RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4067
(1384 letters)
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 397 bits (1023), Expect = e-124
Identities = 189/465 (40%), Positives = 252/465 (54%), Gaps = 104/465 (22%)
Query: 913 GLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITN 972
G++PYP HN +PR T M KQ++G N + R DT + L Y Q P+V+++T I
Sbjct: 138 GMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIG 197
Query: 973 FHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDR 1032
F + PAGQN +AVMSY GY+IEDALIMNKAS++RG GR +R + ++YP DR
Sbjct: 198 FDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDR 257
Query: 1033 ILGPLLEADTR----KPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATP 1088
P + D R + YRH LD+DG+V P ++ E VL+ K+ P
Sbjct: 258 FEIP--DKDVRGYRGEEAYRH--LDEDGLVNPETEVKEGDVLIGKTSP------------ 301
Query: 1089 EYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSS---RHGQKGV 1145
P +LE+ D F I + RR +S R G++G+
Sbjct: 302 -------------PRFLEEP-------DDFGIS---PEKRRE------TSVTMRSGEEGI 332
Query: 1146 IGLIVEQEDMPFNESGICPDIIMNPHGLKGCDRITEYKEVPVSYKGSVPSYLEKVLVSSN 1205
+ ++ +TE +E S L KV V
Sbjct: 333 VDTVI----------------------------LTETEE---------GSRLVKVRV--- 352
Query: 1206 SEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGY 1265
R R PE+GDKF+SRHGQKGVIGLIV QEDMPF ESG+ PD+I+NPH
Sbjct: 353 -----------RDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAI 401
Query: 1266 PSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDIFYSGIT 1325
PSRMTVG ++E++ GK G +EG +GTAF G D++E L + G+ + GK++ Y GIT
Sbjct: 402 PSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGIT 461
Query: 1326 GEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPT-GR 1369
GE +EA I+ G +YYQKL HMV +K+HARSRGP VLTRQPT GR
Sbjct: 462 GEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGR 506
Score = 122 bits (309), Expect = 1e-28
Identities = 51/131 (38%), Positives = 71/131 (54%), Gaps = 15/131 (11%)
Query: 692 FDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQYNKR 751
FDD + +G IEYLD E +++IAV E + THLEI P +LG+ AG+
Sbjct: 89 FDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGM-------- 139
Query: 752 FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI 811
+PYP HN +PR T M KQ++G N + R DT + L Y Q P+V+++T
Sbjct: 140 ------IPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQ 193
Query: 812 RITNFHKLPAG 822
I F + PAG
Sbjct: 194 EIIGFDERPAG 204
>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 = 370 bits (953), Expect = e-111
Identities = 115/266 (43%), Positives = 160/266 (60%), Gaps = 10/266 (3%)
Query: 913 GLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITN 972
L+P+P HNQ+PRN YQ M KQA+G NQQ R+DT +Y L+Y Q+P+V +
Sbjct: 411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIA 470
Query: 973 FHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDR 1032
F +LP GQNA +AVMSYSGY+ EDA+I+NK+S+DRGF R + Y+ + L++ N +
Sbjct: 471 FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI 530
Query: 1033 ILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMP---TISVSAISMATPE 1089
G + + LD+DGI+ PG ++ +LV K P T S +
Sbjct: 531 TRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARD 586
Query: 1090 YKEVPVSYKGSVPSYLEKVLVSS---NSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVI 1146
++ + Y G ++ V + S N L+K+ +RQ R+P+IGDKF+SRHGQKGVI
Sbjct: 587 VRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVI 646
Query: 1147 GLIVEQEDMPFNESGICPDIIMNPHG 1172
I+ QEDMPF E GI PDII+NPHG
Sbjct: 647 SKILPQEDMPFTEDGIPPDIILNPHG 672
Score = 321 bits (825), Expect = 2e-93
Identities = 103/198 (52%), Positives = 134/198 (67%), Gaps = 3/198 (1%)
Query: 1176 CDRITEYKEVPVSYKGSVPSYLEKVLVSS---NSEDAFLIKMLLRQTRRPEIGDKFSSRH 1232
++ + ++ + Y G ++ V + S N L+K+ +RQ R+P+IGDKF+SRH
Sbjct: 581 GEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRH 640
Query: 1233 GQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEG 1292
GQKGVI I+ QEDMPF E GI PDII+NPHG+PSRMT+G+L+E L GKAG + G + +
Sbjct: 641 GQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDA 700
Query: 1293 TAFGGTKLVDVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIH 1352
T F G + D+ E L G NY GK++ Y G TGE LEA I+ GPVYYQ+LKHMV DKIH
Sbjct: 701 TPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIH 760
Query: 1353 ARSRGPRVVLTRQPTGRR 1370
ARS GP +LTRQP R
Sbjct: 761 ARSTGPYSLLTRQPLKGR 778
Score = 159 bits (404), Expect = 2e-39
Identities = 49/116 (42%), Positives = 65/116 (56%), Gaps = 3/116 (2%)
Query: 175 DKIIPKIKAAQFDIVNHMRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISG 234
K + K K + IT+ + + TGNW +RF M+R G++QVL RL+ +S
Sbjct: 268 QKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSE 325
Query: 235 LGMMTRINS-QFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHIT 289
L RI+S + RK R L S WG +CP +TPEGE CGLVKNLALM I+
Sbjct: 326 LSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
Score = 139 bits (353), Expect = 2e-33
Identities = 40/100 (40%), Positives = 55/100 (55%), Gaps = 14/100 (14%)
Query: 724 GVTTHLEIAPFTLLGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCI 783
TH+EI+P +L V A L+P+P HNQ+PRN YQ M KQA+G
Sbjct: 393 KEVTHIEISPSQILSVAAS--------------LIPFPEHNQSPRNLYQSNMQKQAVGTP 438
Query: 784 GYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGK 823
NQQ R+DT +Y L+Y Q+P+V + F +LP G+
Sbjct: 439 ALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQ 478
Score = 135 bits (342), Expect = 5e-32
Identities = 70/239 (29%), Positives = 104/239 (43%), Gaps = 61/239 (25%)
Query: 340 EVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIM 398
+ KP++EE TR+ TP+ECRLRDLTYSAP+ VDI T + ++ V IG +PIM
Sbjct: 44 YLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIM 102
Query: 399 LQSSKCVLRNKTE---------------------------------------YTSSSRR- 418
L+S C L T S +R
Sbjct: 103 LRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVEDSKGKRI 162
Query: 419 ASTSSVTMHSQRTSPLLSCKKLRQKRFQTYKKTPV---DDARDFLSSTCIAHIPVINMRF 475
+ +S+ +S L K +K+ + Y + + ++A ++ RF
Sbjct: 163 YTKTSIPSYSPYRGSWL-EVKSDKKKDRIYVRIDLKRQEEALKYIGK-----------RF 210
Query: 476 KMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKE 534
+ L MIR+++L + LDD D+ GNKR+ LAG LL +F KR E+KE
Sbjct: 211 E----DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKE 265
Score = 56.0 bits (136), Expect = 1e-07
Identities = 19/46 (41%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 128 LVKPHIDSFDYFINVEIKKLMQANANIYS-DVDPLFYLKYLDIHVG 172
LVK IDSF+YF+NV +++++++ I D D LK+ DI++G
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLG 46
>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 = 322 bits (828), Expect = 2e-99
Identities = 106/263 (40%), Positives = 152/263 (57%), Gaps = 7/263 (2%)
Query: 913 GLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITN 972
L+P+ HNQ+PR TYQCAMGKQA+G N+ NR D Y L Y Q+P+V++ +
Sbjct: 5 SLIPFVDHNQSPRITYQCAMGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAVEKGG 64
Query: 973 FHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDR 1032
F +LP GQNA +AVMSY+GY+ EDA+I+NK+S+DRG + + + ++ +
Sbjct: 65 FGELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHIKEYEIEARKTKLGPIEE 124
Query: 1033 ILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTIS--VSAISMATP-E 1089
I +R LD+DGIV G ++ +LV K P + AI +
Sbjct: 125 ITRDPP----NVSEEAYRKLDEDGIVRVGAEVKPGDILVGKITPKGEKLLRAIFGEKARD 180
Query: 1090 YKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLI 1149
K+ + K ++ V + N +K+ +RQ R+P++GDKF+SRHGQKGV+ I
Sbjct: 181 VKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQVGDKFASRHGQKGVVSKI 240
Query: 1150 VEQEDMPFNESGICPDIIMNPHG 1172
+ QEDMPF E GI PDII+NPHG
Sbjct: 241 LPQEDMPFTEDGIPPDIILNPHG 263
Score = 300 bits (772), Expect = 1e-91
Identities = 96/197 (48%), Positives = 128/197 (64%), Gaps = 3/197 (1%)
Query: 1177 DRITEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKG 1236
++ + K+ + K ++ V + N +K+ +RQ R+P++GDKF+SRHGQKG
Sbjct: 176 EKARDVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQVGDKFASRHGQKG 235
Query: 1237 VIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFG 1296
V+ I+ QEDMPF E GI PDII+NPHG PSRMT+G+L+E L GKA + G + + T F
Sbjct: 236 VVSKILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFIDATPFD 295
Query: 1297 GTKLV--DVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHAR 1354
G D+ E L GYN GK++ Y G TGE +A I+ GP+YYQKLKHMV DKIHAR
Sbjct: 296 GASEDVEDIGELLKEAGYNAYGKEVLYDGRTGEPFKAPIFVGPIYYQKLKHMVDDKIHAR 355
Query: 1355 SRGPRVVLTRQPT-GRR 1370
S GP +LT+QP GR
Sbjct: 356 STGPYSLLTQQPLGGRS 372
Score = 99 bits (250), Expect = 4e-22
Identities = 32/68 (47%), Positives = 44/68 (64%)
Query: 756 GLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITN 815
L+P+ HNQ+PR TYQCAMGKQA+G N+ NR D Y L Y Q+P+V++ +
Sbjct: 5 SLIPFVDHNQSPRITYQCAMGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAVEKGG 64
Query: 816 FHKLPAGK 823
F +LP G+
Sbjct: 65 FGELPLGQ 72
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 297 bits (762), Expect = 1e-83
Identities = 82/194 (42%), Positives = 116/194 (59%), Gaps = 4/194 (2%)
Query: 1181 EYKEVPVSYKGSVPSYLEKVLVSSNSEDAF----LIKMLLRQTRRPEIGDKFSSRHGQKG 1236
+ ++ + ++ V V + + L+K+ + Q R+P+IGDK + RHG KG
Sbjct: 784 KVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKG 843
Query: 1237 VIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFG 1296
V+ IV QEDMPF E G PDII+NP G PSRM +G+++E GKA + G + F
Sbjct: 844 VVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFD 903
Query: 1297 GTKLVDVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSR 1356
G D++E L G+ Y GK++ Y G TGE +A I+ G +YYQKL HMV DKIHARS
Sbjct: 904 GAPEEDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHARST 963
Query: 1357 GPRVVLTRQPTGRR 1370
GP ++T+QP G +
Sbjct: 964 GPYSLVTQQPLGGK 977
Score = 291 bits (747), Expect = 1e-81
Identities = 85/271 (31%), Positives = 133/271 (49%), Gaps = 24/271 (8%)
Query: 913 GLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITN 972
L+PYP HNQ+P N Y+ A QA G R DT+ LVYA P V++
Sbjct: 616 SLIPYPEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDTG------ 669
Query: 973 FHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDR 1032
+L GQNA +A M ++GY+ EDA+I+++ S++R + + + +
Sbjct: 670 --ELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKLGPEEI 727
Query: 1033 ILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMP------TISVSAISMA 1086
P + + R+ LD+DGI+ G ++ +LV K P T + +
Sbjct: 728 RDIPNVSEE----ALRN--LDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIF 781
Query: 1087 TPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAF----LIKMLLRQTRRPEIGDKFSSRHGQ 1142
+ ++ + ++ V V + + L+K+ + Q R+P+IGDK + RHG
Sbjct: 782 GEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGN 841
Query: 1143 KGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
KGV+ IV QEDMPF E G PDII+NP G+
Sbjct: 842 KGVVSKIVPQEDMPFLEDGTPPDIILNPLGV 872
Score = 121 bits (306), Expect = 1e-27
Identities = 33/141 (23%), Positives = 60/141 (42%), Gaps = 16/141 (11%)
Query: 192 MRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINS-QFEKTRK 250
+ QD I A+ TG + R ++Q + + + +S L R+++ + R
Sbjct: 364 VPQDLINAKPIHALITGFFG-------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERA 416
Query: 251 VSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHI--TTENDEKNMLKIMYNIGIEH 308
R + + +G +CP +TPEG GL+K+LAL I + + ++ ++
Sbjct: 417 GFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDE 476
Query: 309 IAMFNGEELSSPGVYLVFVNG 329
I E S V+V G
Sbjct: 477 I------EYLSADEEDVYVIG 491
Score = 116 bits (293), Expect = 4e-26
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 28/132 (21%)
Query: 692 FDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQYNKR 751
+ G +EYLD + + IA RPGV TH+EI+P +LG+ A +
Sbjct: 572 EAPLVGTG-MEYLDAEDSGAAVIAK-----RPGVVTHVEISPIVILGIEASL-------- 617
Query: 752 FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI 811
+PYP HNQ+P N Y+ A QA G R DT+ LVYA P V++
Sbjct: 618 ------IPYPEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDTG-- 669
Query: 812 RITNFHKLPAGK 823
+L G+
Sbjct: 670 ------ELALGQ 675
Score = 65.7 bits (161), Expect = 2e-10
Identities = 25/104 (24%), Positives = 41/104 (39%), Gaps = 4/104 (3%)
Query: 435 LSCKKLRQKRFQTYKKTPVDDARDFLSSTCIAHIPVINMR----FKMKAMYLAVMIRRMV 490
L ++ + K+ A+ L + H+ R KA + MI+ ++
Sbjct: 249 LIGSRVFVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLI 308
Query: 491 LALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKE 534
DD D+ GN+RL L G LL +F R ++KE
Sbjct: 309 ELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKE 352
Score = 61.0 bits (149), Expect = 4e-09
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 112 IRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFYLKYLDIHV 171
IRD + + FL LV+ +DS++ F ++++ + I S + L+Y +
Sbjct: 11 IRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESY-NGNTELEYGSYRL 69
Query: 172 GIADKIIPK 180
G K P+
Sbjct: 70 GEPPKFYPE 78
Score = 59.5 bits (145), Expect = 1e-08
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 340 EVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVV--RSDLVIGRMPI 397
E + E + P ECRLR LTYSAP+ V + ++ +G +P+
Sbjct: 63 EYGSYRLGE----PPKFYPEECRLRGLTYSAPLYVKLRLVVNETGEEIKEQEVYMGDIPL 118
Query: 398 MLQ 400
M +
Sbjct: 119 MTR 121
>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 = 281 bits (720), Expect = 7e-82
Identities = 114/268 (42%), Positives = 165/268 (61%), Gaps = 11/268 (4%)
Query: 913 GLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITN 972
+PYP HNQ+PRNT AM KQ++G N + R+DT + L Y Q+P+V+++ + +
Sbjct: 132 STIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIG 191
Query: 973 FHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDR 1032
+ PAGQN +AVMSY GY+IEDALIMNKAS++RG R +R + ++YP DR
Sbjct: 192 YDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDR 251
Query: 1033 ILGPLLEADTR----KPVYRHRALDQDGIVAPGEQICERQVLVNKSMPT---ISVSAISM 1085
P E D R + Y+H LD+DGIV P ++ VL+ K+ P + + +
Sbjct: 252 FEIP--EPDVRGYRGEEAYKH--LDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELRELGL 307
Query: 1086 ATPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 1145
T ++ V+ + ++KV+++ E L+K+ +R R PE+GDKF+SRHGQKGV
Sbjct: 308 VTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGV 367
Query: 1146 IGLIVEQEDMPFNESGICPDIIMNPHGL 1173
IG+IV QEDMPF E GI PD+I+NPH +
Sbjct: 368 IGMIVPQEDMPFTEDGIVPDLIINPHAI 395
Score = 262 bits (672), Expect = 2e-75
Identities = 101/175 (57%), Positives = 131/175 (74%), Gaps = 1/175 (0%)
Query: 1196 YLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGIC 1255
++KV+++ E L+K+ +R R PE+GDKF+SRHGQKGVIG+IV QEDMPF E GI
Sbjct: 326 IVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
Query: 1256 PDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQ 1315
PD+I+NPH PSRMTVG+L+E++AGK +EG +GT F G ++++EL++ G+
Sbjct: 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPD 445
Query: 1316 GKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPT-GR 1369
GK++ Y GITGE LEA I+ G +YYQKL HMV DKIHARSRGP VLTRQPT GR
Sbjct: 446 GKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGR 500
Score = 125 bits (317), Expect = 1e-29
Identities = 48/132 (36%), Positives = 73/132 (55%), Gaps = 15/132 (11%)
Query: 691 RFDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQYNK 750
+DD + +G IEYLD E +++IA+ + P THLEI P +LG+ A
Sbjct: 82 TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-HTHLEIDPSAILGIIAST------- 133
Query: 751 RFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKT 810
+PYP HNQ+PRNT AM KQ++G N + R+DT + L Y Q+P+V+++
Sbjct: 134 -------IPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRV 186
Query: 811 IRITNFHKLPAG 822
+ + + PAG
Sbjct: 187 LELIGYDDRPAG 198
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 278 bits (714), Expect = 3e-77
Identities = 115/265 (43%), Positives = 172/265 (64%), Gaps = 7/265 (2%)
Query: 914 LVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNF 973
++PYP HNQ+PRNTYQ AM KQ++G N + R DT + L Y QRP+V+++ + I +
Sbjct: 637 IIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGY 696
Query: 974 HKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRI 1033
+ PAGQNA +AV+SY+GY+IEDA+IMNKAS++RG R +R + ++YP D+I
Sbjct: 697 NDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKI 756
Query: 1034 LGPLLEADTR--KPVYRHRALDQDGIVAPGEQICERQVLVNKSMP---TISVSAISMATP 1088
P E + R + +R LD+DGIV+P ++ VL+ K+ P + +S+
Sbjct: 757 EIP--EPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQ 814
Query: 1089 EYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGL 1148
E ++ V+ + ++ VL++ + E L+K+ +R R PE+GDKF+SRHGQKGVIG+
Sbjct: 815 ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGM 874
Query: 1149 IVEQEDMPFNESGICPDIIMNPHGL 1173
+V QEDMPF E GI PD+I+NPH +
Sbjct: 875 LVPQEDMPFTEDGIVPDLIINPHAI 899
Score = 267 bits (685), Expect = 1e-73
Identities = 95/175 (54%), Positives = 128/175 (73%), Gaps = 1/175 (0%)
Query: 1196 YLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGIC 1255
++ VL++ + E L+K+ +R R PE+GDKF+SRHGQKGVIG++V QEDMPF E GI
Sbjct: 830 IVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIV 889
Query: 1256 PDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQ 1315
PD+I+NPH PSRMTVG+L+E +AGK +EG + + T F G ++++EL++ GY
Sbjct: 890 PDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPD 949
Query: 1316 GKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPT-GR 1369
G ++ Y G TGE ++A I+ G VYYQKL HMV DKIHAR+RGP +LTRQPT GR
Sbjct: 950 GTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGR 1004
Score = 125 bits (315), Expect = 9e-29
Identities = 53/131 (40%), Positives = 75/131 (57%), Gaps = 15/131 (11%)
Query: 692 FDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQYNKR 751
FDD + G IEYLD E ++++A+ + P THLEI P +LG+ A I
Sbjct: 587 FDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE-HTHLEIWPPAILGITASI-------- 637
Query: 752 FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI 811
+PYP HNQ+PRNTYQ AM KQ++G N + R DT + L Y QRP+V+++ +
Sbjct: 638 ------IPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRAL 691
Query: 812 RITNFHKLPAG 822
I ++ PAG
Sbjct: 692 EIIGYNDRPAG 702
Score = 123 bits (311), Expect = 3e-28
Identities = 56/156 (35%), Positives = 83/156 (53%), Gaps = 7/156 (4%)
Query: 180 KIKAAQFDIVNHMRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMT 239
+ + D+ +R D IT + A+ TGNW R GV+Q+L R +Y+S L +
Sbjct: 365 YARGRKLDLRAIVRPDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLR 419
Query: 240 RINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLK 299
R+ S + + R L G+QWG +CP +TPEG CGLVKNLALM I+ DE+ + +
Sbjct: 420 RVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE 479
Query: 300 IMYNIGIEHIAMFNGEELSSPGVYLVFVNGILAGIT 335
I+Y +G+ + EE V++NG L G
Sbjct: 480 ILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYH 513
Score = 67.3 bits (165), Expect = 5e-11
Identities = 25/72 (34%), Positives = 39/72 (54%)
Query: 340 EVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLVIGRMPIML 399
V +PEI+E+ R TP E RLR+LTY+AP+ + + ++ IG +PIM+
Sbjct: 55 RVGEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMV 114
Query: 400 QSSKCVLRNKTE 411
+S C L +
Sbjct: 115 KSKICPLSGLSP 126
Score = 57.3 bits (139), Expect = 6e-08
Identities = 24/60 (40%), Positives = 34/60 (56%), Gaps = 6/60 (10%)
Query: 478 KAMYLAVMIRR---MVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKE 534
KA +L M + + L +PD D+D+Y NKRL LAG LL+ +F FK+ +LK
Sbjct: 303 KAYFLGQMASKLLELYLGRREPD---DKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
Score = 45.7 bits (109), Expect = 2e-04
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 115 KWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFYLKYLDIHVGIA 174
+W +V ++ KEKGLV+ H+DS++ FI +++++ I +++ P + I VG
Sbjct: 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVG-- 57
Query: 175 DKIIPKIKAAQ 185
P+IK A
Sbjct: 58 ---EPEIKEAD 65
>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 = 144 bits (365), Expect = 1e-34
Identities = 66/161 (40%), Positives = 94/161 (58%), Gaps = 3/161 (1%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
L+K+ + Q R+ ++GDK + RHG KGV+ I+ EDMPF E G DI++NP G PSRM
Sbjct: 826 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMN 885
Query: 1271 VGKLIEL---LAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDIFYSGITGE 1327
+G+++E AGK +G F G +++E L + G GK Y G TGE
Sbjct: 886 IGQILETHLGWAGKKLGRKGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGE 945
Query: 1328 ALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTG 1368
+ + G +Y KL H+V DK+HARS GP ++T+QP G
Sbjct: 946 QFDNPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLG 986
Score = 85.9 bits (213), Expect = 9e-17
Identities = 69/230 (30%), Positives = 106/230 (46%), Gaps = 54/230 (23%)
Query: 976 LPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRN--SKCVLKQYPNQTHDRI 1033
L G+N +A M ++GY+ EDA+++++ LV + + +++Y + D
Sbjct: 671 LALGRNVLVAFMPWNGYNYEDAILISE---------RLVKDDVFTSIHIEEYEVEARDTK 721
Query: 1034 LGPLLEADTR------KPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMAT 1087
LGP E TR + R+ LD++GIV G ++ +LV K P + T
Sbjct: 722 LGP--EEITRDIPNVSEDALRN--LDENGIVRIGAEVKAGDILVGKVTP----KGETELT 773
Query: 1088 PEYK------------------EVPVSYKGSVPSYLEKVLVSSNSEDAFL-------IKM 1122
PE K VP +G+V V V S E L +K+
Sbjct: 774 PEEKLLRAIFGEKARDVRDTSLRVPPGVEGTV----IDVKVFSRKEGDELPPGVNKLVKV 829
Query: 1123 LLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHG 1172
+ Q R+ ++GDK + RHG KGV+ I+ EDMPF E G DI++NP G
Sbjct: 830 YIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLG 879
Score = 34.7 bits (80), Expect = 0.40
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 357 TPHECRLRDLTYSAPITVDIEYT----RGSQRVVRSDLVIGRMPIM 398
EC+ R LTYS P+ V + G++ + ++ +G +P+M
Sbjct: 78 DVEECKERGLTYSVPLKVKLRLINKEEDGTKEIKEQEVYMGDIPLM 123
Score = 32.7 bits (75), Expect = 1.6
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 228 RLSYISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTH 287
RLS + G G +TR + FE R + + +G +CP +TPEG GL+ +L+
Sbjct: 405 RLSAL-GPGGLTRERAGFEV-------RDVHPTHYGRICPIETPEGPNIGLINSLSTYAR 456
Query: 288 I 288
+
Sbjct: 457 V 457
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 136 bits (346), Expect = 2e-32
Identities = 66/158 (41%), Positives = 92/158 (58%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
L+K+ + Q R+ ++GDK + RHG KGV+ I+ EDMP+ E G DI++NP G PSRM
Sbjct: 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMN 928
Query: 1271 VGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDIFYSGITGEALE 1330
+G+++E G A G F G K +++E L G GK Y G TGE +
Sbjct: 929 IGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFD 988
Query: 1331 AYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTG 1368
+ G +Y KL H+V DKIHARS GP ++T+QP G
Sbjct: 989 RPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLG 1026
Score = 64.7 bits (159), Expect = 3e-10
Identities = 25/54 (46%), Positives = 37/54 (68%)
Query: 1119 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHG 1172
L+K+ + Q R+ ++GDK + RHG KGV+ I+ EDMP+ E G DI++NP G
Sbjct: 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLG 922
Score = 41.6 bits (99), Expect = 0.003
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 357 TPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIM 398
EC+ R LTYSAP+ V + ++ V +G +P+M
Sbjct: 82 DVEECKERGLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLM 124
Score = 32.8 bits (76), Expect = 1.9
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 979 GQNATIAVMSYSGYDIEDALIMN 1001
GQN +A M ++GY+ EDA++++
Sbjct: 716 GQNVLVAFMPWNGYNFEDAILIS 738
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 127 bits (322), Expect = 1e-29
Identities = 64/174 (36%), Positives = 89/174 (51%), Gaps = 15/174 (8%)
Query: 1212 IKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTV 1271
I++ + Q R+ ++GDK + RHG KG+I I+ ++DMP+ G PDII+NP G PSRM V
Sbjct: 800 IRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNV 859
Query: 1272 GKLIELLAGKAGLM-----------EGNYKEGT-AFGGTKLVDVQE---ELIRHGYNYQG 1316
G+L E L G AG E E + KL E + G
Sbjct: 860 GQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPG 919
Query: 1317 KDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRR 1370
K + G TG + + G Y KL H+V DKIHAR+ GP ++T+QP G +
Sbjct: 920 KMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGK 973
Score = 75.1 bits (185), Expect = 2e-13
Identities = 60/226 (26%), Positives = 92/226 (40%), Gaps = 52/226 (23%)
Query: 979 GQNATIAVMSYSGYDIEDALIMNK----------ASLDRGFGRCLVYRNSKCVLKQYPNQ 1028
GQN +A M + GY+ EDA+++NK +++ Y K +
Sbjct: 647 GQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEK-------YEIELRQTKLGSEE 699
Query: 1029 THDRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATP 1088
I Y + LD++GI++ G ++ +LV K I+ S P
Sbjct: 700 ITRNIP--------NVSEYSLKNLDENGIISIGSKVLAGDILVGK----ITPKGESDQLP 747
Query: 1089 EYK------------------EVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLR----Q 1126
E K +P G V E S E F + +R Q
Sbjct: 748 EGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKV-EIFSRSKGDELKFGYYLKIRVFIAQ 806
Query: 1127 TRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHG 1172
R+ ++GDK + RHG KG+I I+ ++DMP+ G PDII+NP G
Sbjct: 807 IRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLG 852
Score = 43.5 bits (103), Expect = 0.001
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 223 TQVLSRLSY---ISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLV 279
T LS L++ IS LG +K R R + S +G +CP +TPEG CGL+
Sbjct: 373 TNPLSELTHKRRISILG-----PGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLI 427
Query: 280 KNLALMTHI 288
+LA I
Sbjct: 428 GSLATNARI 436
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 114 bits (289), Expect = 1e-25
Identities = 68/185 (36%), Positives = 98/185 (52%), Gaps = 19/185 (10%)
Query: 1205 NSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHG 1264
+S + I + + Q R ++GDK + RHG KG+I I+ ++DMP+ + G D+++NP G
Sbjct: 797 SSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLG 856
Query: 1265 YPSRMTVGKLIELLAGKAG-LMEGNYK--------EGTAFGGTKLV--DVQEELIRHGY- 1312
PSRM VG++ E L G AG L+ +Y+ E A KLV ++ E +
Sbjct: 857 VPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEA--SRKLVFSELYEASKQTANP 914
Query: 1313 -----NYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPT 1367
Y GK + G TG+ E + G Y KL H V DKIHARS GP ++T+QP
Sbjct: 915 WVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPL 974
Query: 1368 GRRWK 1372
R K
Sbjct: 975 RGRSK 979
Score = 70.3 bits (173), Expect = 6e-12
Identities = 62/218 (28%), Positives = 107/218 (49%), Gaps = 37/218 (16%)
Query: 979 GQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRN--SKCVLKQYPNQTHDRILGP 1036
G+N +A M + GY+ EDA+++++ LVY + + +++Y QTH GP
Sbjct: 652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFHIRKYEIQTHVTSQGP 702
Query: 1037 LLEADTRK----PVYRHRALDQDGIVAPGEQICERQVLVNKSMPTIS-----------VS 1081
E T++ + R LD++GIV G + +LV K P + +
Sbjct: 703 --ERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLR 760
Query: 1082 AI-SMATPEYKE----VPVSYKGSV--PSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGD 1134
AI + KE +P+ +G V +++K SS + I + + Q R ++GD
Sbjct: 761 AIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSY--NPETIHVYILQKREIQVGD 818
Query: 1135 KFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHG 1172
K + RHG KG+I I+ ++DMP+ + G D+++NP G
Sbjct: 819 KVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLG 856
Score = 34.1 bits (79), Expect = 0.71
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 14/54 (25%)
Query: 249 RKVS--GPRSLQG------------SQWGMLCPSDTPEGEACGLVKNLALMTHI 288
RK+S GP L G S +G +CP DT EG GL+ +LA+ I
Sbjct: 391 RKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARI 444
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 108 bits (273), Expect = 1e-24
Identities = 49/132 (37%), Positives = 71/132 (53%), Gaps = 12/132 (9%)
Query: 178 IPKIKAAQFDIVNHMRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGM 237
IK A +R D +T L A+ TGNW R GV+Q+L R Y++ L
Sbjct: 373 ELSIKTA-------VRSDVLTERLEHAMATGNWV-----GGRTGVSQLLDRTDYMATLSH 420
Query: 238 MTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNM 297
+ R+ S +++ R L +QWG +CPS+TPEG CGLVKN A M I+T DE+ +
Sbjct: 421 LRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEV 480
Query: 298 LKIMYNIGIEHI 309
+I+ +G+E
Sbjct: 481 KEILKELGVEPE 492
Score = 64.6 bits (158), Expect = 2e-10
Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 340 EVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLVIGRMPIML 399
V KP ++E+ R+ P E RLR+LTYSAP+ +++ G + ++ IG +P+M+
Sbjct: 60 RVGKPVVKEADGSEREIYPMEARLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMV 119
Query: 400 QSSKCVLRNKTE 411
S C L +E
Sbjct: 120 GSKICNLYGLSE 131
Score = 50.7 bits (122), Expect = 4e-06
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 114 DKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFYLKYLDIHVGI 173
D+ L ++ KE LV+ HIDS++ F++ ++K++ I ++++ Y++ I VG
Sbjct: 4 DRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVG- 62
Query: 174 ADKIIPKIKAAQ 185
P +K A
Sbjct: 63 ----KPVVKEAD 70
Score = 48.0 bits (115), Expect = 2e-05
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 467 HIPVINMRFKMKAMYLAVMIRRMVLALS-DPDMLDDRDYYGNKRLELAGSLLSLMFEDVF 525
H+ V + KA YL M L+ DD+D+Y NKRL+LAG L+ +F F
Sbjct: 295 HLGVEPEVRRAKAHYLGRMAE-ACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAF 353
Query: 526 KRFNSELK 533
R ++K
Sbjct: 354 NRLARDVK 361
>gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Domain 3, s
also known as the fork domain and is proximal to
catalytic site.
Length = 68
Score = 85.8 bits (213), Expect = 3e-20
Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 224 QVLSRLSYISGLGMMTRIN--SQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKN 281
QVL + +++S L R+N K RK R L SQ+G +CP +TPEG CGLV +
Sbjct: 1 QVLDQTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNS 60
Query: 282 LALMTHIT 289
LAL I
Sbjct: 61 LALYARIN 68
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This domain
forms one of the two distinctive lobes of the Rpb2
structure. This domain is also known as the protrusion
domain. The other lobe (pfam04561) is nested within this
domain.
Length = 394
Score = 84.3 bits (209), Expect = 6e-17
Identities = 30/71 (42%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 343 KPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIMLQS 401
KP+I+ES TR+ P E RLR+LTYS+P+ V E T + + + V IG++P+ML+S
Sbjct: 48 KPKIKESDGKTREIYPREARLRNLTYSSPLYVPAELTVNNTEEIEKEKVFIGKIPLMLRS 107
Query: 402 SKCVLRNKTEY 412
+ C+L +E
Sbjct: 108 NACILNGASES 118
Score = 77.4 bits (191), Expect = 1e-14
Identities = 29/98 (29%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 438 KKLRQKRFQTYKKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPD 497
+ K F ++ + A L + H+ V +KA + MI R++L
Sbjct: 266 GRGSAKGFP--RERRILGAVGILDLNLLPHLGVSENTRTLKAQDIGYMIHRLLLLALGRG 323
Query: 498 MLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKET 535
LDD D+ GNKRL LAG LL F + R +++E
Sbjct: 324 PLDDIDHLGNKRLRLAGELLQSQFRILLNRLERDVRER 361
Score = 43.9 bits (104), Expect = 5e-04
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 127 GLVKPHIDSFDYFINVEIKKLMQANANIYSDV-DPLFYLKYLDIHVG 172
GLV+ +DSF++F++ +++ + I + +P F LK I +
Sbjct: 1 GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDEEPEFSLKVGQIKLA 47
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 73.4 bits (180), Expect = 9e-13
Identities = 57/216 (26%), Positives = 93/216 (43%), Gaps = 58/216 (26%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
+K+ + R+ ++GDK + RHG KG++ IV DMP+ G DI++NP G PSRM
Sbjct: 1077 KVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMN 1136
Query: 1271 VGKLIEL---LAGK------AGLMEGNYKEGTAFGGTKLVDV------------------ 1303
+G+++E+ L GK A ++E K+ K++++
Sbjct: 1137 IGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENC 1196
Query: 1304 -QEELIRHGYNYQGKDIF----YSGITGEALEAY-------------IYSGPV------- 1338
EEL+ + ++ + GI+ E +Y G
Sbjct: 1197 SDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRER 1256
Query: 1339 ----YYQKLK-HMVQD-KIHARSRGPRVVLTRQPTG 1368
Y +K H + D K+HARS GP ++T QP G
Sbjct: 1257 VNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVG 1292
Score = 53.0 bits (127), Expect = 1e-06
Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 1119 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
+K+ + R+ ++GDK + RHG KG++ IV DMP+ G DI++NP G+
Sbjct: 1077 KVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGV 1131
Score = 37.6 bits (87), Expect = 0.059
Identities = 30/119 (25%), Positives = 52/119 (43%), Gaps = 17/119 (14%)
Query: 975 KLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRIL 1034
+L G+N +A M ++GY+ EDA+++++ + + Y + R L
Sbjct: 803 ELALGKNVRVAFMPWNGYNFEDAIVVSE---------RITKDDIFTSTHIYEKEVDAREL 853
Query: 1035 GPLLEADTRK-PVYRHRA---LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPE 1089
+E T P + A LD+ GIV G + +LV K+ P + +TPE
Sbjct: 854 KHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIK----STPE 908
Score = 33.4 bits (76), Expect = 1.3
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 255 RSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHI 288
R + + +G +CP +TPEG+ GL+ L+ T +
Sbjct: 562 RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV 595
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 70.0 bits (171), Expect = 9e-12
Identities = 32/58 (55%), Positives = 39/58 (67%)
Query: 1225 GDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKA 1282
GDK + RHG KGVI +V EDMP+ E G DII+NP G PSRM VG+++E G A
Sbjct: 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWA 1141
Score = 55.4 bits (133), Expect = 3e-07
Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 1311 GYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTG 1368
G + G+ + Y G +GE + + G +Y KL H+V KIHARS GP ++T+QP G
Sbjct: 1293 GLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLG 1350
Score = 52.3 bits (125), Expect = 2e-06
Identities = 23/41 (56%), Positives = 28/41 (68%)
Query: 1133 GDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
GDK + RHG KGVI +V EDMP+ E G DII+NP G+
Sbjct: 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGV 1124
Score = 40.8 bits (95), Expect = 0.007
Identities = 35/117 (29%), Positives = 54/117 (46%), Gaps = 19/117 (16%)
Query: 972 NFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHD 1031
N +L GQN +A MS+ GY+ ED++I++ + + + +CV+ HD
Sbjct: 810 NSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVV-------HD 862
Query: 1032 RILGPLLEADTR-------KPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVS 1081
LG E TR + +Y LD GIV G ++ +LV K P S+S
Sbjct: 863 TPLGS--EKITRAIPGVNEENLYH---LDDSGIVKIGTRVGPGYILVGKVTPKPSLS 914
Score = 38.4 bits (89), Expect = 0.034
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 8/61 (13%)
Query: 228 RLSYISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTH 287
RLS + G G +TR + FE R + + +G +CP +TPEG+ GL+ +LA+
Sbjct: 550 RLSAL-GPGGLTRERAGFEV-------RDVHPTHYGRICPIETPEGQNIGLINSLAIYAR 601
Query: 288 I 288
I
Sbjct: 602 I 602
>gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Domain 5,
is also known as the external 2 domain.
Length = 46
Score = 53.7 bits (130), Expect = 2e-09
Identities = 21/46 (45%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 692 FDDFLYEGKIEYLDVNEGNDSHIAVSESGIR----PGVTTHLEIAP 733
F D L EG IEYLD E + IA+S +R TTH EI P
Sbjct: 1 FVDLLKEGVIEYLDAEEEETAMIAMSPEDLRLEDITKTTTHCEIHP 46
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain forms one of the two distinctive lobes of the
Rpb2 structure. This domain is also known as the lobe
domain. DNA has been demonstrated to bind to the concave
surface of the lobe domain, and plays a role in
maintaining the transcription bubble. Many of the
bacterial members contain large insertions within this
domain, as region known as dispensable region 1 (DRI).
Length = 185
Score = 43.1 bits (102), Expect = 3e-04
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 474 RFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLE 511
++KA + MI R++ DD D+ GNKR+
Sbjct: 148 NERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 33.4 bits (77), Expect = 0.43
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 88 VKAVHGTYLTMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDY-FINVEIKK 146
+HG +T E L D+P + + +L FL+ + LV + FD F+ +E +
Sbjct: 50 ATEIHG-----ITPEM--LDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPR 102
Query: 147 LMQANANIYSDVDPLFYLKYL 167
L +D L +
Sbjct: 103 LGIKQPPKLPVIDTLKLARAT 123
>gnl|CDD|184406 PRK13933, PRK13933, stationary phase survival protein SurE;
Provisional.
Length = 253
Score = 32.4 bits (74), Expect = 1.4
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 1275 IELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQ---GKDIFYSGITGEALEA 1331
+E + KA + G + KLV +++ G N G DI YSG A+E
Sbjct: 58 LEGINSKAYSISGTPADCVRVALDKLVPDNIDMVISGINKGLNIGNDILYSGTVSAAIEG 117
Query: 1332 YIYSGP 1337
IY P
Sbjct: 118 AIYKVP 123
>gnl|CDD|223073 PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like
protein; Provisional.
Length = 865
Score = 32.6 bits (75), Expect = 2.0
Identities = 18/50 (36%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 1225 GDKFSSRHGQKGVIGLIVEQEDMPFN----ESGICPDIIMNPHGYPSRMT 1270
G K HGQKGV+ ED E G I ++P Y SR T
Sbjct: 711 GLKICGIHGQKGVLN---GSED--LTEWMAEDGTHAQICLSPISYLSRQT 755
>gnl|CDD|152118 pfam11682, DUF3279, Protein of unknown function (DUF3279). This
family of proteins with unknown function appears to be
restricted to Enterobacteriaceae.
Length = 128
Score = 30.2 bits (68), Expect = 2.7
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 873 EEKEPRLLRKFQYFDVRTPYRLRRLLCWECVLYNKRF 909
EEKE + +++ Q V Y + R+ W CV+ + +
Sbjct: 72 EEKEIQRIKRLQQM-VPDAYPVPRVASWHCVMCHHDY 107
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 31.4 bits (71), Expect = 2.7
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 96 LTMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDY-FINVEIKKLMQ 149
+ +TDE L D+P+ + L F+ L+ H +FD F+ VE ++L
Sbjct: 67 IHGITDE--MLADAPKFAEVLPEFLDFIGGLRLLVAHNAAFDVGFLRVESERLGI 119
>gnl|CDD|214676 smart00463, SMR, Small MutS-related domain.
Length = 80
Score = 28.8 bits (65), Expect = 3.9
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 11/71 (15%)
Query: 678 PTFLNMH--------QFLGFKRFDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHL 729
L++H L K ++ +G + L + G H +SG++P + HL
Sbjct: 1 KWSLDLHGLTVEEALTAL-DKFLNNARLKGLEQKLVIITGKGKHSLGGKSGVKPALKEHL 59
Query: 730 EI--APFTLLG 738
+ F G
Sbjct: 60 RVESFRFAEEG 70
>gnl|CDD|238028 cd00073, H15, linker histone 1 and histone 5 domains; the basic
subunit of chromatin is the nucleosome, consisting of an
octamer of core histones, two full turns of DNA, a
linker histone (H1 or H5) and a variable length of
linker DNA; H1/H5 are chromatin-associated proteins that
bind to the exterior of nucleosomes and dramatically
stabilize the highly condensed states of chromatin
fibers; stabilization of higher order folding occurs
through electrostatic neutralization of the linker DNA
segments, through a highly positively charged carboxy-
terminal domain known as the AKP helix (Ala, Lys, Pro);
thought to be involved in specific protein-protein and
protein-DNA interactions and play a role in suppressing
core histone tail domain acetylation in the chromatin
fiber.
Length = 88
Score = 28.7 bits (65), Expect = 4.7
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 14/69 (20%)
Query: 89 KAVHGTYLTMVTDETSKLKDS-----PEIRDKWKLVLSFLKEKGLVKPHIDSFDYFINVE 143
H Y MVT+ LK+ I+ +++ K K ++F+ + +
Sbjct: 1 PPSHPPYSEMVTEAIKALKERKGSSLQAIK-------KYIEAKY--KVDDENFNKLLKLA 51
Query: 144 IKKLMQANA 152
+KK +
Sbjct: 52 LKKGVAKGK 60
>gnl|CDD|219293 pfam07093, SGT1, SGT1 protein. This family consists of several
eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known
to suppress GCR2 and is highly expressed in the muscle
and heart. The function of this family is unknown
although it has been speculated that SGT1 may be
functionally analogous to the Gcr2p protein of
Saccharomyces cerevisiae which is known to be a
regulatory factor of glycolytic gene expression.
Length = 557
Score = 30.8 bits (70), Expect = 5.8
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 85 LGTVKAVHGTYLTMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEI 144
LG +K G ++ ++ + K ++ +W +L LKEKG K +++ + E
Sbjct: 280 LG-MKLACG--FEILYSKSKREKSDSKVVREWSSLLESLKEKGYFKDNLE-----GSEEY 331
Query: 145 KKLMQANANIYSDVDPLFYLKYLDI 169
K+L++ +S + LD+
Sbjct: 332 KELLEKAEAYFSSTASSPGEEILDL 356
>gnl|CDD|173812 cd07487, Peptidases_S8_1, Peptidase S8 family domain, uncharacterized
subfamily 1. This family is a member of the Peptidases
S8 or Subtilases serine endo- and exo-peptidase clan.
They have an Asp/His/Ser catalytic triad similar to that
found in trypsin-like proteases, but do not share their
three-dimensional structure and are not homologous to
trypsin. The stability of subtilases may be enhanced by
calcium, some members have been shown to bind up to 4
ions via binding sites with different affinity. Some
members of this clan contain disulfide bonds. These
enzymes can be intra- and extracellular, some function at
extreme temperatures and pH values.
Length = 264
Score = 30.2 bits (69), Expect = 6.2
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 16/76 (21%)
Query: 1057 IVAPGEQI--CERQVLVNKSMPT---ISVSAISMATPEYKEVPVSYKGSVPSYLEKVLVS 1111
+VAPGE I C + +S SMATP VS G++ L+ +
Sbjct: 198 VVAPGENIVSCRSPGGNPGAGVGSGYFEMSGTSMATPH-----VS--GAIALLLQANPIL 250
Query: 1112 SNSEDAFLIKMLLRQT 1127
+ E +K +LR T
Sbjct: 251 TPDE----VKCILRDT 262
>gnl|CDD|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated.
Length = 313
Score = 30.2 bits (68), Expect = 7.0
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 94 TYLTMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFD 137
T LT +T+ ++ D+P I + L L+FL +V H SFD
Sbjct: 59 TSLTGITNY--RVSDAPTIEEVLPLFLAFLHTNVIVA-HNASFD 99
>gnl|CDD|130473 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon subunit,
Proteobacterial. This model represents DnaQ, the DNA
polymerase III epsilon subunit, as found in most
Proteobacteria. It consists largely of an exonuclease
domain as described in Pfam model pfam00929. In
Gram-positive bacteria, closely related regions are
found both in the Gram-positive type DNA polymerase III
alpha subunit and as an additional N-terminal domain of
a DinG-family helicase. Both are excluded from this
model, as are smaller proteins, also outside the
Proteobacteria, that are similar in size to the epsilon
subunit but as different in sequence as are the
epsilon-like regions found in Gram-positive bacteria
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 225
Score = 29.7 bits (67), Expect = 8.9
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 9/58 (15%)
Query: 91 VHGTYLTMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDY-FINVEIKKL 147
VHG +TDE L D P+ ++ L F+ LV H +FD F+N E+++L
Sbjct: 55 VHG-----ITDEF--LADKPKFKEIADEFLDFIGGSELVI-HNAAFDVGFLNYELERL 104
>gnl|CDD|143397 cd07078, ALDH, NAD(P)+ dependent aldehyde dehydrogenase family.
The aldehyde dehydrogenase family (ALDH) of NAD(P)+
dependent enzymes, in general, oxidize a wide range of
endogenous and exogenous aliphatic and aromatic
aldehydes to their corresponding carboxylic acids and
play an important role in detoxification. Besides
aldehyde detoxification, many ALDH isozymes possess
multiple additional catalytic and non-catalytic
functions such as participating in metabolic pathways,
or as binding proteins, or as osmoregulants, to mention
a few. The enzyme has three domains, a NAD(P)+
cofactor-binding domain, a catalytic domain, and a
bridging domain; and the active enzyme is generally
either homodimeric or homotetrameric. The catalytic
mechanism is proposed to involve cofactor binding,
resulting in a conformational change and activation of
an invariant catalytic cysteine nucleophile. The
cysteine and aldehyde substrate form an oxyanion
thiohemiacetal intermediate resulting in hydride
transfer to the cofactor and formation of a
thioacylenzyme intermediate. Hydrolysis of the
thioacylenzyme and release of the carboxylic acid
product occurs, and in most cases, the reduced cofactor
dissociates from the enzyme. The evolutionary
phylogenetic tree of ALDHs appears to have an initial
bifurcation between what has been characterized as the
classical aldehyde dehydrogenases, the ALDH family
(ALDH) and extended family members or aldehyde
dehydrogenase-like (ALDH-like) proteins. The ALDH
proteins are represented by enzymes which share a number
of highly conserved residues necessary for catalysis and
cofactor binding and they include such proteins as
retinal dehydrogenase, 10-formyltetrahydrofolate
dehydrogenase, non-phosphorylating glyceraldehyde
3-phosphate dehydrogenase,
delta(1)-pyrroline-5-carboxylate dehydrogenases,
alpha-ketoglutaric semialdehyde dehydrogenase,
alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
aldehyde dehydrogenase and succinate-semialdehyde
dehydrogenase. Included in this larger group are all
human, Arabidopsis, Tortula, fungal, protozoan, and
Drosophila ALDHs identified in families ALDH1 through
ALDH22 with the exception of families ALDH18, ALDH19,
and ALDH20 which are present in the ALDH-like group.
Length = 432
Score = 30.3 bits (69), Expect = 9.0
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 819 LPAGKCQISPGGAEELTARESCHEVLKIISFSISVAV 855
LP G + G +E+ A + H + ISF+ S AV
Sbjct: 151 LPPGVLNVVTGDGDEVGAALASHPRVDKISFTGSTAV 187
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
0.321 0.137 0.411
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 70,851,639
Number of extensions: 7092675
Number of successful extensions: 4906
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4852
Number of HSP's successfully gapped: 84
Length of query: 1384
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1275
Effective length of database: 6,103,016
Effective search space: 7781345400
Effective search space used: 7781345400
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: 65 (28.8 bits)