YD +VR+ G I+QF +G+
Sbjct: 830 AEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGE 889
Query: 776 DGMDPANMEGKSGEPLNFDRLLMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSE 835
DG+DP ++ GE N +R++ K K I ++ GK + +
Sbjct: 890 DGIDPQKLD--HGEAFNLERIIEKQK------------------IEDR-----GKGASKD 924
Query: 836 AFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCFS 895
+++ + L K +L + H + + E +LE
Sbjct: 925 EIEELAKEYTKTFNANLPK---------------LLADAIH-GAELKEDELEAICAEGKE 968
Query: 896 RYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRI 955
+ +VE G AIG I AQSI EPGTQMTL+TFH AG+ +M++T G+ R E+++ +
Sbjct: 969 GFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKP 1028
Query: 956 STPIITAEL--ECN-DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETI 1012
STP + L EC D E A + + E + +A S
Sbjct: 1029 STPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDNANEIKL---------IK 1079
Query: 1013 QDAHLCINADIVKESIVQTPKIKLKQQHIKVL---DFRKLEIFPPVDKSKIHFELYSLKN 1069
D N I E + K + ++ D L++ D+ K L +++N
Sbjct: 1080 PDKRALENGCIPMERFAEIEAALAKGKKFEMELEDDLIILDLVEAADRDKPLATLIAIRN 1139
Query: 1070 VLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKT 1129
+ VKG+ +ER + EK+ R ++ + G+ L AV+ + ID T
Sbjct: 1140 KILDKPVKGVPDIERAWVELVEKDGR--------DEWIIQTSGSNLAAVLEMKCIDIANT 1191
Query: 1130 KSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGI--- 1186
+N FE+ TLGIEAAR I +E+ ++ G+ +D R++ML+AD+M RG + I
Sbjct: 1192 ITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQ 1251
Query: 1187 ---TRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTG 1241
R G S L A+FE T + +A++ G ++I+G+ + +IMG +P+G+G
Sbjct: 1252 AAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
>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 = 670 bits (1731), Expect = 0.0
Identities = 308/790 (38%), Positives = 468/790 (59%), Gaps = 52/790 (6%)
Query: 13 DLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHT 72
DL ++++K A+K +KCP CG +K E F +
Sbjct: 125 DLASTLIEKIVKEAAKRMKCPHCGEEQKKIK---------------FEKPTYF-----YE 164
Query: 73 KESKAAVNVATYILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRP 129
+ + V L P + +++ D D E+L ++ RPE +++T + VPP+ +RP
Sbjct: 165 EGKEGDVK-----LTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRP 219
Query: 130 SVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAG-WETLQVEVAQYINSD 188
S+ ++ + +E+D+T +L II+ N L+ E +EA + + WE LQ VA Y +++
Sbjct: 220 SITLETGERSEDDLTHKLVDIIRINQRLK-ENIEAGAPQLIIEDLWELLQYHVATYFDNE 278
Query: 189 VRGVPFSM-QVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIP 247
+ G+P + + RPL QRLKGK+GRFRGNLSGKRV ++ RTVISPDPN+ I EV +P
Sbjct: 279 LPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVP 338
Query: 248 IRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVEL 307
++A+ LT PERV+ NI++LR+ + NGPD +PGA + PDG + + + +LA L
Sbjct: 339 EQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDENKEELAERL 398
Query: 308 KSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDE 367
+ G +V+RHL DGD+VLFNRQPSLHRMS+M H+ +++P +T R N +VC PYNADFDGDE
Sbjct: 399 EPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDE 458
Query: 368 MNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAF 427
MN+HVPQTEEAR EA LM V+ ++ TP+ G ++ D+++ ++L+T K T + +
Sbjct: 459 MNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEV 518
Query: 428 SLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNK 487
+ +G D P PAI KP E WTGKQ+FS + N + +
Sbjct: 519 QTI---LGVAGYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFEGRAKICSSD------ 569
Query: 488 LIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHAT 547
EE CP+D +V +N +L+ G + K +G K + ++R+YG A
Sbjct: 570 ---ACKKEE------CPHDAYVVIKNGKLLKGVIDKKAIGA-EKGKILHRIVREYGPEAA 619
Query: 548 SGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKL 607
++ + +L R+I GF+ GIDD+ KE ++ +LI + + + I+ Y G+L
Sbjct: 620 RRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGEL 679
Query: 608 QLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMV 667
+ PG +TLE I ++L + R++AG+ L N +IM++ G++GS +NI+QM
Sbjct: 680 EPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMA 739
Query: 668 ACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGRE 727
A VGQQSV G R G+ +R+LPHF + A+GFV +SF GL TE+FFH GGRE
Sbjct: 740 AMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGRE 799
Query: 728 GLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKS 787
GLVDTAV+T+ +GYM RRLI AL+DL ++YD +VR+ G ++QF YG+DG+DP +
Sbjct: 800 GLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDH-- 857
Query: 788 GEPLNFDRLL 797
G+P++ ++
Sbjct: 858 GKPVDVKKIF 867
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 559 bits (1444), Expect = 0.0
Identities = 230/703 (32%), Positives = 332/703 (47%), Gaps = 66/703 (9%)
Query: 86 LNPVNVLFLFKRMTDTDCEVLYLSERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITE 145
L+P V L KR+ D +L + RPE +I+T + VPP +RPS+ +DG + E+D+ +
Sbjct: 156 LSPTKVKKLLKRLKVVDAFLLSGN-RPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLND 214
Query: 146 RLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGF 205
+R+I N L+ L+E + LQ V ++ P ++ RPL
Sbjct: 215 LYRRVINRNNRLK-RLLELAAPIIVRNEKRMLQEAVDALFDN---RRPRAVTGGRPLKSL 270
Query: 206 VQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNI 265
QRLKGKQGRFR NL GKRV+Y+GR+VIS PNLK+ + +P +MA L P V++ NI
Sbjct: 271 SQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNI 330
Query: 266 EKLRQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLF 325
E LR GA+ + L V R + DGD VL
Sbjct: 331 EGLRT----------GAKYAKRMVER--------------RLPEVWDVLREVIDGDPVLL 366
Query: 326 NRQPSLHRMSIMCHRARIMP-WRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALL 384
NR P+LHR+SIM ++P + +R + VC YNADFDGDEM +HVP + EA EA
Sbjct: 367 NRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARG 426
Query: 385 LMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLP 444
LMG Q N+ TP G +VA QD + +L+T D + DR
Sbjct: 427 LMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDR--EK 484
Query: 445 TPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCP 504
AI K +EL TGK + S + A + + V + N+ +
Sbjct: 485 AEAIAKKIELTTGKVIVSTISPDLAELSIIVTT--DGRRIFNRGLP------------ED 530
Query: 505 NDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYG-AHATSGCMNRLAKLSARWI- 562
D V N +LI G + K + + R+YG A+ + L KL I
Sbjct: 531 KDVLVKIVNGKLIKGVIDKKIVT----------IYREYGPEVASKALVKLLDKLKNLGIK 580
Query: 563 GNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAV 622
G GF IGI E D+K +++ E I +Y EG L + + +E +
Sbjct: 581 GIGGFGIGIGRKDI--EAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVL 638
Query: 623 ITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPN 682
+ L + K + + + G G+ +NISQ+V +GQQ V G +
Sbjct: 639 GIEALRNAIIEEIKITLEEQ--GLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISV 696
Query: 683 GFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYM 742
+ F K A+G +SF GL+ E+F H +GGR GLVDTA+KTAD+GY+
Sbjct: 697 L----ARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYL 752
Query: 743 SRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEG 785
+RRL+ +DL +Q D+ V + G ++QF YG+DG D
Sbjct: 753 TRRLVDVAQDLIVQEDDCVTDGIGVVIQFEYGEDGEDLTERIL 795
Score = 109 bits (274), Expect = 5e-24
Identities = 107/361 (29%), Positives = 157/361 (43%), Gaps = 34/361 (9%)
Query: 901 RVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAG--VASMNITQGVPRIKEIINGAKRISTP 958
A G A++ G GTQM + T H+ G VA + T G P + I AK STP
Sbjct: 410 MAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLT-IVDAKLPSTP 468
Query: 959 IITAEL--ECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAH 1016
+ L E D+ A + +IE T + +I SI++ D I +
Sbjct: 469 VGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTISP--DLAELSIIVTTDGRRIFNRG 526
Query: 1017 LCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIF----PPVDKSKIHFELYSLKNVLP 1072
L + D V IV IK V+D + + I+ P V + L LKN
Sbjct: 527 LPEDKD-VLVKIVNGKLIK------GVIDKKIVTIYREYGPEVASKALVKLLDKLKN--- 576
Query: 1073 MVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSN 1132
+ +KGI I K+ E K+ + EG+ L+ ++ E D +T+ N
Sbjct: 577 -LGIKGIGGFGI-GIGRKDIEAEDEKDE-----IVIEAEGSVLKLILQYEEGDLTRTERN 629
Query: 1133 HIFEVQQTLGIEAARICIIDEINETMKAHGMSI-DKRHMMLLADLMTFRGEVLGITRFGI 1191
+I E+ + LGIEA R II+EI T++ G+ D RHM L M V I + G+
Sbjct: 630 NIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGV 689
Query: 1192 QKMDK--SVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRD 1249
M + SVL A+FE T HL A G +EG++E G P+ TG++ +
Sbjct: 690 --MGEKISVLARAAFEVTVKHLE-AEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKT 746
Query: 1250 A 1250
A
Sbjct: 747 A 747
>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 = 510 bits (1315), Expect = e-172
Identities = 201/347 (57%), Positives = 238/347 (68%), Gaps = 48/347 (13%)
Query: 896 RYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRI 955
+Y +VE GTA+GAI AQSIGEPGTQMTLKTFHFAGVASMNIT GVPRIKEIIN +K I
Sbjct: 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNI 60
Query: 956 STPIITAELECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDA 1015
STPIITA+LE + +E +AR+VKGRIEKT LG+VA I+ V + I+I LD + I+
Sbjct: 61 STPIITAKLENDRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDKKIIEKL 120
Query: 1016 HLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVI 1075
L KS ++F L SLK LP V+
Sbjct: 121 QL--------------------------------------SKSNLYFLLQSLKRKLPDVV 142
Query: 1076 VKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIF 1135
V GI V+R VI + +K K KY+LLVEG GL+AVM G+ G +T SNHI
Sbjct: 143 VSGIPEVKRAVINKDKK----------KGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIM 192
Query: 1136 EVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMD 1195
EV++ LGIEAAR II+EI TMK+HGMSID RH+MLLADLMTF+GEVLGITRFGI KM
Sbjct: 193 EVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMK 252
Query: 1196 KSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242
+SVLMLASFEKT DHLFNA+++GR D IEGVSECIIMG PMP+GTG+
Sbjct: 253 ESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGL 299
>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 = 429 bits (1104), Expect = e-138
Identities = 190/491 (38%), Positives = 250/491 (50%), Gaps = 45/491 (9%)
Query: 712 GLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQF 771
GL+ EFFFHTMGGREGL+DTAVKTA+TGY+ RRL+KALEDL +QYD++VRN+GG IVQF
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQF 60
Query: 772 LYGDDGMDPANMEGKSGEPLNFDRLLMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKE 831
LYG+DG+DP +EG+ + L ++ K +
Sbjct: 61 LYGEDGLDPLKIEGQGRFTIEDSDLKLEKKFKIDL-----------------------ND 97
Query: 832 SCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQ 891
SL + + K V K F+
Sbjct: 98 VLLLLSEFSLSTLLFEILLRSGIESKRVR----------------SELTCNSKAGVCFLC 141
Query: 892 TCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIING 951
+YR VE G A+G I AQSIGEPGTQMTL TFHFAGVAS N+T GVPR+KEIIN
Sbjct: 142 YGRDKYRRSLVEPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINV 201
Query: 952 AKRISTPIITAELECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMET 1011
AK P+IT L N + ARV K R EKTLL +I IV+ S + +
Sbjct: 202 AKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLLKKVTIIIVIYYDDDSESTVIKKDR 261
Query: 1012 IQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVL 1071
I + + V E + I K++ K L + K E L
Sbjct: 262 IWVLAYFVIPEEVAEEVALAIIIIGKRKSRKR-KKNNLGVAKDE---KGLEEEELLLLNK 317
Query: 1072 PMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEG-IDGCKTK 1130
++++ GIK V+ VI + K++ L EG LQAVM +G ID KT
Sbjct: 318 ILLVIPGIK-VKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTY 376
Query: 1131 SNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFG 1190
SN I E+ + LGIEAAR I+ EI K G+ +++RH+ LLADLMTF+GE+LGITR G
Sbjct: 377 SNDIREMLKKLGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAG 436
Query: 1191 IQKMDKSVLML 1201
+ + S +++
Sbjct: 437 LNREKSSFILM 447
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 406 bits (1046), Expect = e-132
Identities = 144/302 (47%), Positives = 199/302 (65%), Gaps = 8/302 (2%)
Query: 113 EKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLA 172
E +I+T + VPP +RPSV +DG + E+D+T L+ II+ N L++ L +
Sbjct: 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRN 60
Query: 173 GWETLQVEVAQYINSDVRGVPFSMQVA-RPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRT 231
LQ V I+++ G+P + Q + RPL QRLKGK+GRFR NL GKRV+++ R+
Sbjct: 61 EKRLLQEAVDTLIDNE--GLPRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARS 118
Query: 232 VISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGT 291
VI+PDPNLK+ EV +P +A LT+PE V+ NI+KLR+ ++NGP GA+ I G
Sbjct: 119 VITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP---NGAKYII--RGK 173
Query: 292 ARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRF 351
L ++++A LK G IV+RH+ DGDVVLFNRQP+LHRMSI HR R++ +T+R
Sbjct: 174 KTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
Query: 352 NESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTS 411
N VC+PYNADFDGDEMN+HVPQ+ EAR EA LM V NN+ +PKNG+ ++ QD L
Sbjct: 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLG 293
Query: 412 SF 413
+
Sbjct: 294 LY 295
>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 = 307 bits (789), Expect = 2e-94
Identities = 148/380 (38%), Positives = 219/380 (57%), Gaps = 26/380 (6%)
Query: 869 QILEEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTF 928
+ LEEV K G+T + E I+ Y +E G A+G + AQSIGEPGTQMTL+TF
Sbjct: 5 EKLEEVL-KEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTF 63
Query: 929 HFAGVASMNITQGVPRIKEIINGAKRISTPIITAEL--ECNDNENAARVVKGRIEKTLLG 986
H+AGVA +N+T G+PR+ EI++ K STP +T L E + A V +IE+T L
Sbjct: 64 HYAGVAEINVTLGLPRLIEIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLE 123
Query: 987 QVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDF 1046
+A+ I I + + I I LD E ++D + + D V ++I K+K + + D
Sbjct: 124 NLAEDISIDLFNM--RITIELDEEMLEDRGITV--DDVLKAI---EKLKKGKVGEEG-DV 175
Query: 1047 RKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKY 1106
+ + K EL L + +KGIK ++RV++ ++E E Y
Sbjct: 176 TLIVLKAEEPSIK---ELRKLAEKILNTKIKGIKGIKRVIVRKEEDE------------Y 220
Query: 1107 RLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSID 1166
+ EG+ L+AV+ EG+D +T +N+I E+++ LGIEAAR II+EI T++ G+ +D
Sbjct: 221 VIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVD 280
Query: 1167 KRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGV 1226
RH+ML+AD+MT+ GEV I R GI SVL A+FE T HL +A+V G D + GV
Sbjct: 281 IRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGV 340
Query: 1227 SECIIMGIPMPLGTGILKIR 1246
E II+G P+PLGTG +++
Sbjct: 341 IENIIVGQPIPLGTGDVELT 360
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 304 bits (780), Expect = 5e-93
Identities = 149/382 (39%), Positives = 225/382 (58%), Gaps = 29/382 (7%)
Query: 867 KSQILEEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLK 926
K ++ E++ + +TE+++E I+ Y VE G A+G + AQSIGEPGTQMT++
Sbjct: 23 KEELREKLEER--KLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMR 80
Query: 927 TFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAEL--ECNDNENAARVVKGRIEKTL 984
TFH+AGVA +N+T G+PR+ EI++ K STP++T L E + A V +IE T
Sbjct: 81 TFHYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATT 140
Query: 985 LGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVL 1044
L +AK I + + + +I+I LD E ++D + D VKE+I K K + I
Sbjct: 141 LENLAKDISVDLANM--TIIIELDEEMLEDRG--LTVDDVKEAI---EKKKGGEVEI--- 190
Query: 1045 DFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKK 1104
+ L I P + EL L + + +KGIK ++RV+I KE E
Sbjct: 191 EGNTLIISPKEPSYR---ELRKLAEKIRNIKIKGIKGIKRVIIR---------KEGDE-- 236
Query: 1105 KYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMS 1164
Y + EG+ L+ V+ EG+D +T +N+I E+++ LGIEAAR II+EI T++ G+
Sbjct: 237 -YVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLD 295
Query: 1165 IDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIE 1224
+D RH+ML+AD+MT+ GEV I R G+ SVL A+FE T HL +A+V G D ++
Sbjct: 296 VDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELK 355
Query: 1225 GVSECIIMGIPMPLGTGILKIR 1246
GV+E II+G P+PLGTG +++
Sbjct: 356 GVTENIIVGQPIPLGTGDVELT 377
>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 = 291 bits (746), Expect = 2e-88
Identities = 149/381 (39%), Positives = 219/381 (57%), Gaps = 26/381 (6%)
Query: 871 LEEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHF 930
LEE K +++L+ I+ Y ++ G A+G + AQSIGEPGTQMT++TFH+
Sbjct: 10 LEETVKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHY 69
Query: 931 AGVASMNITQGVPRIKEIINGAKRISTPIITAELECNDNEN---AARVVKGRIEKTLLGQ 987
AGVA +N+T G+PR+ EI++ K STP +T LE ++ A V K +IE T L
Sbjct: 70 AGVAELNVTLGLPRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAK-KIEATKLED 128
Query: 988 VAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFR 1047
VAK I I + +++I LD E +++ + + D V+++I K KL + +D
Sbjct: 129 VAKDISIDLADM--TVIIELDEEQLKERGITV--DDVEKAI---KKAKLGKVIEIDMDGN 181
Query: 1048 KLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYR 1107
+ I PP K EL LK + + +KGIK ++RVVI ++ E Y
Sbjct: 182 TITIKPPKPSLK---ELRKLKEKIKNLHIKGIKGIKRVVIRKEGDE------------YV 226
Query: 1108 LLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDK 1167
+ EG+ L+ V+ EG+D +T +N I E+ + LGIEAAR II+EI T++ G+ +D
Sbjct: 227 IYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDI 286
Query: 1168 RHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVS 1227
RH+ML+ADLMT+ GEV I R GI SVL A+FE T HL +A++ G D + GV
Sbjct: 287 RHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELAGVI 346
Query: 1228 ECIIMGIPMPLGTGILKIRQR 1248
E II+G P+PLGTG + +
Sbjct: 347 ENIIVGQPIPLGTGDVDLVMD 367
>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 = 279 bits (715), Expect = 4e-87
Identities = 101/167 (60%), Positives = 126/167 (75%), Gaps = 2/167 (1%)
Query: 222 GKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPG 281
GKRV+++GR+VI+PDPNLK+ EV +PI MA LT PE V+ NI+KLR+ + NGP+ PG
Sbjct: 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPG 60
Query: 282 ARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRA 341
A+ I+ G R L K R +A+EL G IV RH+ DGDVVL NRQP+LHRMSIM HR
Sbjct: 61 AKYIKRIKGAKRDLEYKKR--IAIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRP 118
Query: 342 RIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGV 388
R++ +T+R N SVC+PYNADFDGDEMN+HVPQ+EEAR EA LM V
Sbjct: 119 RVLEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEARELMLV 165
>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 = 265 bits (680), Expect = 8e-79
Identities = 133/403 (33%), Positives = 205/403 (50%), Gaps = 42/403 (10%)
Query: 881 ITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQ 940
+ ++ + + +R+ V G +G I AQSIGEP TQMTL TFHFAGV++ N+T
Sbjct: 3 LNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTL 62
Query: 941 GVPRIKEIINGAKRISTPIITAELE--CNDNENAARVVKGRIEKTLLGQVAKSIKIVMTS 998
GVPR+KEIIN AK I TP +T LE +E A+ ++ R+E T L V + +I
Sbjct: 63 GVPRLKEIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDP 122
Query: 999 RLASIVIALDMETIQDAHLCINADIVKESI-------------VQTPKIKLKQQHIKVLD 1045
+ VI D E ++ + D+ ++ + + K+ ++Q K+ +
Sbjct: 123 DPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKLSMEQIAKKIKE 182
Query: 1046 FRKLEIF-------------------PPVDKSKIHFELYSLK----NVLPMVIVKGIKTV 1082
K ++ +K + + LK N+L + +KGI+ +
Sbjct: 183 EFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGI 242
Query: 1083 ERVVIAEKEKEKRKVKENGEKKKYR---LLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQ 1139
R V +E +K+ E GE KK L +G L+ V+ G+D +T SN I E+ +
Sbjct: 243 -RKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFE 301
Query: 1140 TLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVL 1199
LGIEAAR ++ E+ + G ++ RH+ LL D+MT RG ++ ITR GI + D L
Sbjct: 302 VLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPL 361
Query: 1200 MLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242
M SFE+T D L A+ G D ++GVSE I++G P+GTG
Sbjct: 362 MRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGC 404
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 260 bits (665), Expect = 1e-75
Identities = 132/379 (34%), Positives = 206/379 (54%), Gaps = 27/379 (7%)
Query: 869 QILEEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTF 928
+ + + K +++ + E ++ Y RV+ A+G + AQSIGEPGTQMT++TF
Sbjct: 147 EEIAKAMKKKE-LSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTF 205
Query: 929 HFAGVASMNITQGVPRIKEIINGAKRISTPIITAEL--ECNDNENAARVVKGRIEKTLLG 986
H+AGVA MN+T G+PR+ EI++ K+ STP +T L + ++E R V +IE T L
Sbjct: 206 HYAGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLI 265
Query: 987 QVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDF 1046
VA I+ S+V+ LD E +++ I D + +I K+ K V
Sbjct: 266 DVAD---IITDIAEMSVVVELDEEKMKERL--IEYDDILAAI---SKLTFK----TVEID 313
Query: 1047 RKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKY 1106
+ P S +LY L + + +KGIK ++R + ++ E+R +
Sbjct: 314 DGIIRLKPQQPS--FKKLYLLAEKVKSLTIKGIKGIKRAIARKENDERR----------W 361
Query: 1107 RLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSID 1166
+ +G+ L+ V+ + +D +T +N I E+ LGIEAAR II E T++ G+++D
Sbjct: 362 VIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVD 421
Query: 1167 KRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGV 1226
RH+ML+AD+MTF G V I R GI SVL A+FE T HL A + G D++ GV
Sbjct: 422 IRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGV 481
Query: 1227 SECIIMGIPMPLGTGILKI 1245
+E II+G P+ LGTG + +
Sbjct: 482 AENIIVGQPITLGTGAVSL 500
>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 = 224 bits (572), Expect = 1e-59
Identities = 182/675 (26%), Positives = 304/675 (45%), Gaps = 144/675 (21%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQ---SNENDI-------TERLKRIIQTNASLQQE 160
RPE +++ I V P +RP V +DG + S+ ND+ RLKR+++ A E
Sbjct: 215 RPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAP---E 271
Query: 161 LVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNL 220
++ N K + LQ V ++ RG P + RPL LKGKQGRFR NL
Sbjct: 272 IIVRNE--KRM-----LQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNL 324
Query: 221 SGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQ 273
GKRV+Y+GR+VI P LK+ + +P +MA L P +R NI+ ++ I+
Sbjct: 325 LGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIE 384
Query: 274 NGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHR 333
+ VL V I + VL NR P+LHR
Sbjct: 385 QEDPEVWD------------VLE-------DV------IKEHP------VLLNRAPTLHR 413
Query: 334 MSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLC 393
+ I ++ + +R + VC +NADFDGD+M +HVP + EA+ EA LM NN+
Sbjct: 414 LGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNIL 473
Query: 394 TPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVE 453
PK+G+ +V +QD + + +T + KP
Sbjct: 474 NPKDGKPIVTPSQDMVLGLYYLTTE-------------------------------KPGA 502
Query: 454 LWTGKQLFSVL---IRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVY 510
GK +FS + IR + N +V+++ + +T L T G + + P +GF Y
Sbjct: 503 KGEGK-IFSNVDEAIRAYDNGKVHLHALIGVRTSGEILETTVG--RVIFNEILP-EGFPY 558
Query: 511 FRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG 570
++E +S K + + L +L +G T+ ++++ L ++ G +I
Sbjct: 559 INDNEPLS----KKEISS-----LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTIS 609
Query: 571 IDDVQPKKELSDKKGKLISE-NYEVCNVKIKEYNEGKLQLKPGCDA-----AQTLEAVIT 624
D+ + D+K +++ E + EV ++ K YN+G + + ++T + V
Sbjct: 610 ASDI----VVPDEKYEILKEADKEVAKIQ-KFYNKGLITDEERYRKVVSIWSETKDKVTD 664
Query: 625 DILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGF 684
++ +++D K N +M+ G++G+ Q+ G + P+G
Sbjct: 665 AMMKLLKKDTYK--------FNPIFMMADSGARGNISQFRQLAGMRGLMA-----KPSGD 711
Query: 685 IDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSR 744
I P K+ SF GL+ E+F T G R+GL DTA+KTAD+GY++R
Sbjct: 712 IIEL----PIKS-----------SFREGLTVLEYFISTHGARKGLADTALKTADSGYLTR 756
Query: 745 RLIKALEDLSIQYDN 759
RL+ +D+ ++ ++
Sbjct: 757 RLVDVAQDVVVREED 771
Score = 84.3 bits (209), Expect = 3e-16
Identities = 35/62 (56%), Positives = 44/62 (70%), Gaps = 4/62 (6%)
Query: 891 QTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVAS--MNITQGVPRIK 946
Q C+ R K VE G A+G I AQSIGEPGTQ+T++TFH GVA +ITQG+PR+K
Sbjct: 855 QKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVK 914
Query: 947 EI 948
E+
Sbjct: 915 EL 916
Score = 59.3 bits (144), Expect = 1e-08
Identities = 58/232 (25%), Positives = 99/232 (42%), Gaps = 56/232 (24%)
Query: 1062 FELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKV---KENGEKKKY------RLLVEG 1112
FE + K+ + V G TVE I + K KR V EN E+KKY +L V+
Sbjct: 917 FEARTPKDKAVIAEVDG--TVEI--IEDIVKNKRVVVIKDENDEEKKYTIPFGAQLRVK- 971
Query: 1113 TGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMML 1172
G G + +G S ++ + GI+A + ++ E+ + + G+ I+ +H+ +
Sbjct: 972 DGDSVSAGDKLTEG----SIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEV 1027
Query: 1173 LADLMT-------------FRGEVLGITRF----------------------GIQKMD-- 1195
+ M GE++ I F GI K
Sbjct: 1028 IVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLN 1087
Query: 1196 -KSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIR 1246
+S L ASF++T L +A++ G+ D + G+ E +I+G +P GTG+ +
Sbjct: 1088 TESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYK 1139
Score = 31.2 bits (71), Expect = 4.3
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 1080 KTVERV------VIAEKEKEKRKVKENGEKKKYRLLVE--GTGLQAVMGAEGI 1124
K +E V V+ + K KE ++ +YR +++ G G +A MGAE I
Sbjct: 115 KELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRAGMGAEAI 167
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 214 bits (547), Expect = 2e-57
Identities = 125/329 (37%), Positives = 193/329 (58%), Gaps = 25/329 (7%)
Query: 921 TQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELE---CNDNENAARVVK 977
T T++TFH+AGVA +N+T G+PR+ EI++ K STPI+T L+ D E A V K
Sbjct: 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAK 600
Query: 978 GRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLK 1037
+IE LG VA SI I + ++ SI + LD ET+ D L I ES+ + + KL
Sbjct: 601 -KIESLTLGDVATSIAIDLWTQ--SIKVELDEETLADRGLTI------ESVEEAIEKKLG 651
Query: 1038 QQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKV 1097
+ + L+ P K+ L + +++KGI +ERV++ ++E E
Sbjct: 652 VKIDRKGTVLYLKPKTPSYKA-----LRKRIPKIKNIVLKGIPGIERVLVKKEEHE---- 702
Query: 1098 KENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINET 1157
++Y L +G+ L+ V EG+D +T +N+I E+Q+ LGIEAAR II+E+ T
Sbjct: 703 ----NDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNT 758
Query: 1158 MKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVN 1217
++ G+ +D RH+ML+AD+MT GEV I R G+ SVL A+FE+T HL++A+ +
Sbjct: 759 LEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEH 818
Query: 1218 GRDDRIEGVSECIIMGIPMPLGTGILKIR 1246
G D+++GV E +I+G P+ LGTG + +R
Sbjct: 819 GEVDKLKGVIENVIVGKPIKLGTGCVDLR 847
Score = 56.1 bits (135), Expect = 1e-07
Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 867 KSQILEEVTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTL 925
K ++ E+++ K G+TE+ +E I S Y VE A+G + AQSIGEPGTQM+L
Sbjct: 20 KDELFEKLS-KRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
>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 = 189 bits (483), Expect = 1e-53
Identities = 108/348 (31%), Positives = 175/348 (50%), Gaps = 48/348 (13%)
Query: 902 VEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEII-NGAKRISTPII 960
VE G A+G + AQSIGEP TQMTL TFHFAG MN+T G+PR++EI+ +K I TP +
Sbjct: 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSM 66
Query: 961 TAELECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCIN 1020
T L + ++A R A+++K RL+ + ++
Sbjct: 67 TLPL--KNGKSAER--------------AETLKK----RLSRVTLS-------------- 92
Query: 1021 ADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSL-KNVLPMVIVKGI 1079
D+V++ V +++ K+L + E+ + S L S+ + + +++ I
Sbjct: 93 -DVVEKVEVTEILKTIERVFKKLLG-KWCEVTIKLPLSSPKLLLLSIVEKLARKAVIREI 150
Query: 1080 KTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVM-GAEGIDGCKTKSNHIFEVQ 1138
+ R + E++K G K KY ++ EG L A+ ++ +D + +N I +
Sbjct: 151 PGITRCFVVEEDK--------GGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAML 202
Query: 1139 QTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSV 1198
T GIEAAR I+ EI+ K +G+++D RH+ L+AD MTF G R G++ S
Sbjct: 203 NTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMES-STSP 261
Query: 1199 LMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIR 1246
L SFE T L A++NG D + S +++G P+ GTG+ +
Sbjct: 262 LQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 194 bits (494), Expect = 5e-50
Identities = 186/733 (25%), Positives = 297/733 (40%), Gaps = 130/733 (17%)
Query: 40 GMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNVATYILNPVNVLFLFKRMT 99
GM +AV L D K E L+ + K KA KR+
Sbjct: 258 GMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQKREKA-----------------VKRLK 300
Query: 100 DTDCEVLYLSERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQ 159
D L P +I+ I V P +RP V +DG + +D+ + +R+I N L++
Sbjct: 301 VVDA-FLKSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKR 359
Query: 160 ELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGN 219
L LQ V ++ RG P + RPL LKGKQGRFR N
Sbjct: 360 LLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLADMLKGKQGRFRQN 419
Query: 220 LSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCI 272
L GKRV+Y+GR+VI P+LK+ + +P MA L P E NI+ ++ +
Sbjct: 420 LLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAV 479
Query: 273 QNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLH 332
G A ++ ++ I D VL NR P+LH
Sbjct: 480 DRG----------------ASYVW---------DVLEEVIQDH------PVLLNRAPTLH 508
Query: 333 RMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNL 392
R+ I ++ + ++ + VC +NADFDGD+M +HVP + +A+ EA +LM NN+
Sbjct: 509 RLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNI 568
Query: 393 CTPKNGEILVASTQDFLTS-SFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKP 451
+P +G L TQD + +L T +D F D ++ D L+
Sbjct: 569 KSPAHGRPLTVPTQDMIIGVYYLTTERDGF---EGEGRTFADFDDALNAYDARADLDLQA 625
Query: 452 VELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVY- 510
+++R +M V + E+T + + I T I + P D Y
Sbjct: 626 ----------KIVVRLSRDMTVRGSYGDLEETKAGERIETTVG-RIIFNQVLPED---YP 671
Query: 511 FRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG 570
+ N +++ +G+ L + Y ++ + K + G ++
Sbjct: 672 YLNYKMVKKDIGR----------LVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVS 721
Query: 571 IDD--VQPKK----ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVIT 624
+ D + K +D+K I E+YE G + + +
Sbjct: 722 VYDATIPDDKPEILAEADEKVAAIDEDYED-----------------GFLSERERHKQVV 764
Query: 625 DILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNG- 683
DI E+ G+A + N +M+ G++G+ I Q+ G + G
Sbjct: 765 DIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMA-----DMKGE 819
Query: 684 FIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMS 743
ID P KA +F GLS E+F T G R+GLVDTA++TAD+GY++
Sbjct: 820 IIDL-----PIKA-----------NFREGLSVLEYFISTHGARKGLVDTALRTADSGYLT 863
Query: 744 RRLIKALEDLSIQ 756
RRL+ +D+ ++
Sbjct: 864 RRLVDVAQDVIVR 876
Score = 76.4 bits (188), Expect = 8e-14
Identities = 38/94 (40%), Positives = 55/94 (58%), Gaps = 13/94 (13%)
Query: 879 SGITEKQLEVFIQTCFSRYRV------------KRVEAGTAIGAIGAQSIGEPGTQMTLK 926
+G+T+ Q+ + TC + Y V + V GTA+G I AQSIGEPGTQ+T++
Sbjct: 937 AGVTKVQIRT-LMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMR 995
Query: 927 TFHFAGVASMNITQGVPRIKEIINGAKRISTPII 960
TFH GVA +ITQG+PR+ E+ K ++
Sbjct: 996 TFHSGGVAGDDITQGLPRVAELFEARKPKGEAVL 1029
Score = 41.4 bits (97), Expect = 0.004
Identities = 24/65 (36%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 1183 VLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242
+LGIT+ + S L ASF++T L +A++ G+ D + G+ E +I+G P+P GTG+
Sbjct: 1179 LLGITKASLAT--DSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236
Query: 1243 LKIRQ 1247
+ R
Sbjct: 1237 SRYRD 1241
>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 = 149 bits (379), Expect = 1e-41
Identities = 65/185 (35%), Positives = 96/185 (51%), Gaps = 28/185 (15%)
Query: 391 NLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILK 450
N+ +P+NG+ ++ +QD + +L+TR+DTF+DR + Y + LP PAILK
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYG------IVLPHPAILK 54
Query: 451 PV-ELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFV 509
P+ LWTGKQ FS L+ N +G + ET+C ND +V
Sbjct: 55 PIKPLWTGKQTFSRLLPNEINP--------------------KGKPKTNEETLCENDSYV 94
Query: 510 YFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSI 569
N ELISG + K G + L ++ ++YG T ++RL KL R++ GFSI
Sbjct: 95 LINNGELISGVIDKKLGG-KSLGSLIHIIYKEYGPEETVKFLDRLQKLGFRYLTKSGFSI 153
Query: 570 GIDDV 574
GIDD+
Sbjct: 154 GIDDI 158
>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 = 146 bits (369), Expect = 2e-40
Identities = 56/108 (51%), Positives = 75/108 (69%)
Query: 1134 IFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQK 1193
I E+ + LGIEAAR II EI + + + G+S+D+RH+ L+AD+MT+ G + G+TR G +
Sbjct: 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRA 109
Query: 1194 MDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTG 1241
S LM ASFEKT HL +A+ G D +EGVSE II+G P PLGTG
Sbjct: 110 SKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
Score = 89.4 bits (222), Expect = 1e-20
Identities = 36/48 (75%), Positives = 43/48 (89%)
Query: 905 GTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGA 952
G A+G + AQSIGEPGTQMTL+TFHFAGVASMN+T G+PR+KEI+N A
Sbjct: 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
>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 = 150 bits (381), Expect = 8e-40
Identities = 73/213 (34%), Positives = 104/213 (48%), Gaps = 16/213 (7%)
Query: 14 LMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHT- 72
+K I C + C +CG NG +K SK + A AI
Sbjct: 128 RLKKINNLCKKKS----ICSKCGEDNGGLKAFEGCGKYQPKISK------DGAEAIKALL 177
Query: 73 -KESKAAVNVATYILNPVNVLFLFKRMTDTDCEVLYLSE---RPEKLIITNIAVPPIAIR 128
+ LNP VL +FK+++ D E+L + RPE +I+T + VPP IR
Sbjct: 178 KNIEIEELKEKLRKLNPEKVLQIFKKISKEDEEILGFNPSGNRPEWMILTVLPVPPPCIR 237
Query: 129 PSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSD 188
PSV +DG + E+D+T +L+ II+ N L++ L E + LQ VA ++D
Sbjct: 238 PSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLEEGAPSHIIREEKRLLQEHVATLFDND 297
Query: 189 VRGVPFSMQ-VARPLSGFVQRLKGKQGRFRGNL 220
+ G P ++Q RPL QRLKGK+GRFRGNL
Sbjct: 298 IPGQPPALQKSGRPLKSISQRLKGKEGRFRGNL 330
>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 = 156 bits (395), Expect = 2e-39
Identities = 107/337 (31%), Positives = 161/337 (47%), Gaps = 53/337 (15%)
Query: 94 LFKRMTDTDCEVLYLSERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQT 153
L KR+ D + S RPE +++ I V P +RP V +DG + +D+ + +R+I
Sbjct: 218 LIKRLRVID-NFIATSSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINR 276
Query: 154 N---ASLQQ----ELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFV 206
N A LQ+ E++ N LQ V I++ RG RPL
Sbjct: 277 NNRLARLQEILAPEIIVRNEK-------RMLQEAVDALIDNGRRGRTVVGANNRPLKSLS 329
Query: 207 QRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYP-------ER 259
++GKQGRFR NL GKRV+Y+GR+VI P LK+ + +P MA L P +
Sbjct: 330 DIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQ 389
Query: 260 VSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLED 319
+NI+ ++ IQ D+ VL + +
Sbjct: 390 GIVNNIKAAKKLIQRADDE------------IWSVL-------------------QEVIT 418
Query: 320 GDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEAR 379
G V+ NR P+LHR+ I ++ R ++ + VC +NADFDGD+M +HVP + EA+
Sbjct: 419 GHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQ 478
Query: 380 TEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLIT 416
TEA LLM NN+ +P GE +V +QD + + +T
Sbjct: 479 TEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLT 515
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 158 bits (400), Expect = 9e-39
Identities = 173/673 (25%), Positives = 286/673 (42%), Gaps = 106/673 (15%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +I+T I + P +RP V ++ + +D+ + II N L++ L
Sbjct: 1665 RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMI 1724
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQ-RLKGKQGRFRGNLSGKRVEYTG 229
LQ V ++ R + A + LKGKQGRFR NL GKRV+Y+G
Sbjct: 1725 RNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSG 1784
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPD 289
R+VI P LK+ + +P RMA L P S + Y A I++
Sbjct: 1785 RSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKM-------------YGMAPTIKFAS 1831
Query: 290 GTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTL 349
R + + L +K VL NR P+LHR+ I ++ + +
Sbjct: 1832 KLIRAEKPEVWDMLEEVIKE-----------HPVLLNRAPTLHRLGIQAFEPILIEGKAI 1880
Query: 350 RFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFL 409
+ + VC +NADFDGD+M +HVP + EA+ EA +LM NN+ +P NG ++ ++D +
Sbjct: 1881 QLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIV 1940
Query: 410 TSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHA 469
+ +T ++ D DLP+ VE L + H+
Sbjct: 1941 LGIYYLTLQEPKED------------------DLPSFGAFCEVE----HSLSDGTLHIHS 1978
Query: 470 NMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDG----FVYFRNSELISGQLGKAT 525
+++ Y + I + G E +T+C G + F E + L
Sbjct: 1979 SIK-----------YRMEYINSSG--ETHYKTICTTPGRLILWQIFPKHENLGFDLINQV 2025
Query: 526 LGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG-IDDVQPKKE---LS 581
L + ++ R+ G AT ++L L + G S D V P+ + +
Sbjct: 2026 LTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVD 2085
Query: 582 DKKG--KLISENYEVCNV-KIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKAC 638
+G K S Y+ + + + YN K + ++ + + D+L I G +
Sbjct: 2086 HARGEIKKFSMQYQDGLITRSERYN------KVIDEWSKCTDMIANDMLKAISIYDGNSK 2139
Query: 639 MGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKE 698
NS +M G++GS SQM G + G P+G I +
Sbjct: 2140 Y------NSVYMMVNSGARGS---TSQMKQLAGMR--GLMTKPSGEI----------IET 2178
Query: 699 PAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALED-LSIQY 757
P + ++F GL+ E+F T G R+GL DTA+KTA++GY++RRL+ ++ + ++
Sbjct: 2179 P-----IISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKH 2233
Query: 758 DNSVRNAGGCIVQ 770
D +N G +V+
Sbjct: 2234 DCKTKN--GLVVR 2244
Score = 52.3 bits (125), Expect = 2e-06
Identities = 24/43 (55%), Positives = 31/43 (72%), Gaps = 4/43 (9%)
Query: 900 KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGV 942
K V G A+G I AQS+GEPGTQ+T++TFH GV +T+GV
Sbjct: 2328 KIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGV 2366
Score = 47.3 bits (112), Expect = 7e-05
Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 44/166 (26%)
Query: 1134 IFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLL-------------ADLMTFR 1180
+ ++ + LG+EA +I EI + + G+ ID +H+ ++ D M
Sbjct: 2638 LHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLV 2697
Query: 1181 GEVL---------------------------GITRFGIQKMDKSVLMLASFEKTADHLFN 1213
GE + GITR ++ S + ASF++T L
Sbjct: 2698 GESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLET--SSFISAASFQETTKVLTE 2755
Query: 1214 ASVNGRDDRIEGVSECIIMGIPMPLGTGIL--KIRQRDAVPPMLKY 1257
A+ G+ D + G+ E +I+G +P GTG++ K+R + KY
Sbjct: 2756 AAFCGKSDPLSGLKENVIVGRLIPAGTGLIMNKVRALSLCDNVDKY 2801
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 148 bits (376), Expect = 6e-37
Identities = 101/320 (31%), Positives = 153/320 (47%), Gaps = 52/320 (16%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTN---ASLQQ----ELVE 163
RPE +++ I V P +RP V +DG + +D+ + +R+I N A LQ+ E++
Sbjct: 241 RPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIV 300
Query: 164 ANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGK 223
N LQ V I++ RG RPL ++GKQGRFR NL GK
Sbjct: 301 RNEK-------RMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGK 353
Query: 224 RVEYTGRTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQNGP 276
RV+Y+GR+VI P LK+ + +P MA L P + +NI+ ++ IQ
Sbjct: 354 RVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRAD 413
Query: 277 DKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSI 336
+ +VL + +G VL NR P+LHR+ I
Sbjct: 414 PE------------VWQVL-------------------EEVIEGHPVLLNRAPTLHRLGI 442
Query: 337 MCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPK 396
++ R ++ + VC +NADFDGD+M +HVP + EA+ EA LLM NN+ +P
Sbjct: 443 QAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPA 502
Query: 397 NGEILVASTQDFLTSSFLIT 416
GE +V +QD + + +T
Sbjct: 503 TGEPIVTPSQDMVLGCYYLT 522
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 141 bits (358), Expect = 2e-34
Identities = 94/306 (30%), Positives = 145/306 (47%), Gaps = 36/306 (11%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
PE +++ + V P +RP + +DG + +D+ E +R+I N +L L + S
Sbjct: 260 EPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGE 319
Query: 171 LAGWET--LQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYT 228
L + LQ V +++ +RG P +P F ++GK+GRFR NL GKRV+Y+
Sbjct: 320 LVMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYS 379
Query: 229 GRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGA--RMIR 286
GR+VI P+L + + +P +A L P +R I+ A IR
Sbjct: 380 GRSVIVVGPSLSLHQCGLPREIAIELFQP--------FVIRGLIRQHLASNIRAAKSKIR 431
Query: 287 YPDGTARVLYGKFRNQLAVELKSGCIVDRHLE---DGDVVLFNRQPSLHRMSIMCHRARI 343
+ IV L+ G VL NR P+LHR+ I + +
Sbjct: 432 ---------------------EKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPIL 470
Query: 344 MPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVA 403
+ R + + VC +NADFDGD+M +HVP + EA+ EA LLM NL +P G+ +
Sbjct: 471 VEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISV 530
Query: 404 STQDFL 409
+QD L
Sbjct: 531 PSQDML 536
>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 = 126 bits (319), Expect = 3e-34
Identities = 48/108 (44%), Positives = 66/108 (61%), Gaps = 1/108 (0%)
Query: 599 IKEYNE-GKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSK 657
I + GKL+ G +T EA+I +ILN+ R+ AG SL NS +M+ G+K
Sbjct: 1 ITDAERYGKLEDIWGMTLEETFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAK 60
Query: 658 GSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFV 705
GS INISQ+ C GQQ+V G+R P GF R+LPHF + + P ++GFV
Sbjct: 61 GSIINISQIAGCRGQQNVEGKRIPFGFSGRTLPHFKKDDEGPESRGFV 108
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 134 bits (339), Expect = 1e-31
Identities = 96/302 (31%), Positives = 153/302 (50%), Gaps = 30/302 (9%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +++T + V P +RP V +DG + +D+ E +R+I N L++ L+E +
Sbjct: 1622 RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKR-LMELGAPEII 1680
Query: 171 LAGWE-TLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTG 229
+ + LQ V ++ RPL + +KGKQGRFR NL GKRV+++G
Sbjct: 1681 VRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSG 1740
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPD 289
R+VI PNLK+ E +P MA L P H + KL +
Sbjct: 1741 RSVIVVGPNLKMDECGLPKNMALELFKP-----HLLSKLEE------------------R 1777
Query: 290 GTARVLYGKFRNQLAVELKSGCIVD--RHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWR 347
G A L R +E KS + + + + +G VL NR P+LH+ SI +++ +
Sbjct: 1778 GYATTLKQAKR---MIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGK 1834
Query: 348 TLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQD 407
++ + VC+ +NADFDGD+M +HVP ++EA E +LM N+ P +G+ + +QD
Sbjct: 1835 AIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQD 1894
Query: 408 FL 409
+
Sbjct: 1895 MV 1896
Score = 65.3 bits (159), Expect = 2e-10
Identities = 61/242 (25%), Positives = 106/242 (43%), Gaps = 35/242 (14%)
Query: 543 GAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEY 602
G T+ ++ L L R+ G SI ++D+ K K++ E V++K+
Sbjct: 1989 GIGITATFLDNLKTLGFRYATKAGISISMEDII----TPKDKQKMV----EKAKVEVKKI 2040
Query: 603 NEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWR----NSPLIMSQCGSKG 658
+ Q G Q I D + + K M ++ NS +M+ G++G
Sbjct: 2041 ---QQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARG 2097
Query: 659 SPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEF 718
S I Q+ A G + P+G I + P + ++F GL+ E+
Sbjct: 2098 SAAQIRQLSAMRGLMT-----KPDGSI----------IETP-----IISNFKEGLNVLEY 2137
Query: 719 FFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGM 778
F T G R+GL DTA+KTA+ GY++R+LI +++ + D+ + G I G + +
Sbjct: 2138 FNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELI 2197
Query: 779 DP 780
+P
Sbjct: 2198 EP 2199
Score = 54.9 bits (132), Expect = 3e-07
Identities = 22/36 (61%), Positives = 26/36 (72%)
Query: 900 KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVAS 935
K G A+G + AQSIGEPGTQ+TL+TFH G AS
Sbjct: 2272 KMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTAS 2307
Score = 43.8 bits (103), Expect = 7e-04
Identities = 23/62 (37%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 1183 VLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242
+LGITR I S++ ASF++T L AS+ + D +E + E +++G +P+GTG+
Sbjct: 2816 LLGITRAAIGS--DSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGM 2873
Query: 1243 LK 1244
K
Sbjct: 2874 YK 2875
>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 = 84.1 bits (209), Expect = 3e-18
Identities = 31/49 (63%), Positives = 41/49 (83%), Gaps = 1/49 (2%)
Query: 900 KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEI 948
K VE G A+G I AQSIGEPGTQ+T++TFH GVA+ +ITQG+PR++E+
Sbjct: 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEEL 48
Score = 47.5 bits (114), Expect = 1e-05
Identities = 35/157 (22%), Positives = 70/157 (44%), Gaps = 44/157 (28%)
Query: 1127 CKTKSNH-IFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMT------- 1178
+ + H + ++ LG EA + +++EI + ++ G++I+ +H+ ++ MT
Sbjct: 51 ARKINPHDLLRIK-FLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIID 109
Query: 1179 ------FRGE---------------------------VLGITRFGIQKMDKSVLMLASFE 1205
GE +LGIT+ + +S + ASF+
Sbjct: 110 PGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNT--ESFISAASFQ 167
Query: 1206 KTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242
+T L A++ G+ D + G+ E +I+G +P GTG+
Sbjct: 168 ETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 79.7 bits (198), Expect = 7e-15
Identities = 40/105 (38%), Positives = 56/105 (53%), Gaps = 28/105 (26%)
Query: 860 EDIGWDDKSQILEEVTHKTSGITEKQLEVFIQ---TCFSRYRV------------KRVEA 904
I ++ + +EE +GI E V I+ TC +R+ V K V
Sbjct: 829 TLID-EEIADKIEE-----AGIEE----VKIRSVLTCETRHGVCAKCYGRDLATGKLVNI 878
Query: 905 GTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEII 949
G A+G I AQSIGEPGTQ+T++TFH GV +IT G+PR+ E+
Sbjct: 879 GEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELF 920
Score = 78.6 bits (195), Expect = 2e-14
Identities = 40/106 (37%), Positives = 58/106 (54%), Gaps = 25/106 (23%)
Query: 316 HLED---GDVVLFNRQPSLHRMSIMCHRA-----------RIMPWRTLRFNESVCNPYNA 361
LE+ VL NR P+LHR+ I +A ++ P L VC +NA
Sbjct: 401 VLEEVIKEHPVLLNRAPTLHRLGI---QAFEPVLIEGKAIQLHP---L-----VCTAFNA 449
Query: 362 DFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQD 407
DFDGD+M +HVP + EA+ EA +LM NN+ +P NG+ ++ +QD
Sbjct: 450 DFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQD 495
Score = 77.8 bits (193), Expect = 2e-14
Identities = 64/222 (28%), Positives = 101/222 (45%), Gaps = 55/222 (24%)
Query: 540 RDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISE-NYEVCNVK 598
R YG T ++++ L ++ G SIGIDD+ + +K ++I E EV ++
Sbjct: 588 RRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDI----VIPPEKKEIIEEAEKEVAEIE 643
Query: 599 IKEYNEGKLQLKPGCDAAQTLE----AVITDILNRIREDAGKACMGSLPWRNSPL----I 650
K+Y G + T VI DI ++ ++ KA M +L +
Sbjct: 644 -KQYRRGLI----------TDGERYNKVI-DIWSKATDEVAKAMMKNLSKDQESFNPIYM 691
Query: 651 MSQCGSKGSPINISQMVACVGQQSVGGRR----APNG-FIDRSLPHFPRKAKEPAAKGFV 705
M+ G++GS I Q+ G R P+G I+ P K+
Sbjct: 692 MADSGARGSASQIRQL---------AGMRGLMAKPSGEIIET-----PIKS--------- 728
Query: 706 ANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLI 747
+F GL+ E+F T G R+GL DTA+KTAD+GY++RRL+
Sbjct: 729 --NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLV 768
Score = 74.3 bits (184), Expect = 3e-13
Identities = 55/157 (35%), Positives = 79/157 (50%), Gaps = 32/157 (20%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDG---SQSNENDI-------TERLKRIIQTNAS---L 157
+PE +I+ + V P +RP V +DG + S+ ND+ RLKR+++ A +
Sbjct: 223 KPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIV 282
Query: 158 QQE---LVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQG 214
+ E L EA V ++ RG P + RPL LKGKQG
Sbjct: 283 RNEKRMLQEA----------------VDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQG 326
Query: 215 RFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMA 251
RFR NL GKRV+Y+GR+VI P LK+ + +P +MA
Sbjct: 327 RFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA 363
Score = 48.5 bits (117), Expect = 2e-05
Identities = 57/219 (26%), Positives = 98/219 (44%), Gaps = 58/219 (26%)
Query: 1084 RVVIAEKEKEKRKVK---ENGEKKKY------RLLV-EGTGLQAVMGAEGIDGCKTKSNH 1133
V ++ K KR++ ++GE+++Y LLV EG ++A G + DG +
Sbjct: 937 TVSFGKETKGKRRIVITPDDGEEREYLIPKGKHLLVQEGDHVEA--GDKLTDGSID-PHD 993
Query: 1134 IFEVQQTLGIEAARICIIDEINETMKAHGMSI-DK------RHMM-------------LL 1173
I V LG+EA + +++E+ + + G+ I DK R M+ L
Sbjct: 994 ILRV---LGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLP 1050
Query: 1174 ADLM--------------------TFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFN 1213
+L+ T R +LGIT+ + +S L ASF++T L
Sbjct: 1051 GELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLAT--ESFLSAASFQETTRVLTE 1108
Query: 1214 ASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDAVP 1252
A++ G+ D + G+ E +I+G +P GTG+ + R P
Sbjct: 1109 AAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEP 1147
>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA
polymerase IV, C-terminal domain. Higher plants have
five multi-subunit nuclear RNA polymerases: RNAP I, RNAP
II and RNAP III, which are essential for viability; plus
the two isoforms of the non-essential polymerase RNAP IV
(IVa and IVb), which specialize in small RNA-mediated
gene silencing pathways. RNAP IVa and/or RNAP IVb might
be involved in RNA-directed DNA methylation of endogenous
repetitive elements, silencing of transgenes, regulation
of flowering-time genes, inducible regulation of adjacent
gene pairs, and spreading of mobile silencing signals.
NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b
is the largest subunit of RNAP IVb. The full subunit
compositions of RNAP IVa and RNAP IVb are not known, nor
are their templates or enzymatic products. However, it
has been shown that RNAP IVa and, to a lesser extent,
RNAP IVb are crucial for several RNA-mediated gene
silencing phenomena.
Length = 381
Score = 66.7 bits (163), Expect = 3e-11
Identities = 80/380 (21%), Positives = 149/380 (39%), Gaps = 49/380 (12%)
Query: 905 GTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEII-NGAKRISTP----I 959
G +G++ A +I EP + L + + +KE++ +K S +
Sbjct: 1 GEPVGSLAATAISEPAYKALLDP------PQSLESSPLELLKEVLECRSKSKSKENDRRV 54
Query: 960 ITAELECNDN-----ENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQD 1014
I + C + E AA VK +E+ L +A + I + + ++ + +
Sbjct: 55 ILSLHLCKCDHGFEYERAALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNT 114
Query: 1015 AHLCINADIVKESIVQTPK------IKLKQQHIKVLDFRKLEIFPPVDKSK-IHFELYSL 1067
I S+ T L ++ K+ D L + SK L L
Sbjct: 115 KKKGKKKAIFSTSLKITKFSPWVCHFHLDKECQKLSDGPCLTFSVSKEVSKSSEELLDVL 174
Query: 1068 KN-VLPM---VIVKGIKTVERVVIAEKEKEKR-KVKENGEKKKYRLLVE----------- 1111
++ ++P ++KG + ++ V I ++ VK G+ + L++E
Sbjct: 175 RDRIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKTR 234
Query: 1112 GTGLQAVMGA-----EGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSID 1166
G VM A + ID ++ I +++ LGI+AA + + + G S+
Sbjct: 235 GNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVL 294
Query: 1167 KRHMMLLADLMTFRGEVLGITRFGIQKMDKSV-----LMLASFEKTADHLFNASVNGRDD 1221
+ H++L+AD MT+ GE +G+ G + +S+ A F A+ G D
Sbjct: 295 REHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASD 354
Query: 1222 RIEGVSECIIMGIPMPLGTG 1241
+ GV + G P+GTG
Sbjct: 355 SLSGVLDACAWGKEAPVGTG 374
>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 = 66.0 bits (161), Expect = 1e-10
Identities = 70/261 (26%), Positives = 113/261 (43%), Gaps = 68/261 (26%)
Query: 511 FRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG 570
F+N + L L S + YG T+ ++L L R+ G SI
Sbjct: 2 FKNRVVDKKALKN----------LISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSIS 51
Query: 571 IDD--VQPKK----ELSDKKGKLISENY---EVCNVK-----IKEYNEGKLQLKPGCDAA 616
+DD V P K E ++K+ + E Y E+ V+ I +N
Sbjct: 52 VDDLKVPPAKQDLLEAAEKEIRATEERYRRGEITEVERFQKVIDTWNG------------ 99
Query: 617 QTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVG 676
T E + +++N R+ NS +M+ G++G N+SQ+ VG + G
Sbjct: 100 -TNEELKDEVVNNFRQTDP---------LNSVYMMAFSGARG---NMSQVRQLVGMR--G 144
Query: 677 GRRAPNG-FIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVK 735
P G ID LP + +F GL+ TE+ + G R+GLVDTA++
Sbjct: 145 LMANPQGEIID--LP--------------IKTNFREGLTVTEYVISSYGARKGLVDTALR 188
Query: 736 TADTGYMSRRLIKALEDLSIQ 756
TAD+GY++RRL+ +D+ ++
Sbjct: 189 TADSGYLTRRLVDVSQDVIVR 209
Score = 54.9 bits (132), Expect = 3e-07
Identities = 22/43 (51%), Positives = 30/43 (69%)
Query: 900 KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGV 942
V+ G A+G I AQSIGEPGTQ+T++TFH GV + + + V
Sbjct: 304 HLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQV 346
Score = 39.8 bits (93), Expect = 0.012
Identities = 30/138 (21%), Positives = 57/138 (41%), Gaps = 38/138 (27%)
Query: 1142 GIEAARICIIDEINETMKAHGMSIDKRHM--------------------MLLADLMTFR- 1180
++ + +++E+ ++ G+ I +H+ +L +L+ R
Sbjct: 1084 SLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQ 1143
Query: 1181 ----GEVLGIT----------RFGIQKMD---KSVLMLASFEKTADHLFNASVNGRDDRI 1223
E + IT GI K S + ASF++T L A++ G+ D +
Sbjct: 1144 VEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWL 1203
Query: 1224 EGVSECIIMGIPMPLGTG 1241
G+ E +I+G +P GTG
Sbjct: 1204 RGLKENVIIGRLIPAGTG 1221
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 61.1 bits (149), Expect = 4e-09
Identities = 23/41 (56%), Positives = 28/41 (68%)
Query: 902 VEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGV 942
VE G A+G I QSIGEPGTQ+TL+TFH GV + + V
Sbjct: 312 VELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQV 352
Score = 55.3 bits (134), Expect = 2e-07
Identities = 21/36 (58%), Positives = 28/36 (77%)
Query: 712 GLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLI 747
GLS TE+ G R+G+VDTAV+TAD GY++RRL+
Sbjct: 172 GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
Score = 31.4 bits (72), Expect = 4.3
Identities = 23/66 (34%), Positives = 39/66 (59%), Gaps = 2/66 (3%)
Query: 1183 VLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGI 1242
+LGIT+ + +S + ASF++T L A++ GR D ++G+ E +I+G +P GTG
Sbjct: 1260 LLGITKASLNT--QSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
Query: 1243 LKIRQR 1248
+ R
Sbjct: 1318 KGLVHR 1323
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 60.8 bits (148), Expect = 4e-09
Identities = 71/265 (26%), Positives = 113/265 (42%), Gaps = 84/265 (31%)
Query: 511 FRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG 570
FRN + L L + ++YG T+ + L L R+ G SI
Sbjct: 3 FRNRVVDKKALKN----------LIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSIS 52
Query: 571 IDDVQ---PKKELSDKKGKLIS---ENY---EVCNVK-----IKEYNEGKLQLKPGCDAA 616
+DD++ K++L ++ + I+ E Y E+ V+ I +NE +LK
Sbjct: 53 VDDLKVPPAKRDLLEQAEEEITATEERYRRGEITEVERFQKVIDTWNETNERLK------ 106
Query: 617 QTLEAVI-----TDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVG 671
+ V+ D L NS +M+ G++G N+SQ+
Sbjct: 107 ---DEVVKNFRQNDPL------------------NSVYMMAFSGARG---NMSQV----- 137
Query: 672 QQSVGGR---RAPNG-FIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGRE 727
+Q VG R P G ID LP + +F GL+ TE+ + G R+
Sbjct: 138 RQLVGMRGLMANPQGEIID--LP--------------IKTNFREGLTVTEYVISSYGARK 181
Query: 728 GLVDTAVKTADTGYMSRRLIKALED 752
GLVDTA++TAD+GY++RRL+ +D
Sbjct: 182 GLVDTALRTADSGYLTRRLVDVSQD 206
Score = 58.1 bits (141), Expect = 3e-08
Identities = 21/32 (65%), Positives = 26/32 (81%)
Query: 902 VEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGV 933
V+ G A+G I AQSIGEPGTQ+T++TFH GV
Sbjct: 308 VDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 339
Score = 31.5 bits (72), Expect = 3.5
Identities = 31/139 (22%), Positives = 58/139 (41%), Gaps = 38/139 (27%)
Query: 1141 LGIEAARICIIDEINETMKAHGMSIDKRHM--------------------MLLADLMTFR 1180
++ + +++E+ ++ G+ I +H+ ML +L+ R
Sbjct: 1084 EALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELR 1143
Query: 1181 -----GEVLGIT-----RF-----GIQKMD---KSVLMLASFEKTADHLFNASVNGRDDR 1222
E + IT + GI K S + ASF++T L A++ G+ D
Sbjct: 1144 QVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDW 1203
Query: 1223 IEGVSECIIMGIPMPLGTG 1241
+ G+ E +I+G +P GTG
Sbjct: 1204 LRGLKENVIIGRLIPAGTG 1222
>gnl|CDD|178515 PLN02927, PLN02927, antheraxanthin epoxidase/zeaxanthin epoxidase.
Length = 668
Score = 33.5 bits (76), Expect = 0.93
Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 11/85 (12%)
Query: 1044 LDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVV-------IAEKEKEKRK 1096
LDF + +F PV K + + +L S P + G ++ + ++ + EKE+++
Sbjct: 17 LDFTRTHVFSPVAK-QFYLDLSSFSGK-PGGGLSGFRSRKALLGVKAATALVEKEEKREA 74
Query: 1097 VKENGEKKKYRLLVEGTGLQAVMGA 1121
V E +KKK R+LV G G+ ++ A
Sbjct: 75 VTE--KKKKSRVLVAGGGIGGLVFA 97
>gnl|CDD|178137 PLN02522, PLN02522, ATP citrate (pro-S)-lyase.
Length = 608
Score = 33.3 bits (76), Expect = 1.00
Identities = 24/65 (36%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 37 YINGMVKKAVAVLGIIH------DRSKVTESLQEFA-SAITHTKESKAAVNVATYILNPV 89
++ GM KK + V GI H +R K E LQ++A + K + AV V TY L+
Sbjct: 472 FVEGMKKKGIRVPGIGHRIKSRDNRDKRVELLQKYARTHFPSVKYMEYAVQVETYTLSKA 531
Query: 90 NVLFL 94
N L L
Sbjct: 532 NNLVL 536
>gnl|CDD|88524 cd05623, STKc_MRCK_alpha, Catalytic domain of the Protein
Serine/Threonine Kinase, DMPK-related cell division
control protein 42 binding kinase alpha.
Serine/Threonine Kinases (STKs), DMPK-like subfamily,
DMPK-related cell division control protein 42 (Cdc42)
binding kinase (MRCK) alpha isoform, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The DMPK-like subfamily
is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. MRCK is activated via interaction with the
small GTPase Cdc42. MRCK/Cdc42 signaling mediates
myosin-dependent cell motility. MRCKalpha is expressed
ubiquitously in many tissues. It plays a role in the
regulation of peripheral actin reorganization and
neurite outgrowth. It may also play a role in the
transferrin iron uptake pathway.
Length = 332
Score = 32.7 bits (74), Expect = 1.2
Identities = 32/143 (22%), Positives = 58/143 (40%), Gaps = 24/143 (16%)
Query: 727 EGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVR--NAGGCIVQFLYGDDGMDPANME 784
+G V ++V Y+S +++A+ED +Y + G C+ + LYG+ ++
Sbjct: 155 DGTVQSSVAVGTPDYISPEILQAMEDGKGKYGPECDWWSLGVCMYEMLYGETPFYAESLV 214
Query: 785 GKSGEPLNFDRLLMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKF 844
G+ +N +R+ P QV+++ E + CS R+
Sbjct: 215 ETYGKIMNHK--------------ERFQFPAQVTDVSEDAKDLIRRLICS-------REH 253
Query: 845 FEGQQDKLD-KKIKFVEDIGWDD 866
GQ D K+ F I WD+
Sbjct: 254 RLGQNGIEDFKQHPFFTGIDWDN 276
>gnl|CDD|131490 TIGR02437, FadB, fatty oxidation complex, alpha subunit FadB.
Members represent alpha subunit of multifunctional enzyme
complex of the fatty acid degradation cycle. Activities
include: enoyl-CoA hydratase (EC 4.2.1.17),
dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8),
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadB. This model excludes the
FadJ family represented by SP:P77399 [Fatty acid and
phospholipid metabolism, Degradation].
Length = 714
Score = 32.9 bits (75), Expect = 1.2
Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 23/104 (22%)
Query: 932 GVASMNITQGVPRIKEIINGAKRISTPIITAELECNDNENAARVVKGRIEKTLLGQVAKS 991
G+A + ++G P + + IN L+ E AA+++ ++E+ +
Sbjct: 327 GIAYQSASKGTPIVMKDIN----------QHSLDLGLTE-AAKLLNKQVER------GRI 369
Query: 992 IKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIK 1035
M L I L N DIV E++V+ PK+K
Sbjct: 370 TPAKMAGVLNGITPTLSYAGFD------NVDIVVEAVVENPKVK 407
>gnl|CDD|132569 TIGR03530, GldJ_short, gliding motility-associated lipoprotein
GldJ. Members of this protein family are exclusive to
the Bacteroidetes phylum (previously
Cytophaga-Flavobacteria-Bacteroides). GldJ is a
lipoprotein linked to a type of rapid surface gliding
motility found in certain Bacteroidetes, such as
Flavobacterium johnsoniae. Knockouts of GldJ abolish the
gliding phenotype. GldJ is homologous to GldK. This
model represents the GldJ homolog in Cytophaga
hutchinsonii and several other species which is of
shorter architecture than that found in Flavobacterium
johnsoniae and is represented by a separate model
(TIGR03524). Gliding motility appears closely linked to
chitin utilization in the model species Flavobacterium
johnsoniae. Bacteroidetes with members of this protein
family appear to have all of the genes associated with
gliding motility.
Length = 402
Score = 32.3 bits (73), Expect = 1.8
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 13/74 (17%)
Query: 342 RIMPW--RTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGE 399
RI PW LR NPYN G +M + + R + + G + N +G
Sbjct: 240 RIYPWDGHALR------NPYNVKRKGKQMGDFLANFKRGRGDYAGIAGNKLN-----DGA 288
Query: 400 ILVASTQDFLTSSF 413
I+ + DF + F
Sbjct: 289 IIPTNIYDFAPNDF 302
>gnl|CDD|223299 COG0221, Ppa, Inorganic pyrophosphatase [Energy production and
conversion].
Length = 171
Score = 31.1 bits (71), Expect = 2.2
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 833 CSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTH 876
E L+ ++ FFE K +K K+V+ GW+D + +E+
Sbjct: 123 LPEHLLDEIQHFFETY--KDLEKGKWVKVEGWEDAEEAKKEIKE 164
>gnl|CDD|237754 PRK14554, PRK14554, putative pseudouridylate synthase; Provisional.
Length = 422
Score = 31.1 bits (71), Expect = 3.7
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 7/42 (16%)
Query: 1073 MVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTG 1114
V V+ ++ R KE ++KE K YR LVE
Sbjct: 286 KVEVENLRFATR-------KEVERIKEEKASKTYRALVESDE 320
>gnl|CDD|183293 PRK11730, fadB, multifunctional fatty acid oxidation complex subunit
alpha; Reviewed.
Length = 715
Score = 31.4 bits (72), Expect = 4.3
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 17/64 (26%)
Query: 972 AARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQT 1031
+V +G+I+ + V L+SI LD + D+V E++V+
Sbjct: 361 NKQVERGKIDGAKMAGV-----------LSSIRPTLDYAGFERV------DVVVEAVVEN 403
Query: 1032 PKIK 1035
PK+K
Sbjct: 404 PKVK 407
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 31.0 bits (70), Expect = 4.9
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 579 ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKP---GCDAAQTLEAVITDILNRIREDAG 635
EL +GK+++ + +++ E + +L+L A+ L + D +RI DA
Sbjct: 257 ELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADAERLTEYVQDTFDRILVDAP 316
Query: 636 KACMGSLPWRNSPLIM 651
+G+ RN P ++
Sbjct: 317 CTSLGTA--RNHPEVL 330
>gnl|CDD|177640 PHA03412, PHA03412, putative methyltransferase; Provisional.
Length = 241
Score = 30.4 bits (68), Expect = 6.1
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 37/147 (25%)
Query: 179 VEVAQYINSDVRGVPFS----MQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVIS 234
V A +IN+D F M ++ P G K K F+G +G EY
Sbjct: 96 VPEATWINADALTTEFDTLFDMAISNPPFG-----KIKTSDFKGKYTGAEFEY------- 143
Query: 235 PDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARV 294
K+ E A I P+ ++ +Y G R + T
Sbjct: 144 -----KVIERASQIARQGTFIIPQMSANF--------------RYSGTHYFRQDESTTSS 184
Query: 295 LYGKFRNQLAVELKSGCIVDR--HLED 319
KF ++ +E+ GC +D +LED
Sbjct: 185 KCKKFLDETGLEMNPGCGIDTGYYLED 211
>gnl|CDD|205373 pfam13192, Thioredoxin_3, Thioredoxin domain.
Length = 76
Score = 27.9 bits (63), Expect = 8.0
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 32 CPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFAS 67
C +C + VK+AVA LGI + KVT+ E A
Sbjct: 10 CAKCPKLEEAVKEAVAELGIDAEVEKVTD-FPEIAK 44
>gnl|CDD|237296 PRK13188, PRK13188, bifunctional UDP-3-O-[3-hydroxymyristoyl]
N-acetylglucosamine
deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein]
dehydratase; Reviewed.
Length = 464
Score = 30.3 bits (69), Expect = 8.6
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 1163 MSIDK---RHMMLLADLMTFRGEVLGITRFGIQKMD 1195
M IDK R ++ D + F+ E+L R GI +M
Sbjct: 405 MKIDKVKFRQKVVPGDTLIFKVELLSPIRRGICQMQ 440
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 30.1 bits (68), Expect = 8.9
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 116 IITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQT--NASL-QQELVEANSAFKSLA 172
I +I P+ IRP+ + G+ E + I + AS+ Q LVE KSL
Sbjct: 174 IAEDIGEFPLIIRPAFTLGGTGGGIAYNKEEFETICKAGLAASITSQVLVE-----KSLL 228
Query: 173 GWETLQVEVAQYINSDV 189
GW+ ++EV + + +V
Sbjct: 229 GWKEYELEVMRDLADNV 245
>gnl|CDD|187622 cd05364, SDR_c11, classical (c) SDR, subgroup 11. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 253
Score = 29.7 bits (67), Expect = 9.3
Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 12/83 (14%)
Query: 656 SKGSPINISQMVACVGQQSVGGRRAPNGFIDRS-LPHFPR-KAKEPAAKGFVANSFYSGL 713
+KG +N+S + G +S G I ++ L F R A E A KG NS G+
Sbjct: 132 TKGEIVNVS---SVAGGRSFPG--VLYYCISKAALDQFTRCTALELAPKGVRVNSVSPGV 186
Query: 714 SATEFFFHTMGGREGLVDTAVKT 736
T F R G+ +
Sbjct: 187 IVTGF-----HRRMGMPEEQYIK 204
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 30.4 bits (69), Expect = 9.3
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 124 PIAIRPSVIMDGSQSNENDITERLKRIIQTNASL---QQELVEANSAFKSLAGWETLQVE 180
P+ +RP+ + G+ E LK I + S Q LVE KSLAGW+ ++ E
Sbjct: 164 PVIVRPAFTLGGTGGGIAYNREELKEIAERALSASPINQVLVE-----KSLAGWKEIEYE 218
Query: 181 V 181
V
Sbjct: 219 V 219
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
0.319 0.135 0.391
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 63,994,101
Number of extensions: 6439699
Number of successful extensions: 5730
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5638
Number of HSP's successfully gapped: 98
Length of query: 1265
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1157
Effective length of database: 6,147,370
Effective search space: 7112507090
Effective search space used: 7112507090
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 65 (28.6 bits)