RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7583
(451 letters)
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit. RNA
polymerases catalyse the DNA dependent polymerization of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Each RNA
polymerase complex contains two related members of this
family, in each case they are the two largest
subunits.The clamp is a mobile structure that grips DNA
during elongation.
Length = 866
Score = 551 bits (1423), Expect = 0.0
Identities = 194/488 (39%), Positives = 242/488 (49%), Gaps = 95/488 (19%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G N RMDT ++L YP KPLV T EY+ F ELP G N+IVA++ Y+GYN ED
Sbjct: 435 VGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFED 494
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
++I+N S+V+RG+FRS
Sbjct: 495 AIIINKSSVDRGFFRS-------------------------------------------- 510
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
+ ++ Y+ K EE R + LD+DGII PG RV D+++
Sbjct: 511 -IHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLT---LNVDGYKFCKIRVR 237
GK E E K RD S E GIVD V + LN G K K+ +R
Sbjct: 566 GKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIR 625
Query: 238 SVRIPQIGDKFASRHGQKGTCGIQYRQE-------------------------------- 265
R PQIGDKFASRHGQKG QE
Sbjct: 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLES 685
Query: 266 ----VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLG 321
+ G+ GDATPF D + IS LL E G G EV+++G TG + A +F+G
Sbjct: 686 LLGKAGALLGKFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVG 744
Query: 322 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 381
P YYQRLKHMVDDKIH+R+ GP +L RQP++GR+R GG RFGEMERD I+HGAA L+
Sbjct: 745 PVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQ 804
Query: 382 ERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMS 441
ERL SD VC CG+I AN+ C+ CK T IS+V +PYA KLLFQEL S
Sbjct: 805 ERLTIKSDDVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQS 858
Query: 442 MNIAPRLM 449
MNI PRL
Sbjct: 859 MNIDPRLK 866
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 484 bits (1249), Expect = e-161
Identities = 212/490 (43%), Positives = 278/490 (56%), Gaps = 90/490 (18%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G+Y NF +R DT H+L+YP +PLV TR++E + GYN
Sbjct: 660 LGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEII-------------------GYN--- 697
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
+ PAG N++VA+L YTGYN ED++I+N +++ERG R
Sbjct: 698 -----------------------DRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLAR 734
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMR-NAIYDKLDDDGIIAPGLRVSGDDVV 179
S FFR+Y+ E K G QE++ E P +G R Y KLD+DGI++P + V G DV+
Sbjct: 735 STFFRTYETEERKYPGGQEDKIEIPE-PNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVL 793
Query: 180 IGKTIT---LPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRV 236
IGKT L E E+ G +R RD S +R+ E GIVD V++T + +G K K+RV
Sbjct: 794 IGKTSPPRFLEELEELSLGLQER---RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRV 850
Query: 237 RSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------- 265
R +RIP++GDKFASRHGQKG G+ QE
Sbjct: 851 RDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 910
Query: 266 -----VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFL 320
V++ +G DATPF +++ L + GY+ G EVM++G TG KI A +F+
Sbjct: 911 SIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFI 969
Query: 321 GPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFL 380
G YYQ+L HMV DKIH+RARGPVQIL RQP EGRAR+GGLRFGEMERDC I HGAA L
Sbjct: 970 GVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLL 1029
Query: 381 RERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELM 440
+ERL + SD I+VC CG IA + R N + C +K IS V + YA KLL QELM
Sbjct: 1030 KERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELM 1089
Query: 441 SMNIAPRLMV 450
SM I+PRL +
Sbjct: 1090 SMGISPRLKL 1099
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B. This
model represents the archaeal version of DNA-directed
RNA polymerase subunit B (rpoB) and is observed in all
archaeal genomes.
Length = 599
Score = 457 bits (1178), Expect = e-157
Identities = 198/490 (40%), Positives = 271/490 (55%), Gaps = 90/490 (18%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G+Y N+ +R+DT H+L+YP KPLV TR +E + GY+
Sbjct: 156 LGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELI-------------------GYD--- 193
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
+ PAG N +VA++ Y GYN ED++I+N +++ERG R
Sbjct: 194 -----------------------DRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLAR 230
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNA-IYDKLDDDGIIAPGLRVSGDDVV 179
S FFR+Y+ E + G QE++FE P +G R Y LD+DGI+ P + V G DV+
Sbjct: 231 STFFRTYEAEERRYPGGQEDRFEIPE-PDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVL 289
Query: 180 IGKTIT---LPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRV 236
IGKT L E + T +R RD S +R+ E GIVD+V++T +G K K+RV
Sbjct: 290 IGKTSPPRFLEELRELGLVTERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRV 346
Query: 237 RSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------- 265
R +RIP++GDKFASRHGQKG G+ QE
Sbjct: 347 RDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 406
Query: 266 -----VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFL 320
V++ +G D TPF + +++ L + G++ G EVM++G TG K+ A++F+
Sbjct: 407 MIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFI 465
Query: 321 GPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFL 380
G YYQ+L HMV DKIH+R+RGPVQ+L RQP EGRAR+GGLRFGEMERD I HGAA L
Sbjct: 466 GVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLL 525
Query: 381 RERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELM 440
+ERL + SD Y ++VC CG IA + R T C C IS V + YA KLL EL
Sbjct: 526 KERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELK 585
Query: 441 SMNIAPRLMV 450
S+ I+PRL +
Sbjct: 586 SLGISPRLEL 595
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 434 bits (1118), Expect = e-148
Identities = 193/490 (39%), Positives = 266/490 (54%), Gaps = 90/490 (18%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G+ N+ +R DT H+L+YP PLV T++ E + F E PAG N +VA++ Y GYN ED
Sbjct: 162 LGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIED 221
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
++I+N +++ERG RS
Sbjct: 222 ALIMNKASIERGLGRSH------------------------------------------- 238
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNA-IYDKLDDDGIIAPGLRVSGDDVV 179
FFR+Y+ E + G QE++FE P+ + +G R Y LD+DG++ P V DV+
Sbjct: 239 --FFRTYEGEERRYPGGQEDRFEIPD-KDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVL 295
Query: 180 IGKTIT---LPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRV 236
IGKT L E +D KR R+ S +R+ E GIVD V+LT +G + K+RV
Sbjct: 296 IGKTSPPRFLEEPDDFGISPEKR---RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRV 352
Query: 237 RSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------- 265
R +RIP++GDKFASRHGQKG G+ QE
Sbjct: 353 RDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLE 412
Query: 266 -----VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFL 320
V S +G D T F+ + + + L++ G++ G EVM++G TG KI A++F+
Sbjct: 413 MIGGKVGSLEGRRVDGTAFSG-EDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFV 471
Query: 321 GPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFL 380
G YYQ+L HMV +K+H+R+RGPVQ+L RQP EGRAR+GGLRFGEMERD I HGAA L
Sbjct: 472 GVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLL 531
Query: 381 RERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELM 440
+ERL + SD I+VC CG+IAI + + N C C +T I V + YA KLL EL
Sbjct: 532 KERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELK 591
Query: 441 SMNIAPRLMV 450
S+ IAPRL +
Sbjct: 592 SLGIAPRLEL 601
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 410 bits (1055), Expect = e-133
Identities = 148/495 (29%), Positives = 205/495 (41%), Gaps = 123/495 (24%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
G+ R DT+ L Y P
Sbjct: 640 TGINQRPLVKRGDTVEKGLVYADGP----------------------------------- 664
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
+V+ G EL G N++VA + + GYN ED++I++ +VER F
Sbjct: 665 -------SVDTG-----------ELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFT 706
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
S+ Y+ EE + PN LD+DGII G V G D+++
Sbjct: 707 SIHIEEYETEARDTKLGPEEIRDIPNVS------EEALRNLDEDGIIRIGAEVKGGDILV 760
Query: 181 GKTITLPENEDEL---EGTTKRF--SKRDGSTFLRNSETGIVDQVMLTLNVDG----YKF 231
GK P+ E EL E + F RD S + + E GIVD V + DG K
Sbjct: 761 GKVT--PKGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKL 818
Query: 232 CKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE-------------------------- 265
K+ V R PQIGDK A RHG KG QE
Sbjct: 819 VKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNI 878
Query: 266 ----------VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKIN 315
++ G D F D + I LL+E G+ G EV+++G TG +
Sbjct: 879 GQILETHLGKAAALLGIPVDTPVF-DGAPEEDIRELLKEAGFPYSGKEVLYDGRTGEPFD 937
Query: 316 AQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHG 375
A +F+G YYQ+L HMVDDKIH+R+ GP ++ +QP+ G+A+ GG RFGEME ++G
Sbjct: 938 APIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 997
Query: 376 AAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLL 435
AA L+ERL SD CG R +EC I +V +P + K+L
Sbjct: 998 AAYTLQERLTVKSDDV-------CG-------RIKIYECIVK--GENIPEVGIPESFKVL 1041
Query: 436 FQELMSMNIAPRLMV 450
+EL S+ I RL +
Sbjct: 1042 LKELRSLGIDVRLEL 1056
>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This domain
represents the hybrid binding domain and the wall
domain. The hybrid binding domain binds the nascent RNA
strand / template DNA strand in the Pol II transcription
elongation complex. This domain contains the important
structural motifs, switch 3 and the flap loop and binds
an active site metal ion. This domain is also involved
in binding to Rpb1 and Rpb3. Many of the bacterial
members contain large insertions within this domain, as
region known as dispensable region 2 (DRII).
Length = 373
Score = 351 bits (903), Expect = e-119
Identities = 134/395 (33%), Positives = 188/395 (47%), Gaps = 88/395 (22%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G+Y N + R D ++L YP KPLV T ++E F ELP G N++VA++ YTGYNQED
Sbjct: 29 IGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAVEKGGFGELPLGQNALVAVMSYTGYNQED 88
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
++I+N S+V+RG F S
Sbjct: 89 AIIINKSSVDRGLFTS-------------------------------------------- 104
Query: 121 SVFFRSYK-DAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVV 179
+ + Y+ +A ++G EE P + Y KLD+DGI+ G V D++
Sbjct: 105 -IHIKEYEIEARKTKLGPIEEITRDPPN-----VSEEAYRKLDEDGIVRVGAEVKPGDIL 158
Query: 180 IGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSV 239
+GK E K +D S +++ E G VD V + LN G K K+ +R
Sbjct: 159 VGKITPKGEKLLRAIFGEKARDVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQK 218
Query: 240 RIPQIGDKFASRHGQKGTCGIQYRQE---------------------------------- 265
R PQ+GDKFASRHGQKG QE
Sbjct: 219 RKPQVGDKFASRHGQKGVVSKILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLESLL 278
Query: 266 --VSSNKGEIGDATPFNDAVN-VQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGP 322
++ G+ DATPF+ A V+ I LL+E GY G EV+++G TG A +F+GP
Sbjct: 279 GKAAALLGKFIDATPFDGASEDVEDIGELLKEAGYNAYGKEVLYDGRTGEPFKAPIFVGP 338
Query: 323 TYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRAR 357
YYQ+LKHMVDDKIH+R+ GP +L +QP+ GR+R
Sbjct: 339 IYYQKLKHMVDDKIHARSTGPYSLLTQQPLGGRSR 373
>gnl|CDD|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain comprised of the structural domains anchor and
clamp. The clamp region (C-terminal) contains a
zinc-binding motif. The clamp region is named due to its
interaction with the clamp domain found in Rpb1. The
domain also contains a region termed "switch 4". The
switches within the polymerase are thought to signal
different stages of transcription.
Length = 78
Score = 126 bits (318), Expect = 1e-35
Identities = 37/93 (39%), Positives = 45/93 (48%), Gaps = 15/93 (16%)
Query: 359 GGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCK 418
GG RFGEME ++GAA L+ERL SD VC CG A CK
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVCGRCGAYAA-----------ICK 45
Query: 419 NKTQISQVRLPYAAKLLFQELMSMNIAPRLMVV 451
KT I +P + KLL QEL S+ + RL +
Sbjct: 46 GKTIIEPGDIPESFKLLLQELRSLGLDIRLFLE 78
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit. This
model describes orthologs of the beta subunit of
Bacterial RNA polymerase. The core enzyme consists of two
alpha chains, one beta chain, and one beta' subunit
[Transcription, DNA-dependent RNA polymerase].
Length = 1065
Score = 132 bits (333), Expect = 6e-33
Identities = 106/383 (27%), Positives = 167/383 (43%), Gaps = 74/383 (19%)
Query: 62 VILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRS 121
V+ + + + G EL G N +VA + + GYN ED+++++ V+ F S
Sbjct: 659 VLADGPSTDLG-----------ELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTS 707
Query: 122 VFFRSYK-DAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
+ Y+ +A ++G +E + PN + LD++GI+ G V D+++
Sbjct: 708 IHIEEYEVEARDTKLGPEEITRDIPN------VSEDALRNLDENGIVRIGAEVKAGDILV 761
Query: 181 GKTITLPENEDELEGTTKRFSK---------RDGSTFLRNSETGIVDQVMLTLNVDG--- 228
GK P+ E EL K RD S + G V V + +G
Sbjct: 762 GKVT--PKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKEGDEL 819
Query: 229 ----YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------- 265
K K+ + R Q+GDK A RHG KG E
Sbjct: 820 PPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLG 879
Query: 266 VSS--NKGEIGD-----------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMF 306
V S N G+I + ATP D + ++I L++ G G ++
Sbjct: 880 VPSRMNIGQILETHLGWAGKKLGRKGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLY 939
Query: 307 NGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEM 366
+G TG + + V +G Y +L H+VDDK+H+R+ GP ++ +QP+ G+A+ GG RFGEM
Sbjct: 940 DGRTGEQFDNPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEM 999
Query: 367 ERDCQISHGAAQFLRERLFEVSD 389
E ++GAA L+E L SD
Sbjct: 1000 EVWALEAYGAAYTLQEMLTVKSD 1022
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 131 bits (332), Expect = 9e-33
Identities = 112/426 (26%), Positives = 179/426 (42%), Gaps = 87/426 (20%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQF 142
EL G N +VA + + GYN ED++++N V F S+ Y+ + ++G +E
Sbjct: 643 ELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITR 702
Query: 143 EKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKR--F 200
PN ++ LD++GII+ G +V D+++GK E++ EG R F
Sbjct: 703 NIPNVS-----EYSLK-NLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIF 756
Query: 201 SK-----RDGSTFLRNSETG-IVDQVMLTLNV-DGYKF-----CKIRVRSVRIPQIGDKF 248
+ +D S + N G ++ + + + D KF ++ + +R Q+GDK
Sbjct: 757 GEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKL 816
Query: 249 ASRHGQKGTCG-IQYRQE------------------VSS--NKGEIGDA----------- 276
A RHG KG I RQ+ V S N G++ +
Sbjct: 817 AGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNK 876
Query: 277 ----TPFNDAVNVQKISTLLQEYGYQLR--------------GNEVMFNGHTGRKINAQV 318
PF++ + L+ Q G V+ +G TG K V
Sbjct: 877 RFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPV 936
Query: 319 FLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQ 378
+G Y +L H+VDDKIH+R GP ++ +QP+ G+A+ GG RFGEME + GAA
Sbjct: 937 TVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAY 996
Query: 379 FLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQE 438
L+E L SD +M+ I + P + K+L +E
Sbjct: 997 TLKELLTIKSD----------------DMQGRNETLNAIVKGQPIPKPGTPESFKVLMRE 1040
Query: 439 LMSMNI 444
L S+ +
Sbjct: 1041 LQSLGL 1046
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 106 bits (267), Expect = 2e-24
Identities = 111/359 (30%), Positives = 163/359 (45%), Gaps = 71/359 (19%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQF 142
EL G N +VA + + GYN ED+++++ V+ F S+ Y+ +A ++G +E
Sbjct: 712 ELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITR 771
Query: 143 EKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL--------- 193
+ PN + LD+ GI+ G V D+++GK +T P+ E EL
Sbjct: 772 DIPN------VSEEALRNLDESGIVRIGAEVKPGDILVGK-VT-PKGETELTPEEKLLRA 823
Query: 194 ---EGTTKRFSKRDGSTFLR--NSETGIV-DQVMLTLNVDGY-------KFCKIRVRSVR 240
E K +D S LR + E G V D + T G K K+ + R
Sbjct: 824 IFGE---KARDVKDTS--LRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKR 878
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQE-------------------VSS--NKGEI------ 273
Q+GDK A RHG KG E V S N G+I
Sbjct: 879 KIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLG 938
Query: 274 ------GD--ATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYY 325
G ATP D ++I LL+E G G +++G TG + V +G Y
Sbjct: 939 WAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYM 998
Query: 326 QRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
+L H+VDDKIH+R+ GP ++ +QP+ G+A+ GG RFGEME ++GAA L+E L
Sbjct: 999 LKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1057
Score = 28.9 bits (66), Expect = 6.4
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 39 ELPAGINSIVAILCYTGYNQEDSVILN 65
EL G N +VA + + GYN ED+++++
Sbjct: 712 ELALGQNVLVAFMPWNGYNFEDAILIS 738
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 84.2 bits (208), Expect = 4e-17
Identities = 41/114 (35%), Positives = 66/114 (57%)
Query: 276 ATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDK 335
A P + ++ +K L + + G +++G TG K+ +V +G Y +L H+VD+K
Sbjct: 1215 AIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEK 1274
Query: 336 IHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSD 389
+H+R+ GP ++ QP+ G+A GG RFGEME ++GAA L+E L SD
Sbjct: 1275 VHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
Score = 42.2 bits (99), Expect = 6e-04
Identities = 28/101 (27%), Positives = 48/101 (47%), Gaps = 7/101 (6%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSV-FFRSYKDAESKRIGDQEEQF 142
EL G N VA + + GYN ED+++++ + F S + DA + G +E
Sbjct: 803 ELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTA 862
Query: 143 EKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKT 183
+ P+ ++ LD+ GI+ G VS +++GKT
Sbjct: 863 DIPD------VKEEALAHLDESGIVKVGTYVSAGMILVGKT 897
Score = 33.4 bits (76), Expect = 0.31
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 39 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSM----EYLRFRELPAGINSIVA 94
EL G N VA + + GYN ED+++++ + F S + + REL G+ A
Sbjct: 803 ELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTA 862
Score = 31.0 bits (70), Expect = 1.5
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 230 KFCKIRVRSVRIPQIGDKFASRHGQKG 256
K K+ + + R ++GDK A RHG KG
Sbjct: 1076 KKVKLYIATKRKLKVGDKMAGRHGNKG 1102
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 80.8 bits (199), Expect = 5e-16
Identities = 42/114 (36%), Positives = 67/114 (58%)
Query: 276 ATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDK 335
A P + ++I+ L + G G V+++G +G K + +V +G Y +L H+VD K
Sbjct: 1273 AAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGK 1332
Query: 336 IHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSD 389
IH+R+ GP ++ +QP+ G++ GG RFGEME ++GAA L+E L SD
Sbjct: 1333 IHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
Score = 49.2 bits (117), Expect = 4e-06
Identities = 39/138 (28%), Positives = 62/138 (44%), Gaps = 16/138 (11%)
Query: 50 ILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVIL 109
++C Y +E VI + A+ G EL G N +VA + + GYN EDS+I+
Sbjct: 790 LVCVGDYVKEGDVIADGPAINSG-----------ELALGQNLLVAFMSWQGYNFEDSIII 838
Query: 110 NASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAP 169
++ V++ F S+ ++ + D EK R +Y LDD GI+
Sbjct: 839 SSEVVKKDLFTSIHIEEFECV----VHDTPLGSEKITRAIPGVNEENLY-HLDDSGIVKI 893
Query: 170 GLRVSGDDVVIGKTITLP 187
G RV +++GK P
Sbjct: 894 GTRVGPGYILVGKVTPKP 911
Score = 38.8 bits (90), Expect = 0.006
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 39 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRF----RELPAGINSIVA 94
EL G N +VA + + GYN EDS+I+++ V++ F S+ F + P G I
Sbjct: 813 ELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITR 872
Query: 95 ILCYTGYNQEDSVILNASAV 114
+ G N+E+ L+ S +
Sbjct: 873 AI--PGVNEENLYHLDDSGI 890
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 70.7 bits (174), Expect = 6e-13
Identities = 36/84 (42%), Positives = 48/84 (57%)
Query: 306 FNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGE 365
F+G TG V +G Y +L H VDDKIH+R+ GP ++ +QP+ GR++ GG R GE
Sbjct: 928 FDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGE 987
Query: 366 MERDCQISHGAAQFLRERLFEVSD 389
ME G A L+E L SD
Sbjct: 988 MEVWALEGFGVAYILQEMLTYKSD 1011
Score = 38.3 bits (90), Expect = 0.008
Identities = 53/189 (28%), Positives = 83/189 (43%), Gaps = 24/189 (12%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFE 143
EL G N +VA + + GYN ED+V+++ V + S R Y + ++ E+
Sbjct: 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERIT 706
Query: 144 K--PNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL---EGTTK 198
K P+ + +RN LD +GI+ G V D+++GK +T E E+ EG
Sbjct: 707 KEIPHLEA-HLLRN-----LDKNGIVMLGSWVETGDILVGK-LTPQEAEESSYAPEGRLL 759
Query: 199 R-------FSKRDGSTFLRNSETG-IVDQVMLTLNVD-GYKFCKIRVRSV--RIPQIGDK 247
R + ++ L G ++D + Y I V + R Q+GDK
Sbjct: 760 RAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDK 819
Query: 248 FASRHGQKG 256
A RHG KG
Sbjct: 820 VAGRHGNKG 828
>gnl|CDD|100054 cd04649, LbH_THP_succinylT_putative, Putative
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP)
N-succinyltransferase (THP succinyltransferase),
C-terminal left-handed parallel alpha-helix (LbH)
domain: This group is composed of mostly uncharacterized
proteins containing an N-terminal domain of unknown
function and a C-terminal LbH domain with similarity to
THP succinyltransferase LbH. THP succinyltransferase
catalyzes the conversion of tetrahydrodipicolinate and
succinyl-CoA to N-succinyltetrahydrodipicolinate and
CoA. It is the committed step in the succinylase pathway
by which bacteria synthesize L-lysine and
meso-diaminopimelate, a component of peptidoglycan. The
enzyme is trimeric and displays the left-handed parallel
alpha-helix (LbH) structural motif encoded by the
hexapeptide repeat motif.
Length = 147
Score = 31.6 bits (72), Expect = 0.35
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 161 LDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTK--RFSKRDGSTFLRNSETGIV 217
L D+ I+ GL V+ G +TLP+NE+ + K S ++G F RNS++G V
Sbjct: 92 LGDNCIVEAGLYVTA-----GTKVTLPDNEEFEKNVVKARELSGKNGLLFRRNSQSGKV 145
>gnl|CDD|131337 TIGR02284, TIGR02284, conserved hypothetical protein. Members of
this protein family are found mostly in the
Proteobacteria, although one member is found in the the
marine planctomycete Pirellula sp. strain 1. The
function is unknown.
Length = 139
Score = 27.9 bits (62), Expect = 5.7
Identities = 11/52 (21%), Positives = 25/52 (48%)
Query: 221 MLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVSSNKGE 272
++ +++DG + V+ P++ F G+K + +Q V+S G+
Sbjct: 8 LIEISIDGKDGFEESAEEVKDPELATLFRRIAGEKSAIVSELQQVVASLGGK 59
>gnl|CDD|176695 cd08347, PcpA_C_like, C-terminal domain of Sphingobium
chlorophenolicum 2,6-dichloro-p-hydroquinone
1,2-dioxygenase (PcpA), and similar proteins. The
C-terminal domain of Sphingobium chlorophenolicum
(formerly Sphingomonas chlorophenolica)
2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and
similar proteins. PcpA is a key enzyme in the
pentachlorophenol (PCP) degradation pathway, catalyzing
the conversion of 2,6-dichloro-p-hydroquinone to
2-chloromaleylacetate. This domain belongs to a
conserved domain superfamily that is found in a variety
of structurally related metalloproteins, including the
bleomycin resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases.
Length = 157
Score = 27.9 bits (63), Expect = 7.1
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 114 VERGYFRSVFFR 125
V+R YF+S++FR
Sbjct: 97 VDRFYFKSLYFR 108
>gnl|CDD|221029 pfam11209, DUF2993, Protein of unknown function (DUF2993). This
family of proteins with unknown function appears to be
restricted to Cyanobacteria.
Length = 214
Score = 27.8 bits (62), Expect = 9.3
Identities = 18/95 (18%), Positives = 38/95 (40%), Gaps = 5/95 (5%)
Query: 151 QGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLR 210
+R A + G+ ++++GD V + T+ L + L T + +
Sbjct: 111 PLLRAAGVLLISLLGLTEGEVKLTGDVVTVSATLRLVGGDGGLRLTLTDVTLGPALLAPQ 170
Query: 211 NSETGIVDQVM----LTLNVDGYKFCKIRVRSVRI 241
+ D ++ L L++D F +R+ SV +
Sbjct: 171 ALPPELTDALLDALSLLLDLDDLPF-GLRLTSVEV 204
>gnl|CDD|183782 PRK12834, PRK12834, putative FAD-binding dehydrogenase; Reviewed.
Length = 549
Score = 28.3 bits (64), Expect = 9.3
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 7/43 (16%)
Query: 355 RARDGGL--RFGEMERDCQIS--HGAAQFLRERLFEVSDPYRI 393
ARD + F +D QI+ A ++L +RL V+ P+R+
Sbjct: 425 EARDREVANPFS---KDAQITAIRNARRYLGDRLIRVAKPHRL 464
>gnl|CDD|235620 PRK05841, flgE, flagellar hook protein FlgE; Validated.
Length = 603
Score = 28.3 bits (63), Expect = 9.6
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 8/41 (19%)
Query: 189 NEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGY 229
N+D + RDGS F R+++ +V N +GY
Sbjct: 110 NKDGFSKKQDNYFTRDGS-FARDADGYLV-------NPEGY 142
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.138 0.407
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,941,194
Number of extensions: 2234601
Number of successful extensions: 1595
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1566
Number of HSP's successfully gapped: 50
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.4 bits)