BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 020983
(319 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|Q39211|RPB3A_ARATH DNA-directed RNA polymerase II subunit RPB3-A OS=Arabidopsis
thaliana GN=RPB36A PE=2 SV=1
Length = 319
Score = 550 bits (1416), Expect = e-156, Method: Compositional matrix adjust.
Identities = 264/319 (82%), Positives = 292/319 (91%)
Query: 1 MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSS 60
MDGA+YQRFPK+KIRELKDDYAKFELR+TD SMANALRRVMI+EVPT+AIDLVEIEVNSS
Sbjct: 1 MDGATYQRFPKIKIRELKDDYAKFELRETDVSMANALRRVMISEVPTVAIDLVEIEVNSS 60
Query: 61 VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDV 120
VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEF L +KC +DQTLDV
Sbjct: 61 VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDV 120
Query: 121 TSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
TS+DLYS+D +V PVDF + + + +GIIIVKLRRGQEL+LRAIARKGIGKDHAKW
Sbjct: 121 TSRDLYSADPTVTPVDFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKW 180
Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
SPAATVTFMYEP+I INED+M++LS EEK +ESSPTKVF +DP T QV VVD EAYTY
Sbjct: 181 SPAATVTFMYEPDIIINEDMMDTLSDEEKIDLIESSPTKVFGMDPVTRQVVVVDPEAYTY 240
Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSE 300
D+EVIKKAEAMGKPGL+EI K+DSFIFTVESTGA+KASQLVLNAI++LKQKLDAVRLS+
Sbjct: 241 DEEVIKKAEAMGKPGLIEISPKDDSFIFTVESTGAVKASQLVLNAIDLLKQKLDAVRLSD 300
Query: 301 DTVEADDQFGELGAHMRGG 319
DTVEADDQFGELGAHMRGG
Sbjct: 301 DTVEADDQFGELGAHMRGG 319
>sp|Q39212|RPB3B_ARATH DNA-directed RNA polymerase II subunit RPB3-B OS=Arabidopsis
thaliana GN=RPB36B PE=1 SV=2
Length = 319
Score = 511 bits (1315), Expect = e-144, Method: Compositional matrix adjust.
Identities = 245/319 (76%), Positives = 281/319 (88%)
Query: 1 MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSS 60
MDG +YQRFP VKIRELKDDYAKFELR+TD SMANALRRVMI+EVPT+AI LV+IEVNSS
Sbjct: 1 MDGVTYQRFPTVKIRELKDDYAKFELRETDVSMANALRRVMISEVPTMAIHLVKIEVNSS 60
Query: 61 VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDV 120
VLNDEFIA RL LIPLTSERAMSMRF +DC+ C+GD CEFCSVEF L AKC +DQTLDV
Sbjct: 61 VLNDEFIAQRLSLIPLTSERAMSMRFCQDCEDCNGDEHCEFCSVEFPLSAKCVTDQTLDV 120
Query: 121 TSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
TS+DLYS+D +V PVDF + + + +GIII KLRRGQEL+L+A+ARKGIGKDHAKW
Sbjct: 121 TSRDLYSADPTVTPVDFTSNSSTSDSSEHKGIIIAKLRRGQELKLKALARKGIGKDHAKW 180
Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
SPAATVT+MYEP+I INE++M +L+ EEK +ESSPTKVF IDP TGQV VVD EAYTY
Sbjct: 181 SPAATVTYMYEPDIIINEEMMNTLTDEEKIDLIESSPTKVFGIDPVTGQVVVVDPEAYTY 240
Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSE 300
D+EVIKKAEAMGKPGL+EI+ K DSF+FTVESTGA+KASQLVLNAI++LKQKLDA+RLS+
Sbjct: 241 DEEVIKKAEAMGKPGLIEIHPKHDSFVFTVESTGALKASQLVLNAIDILKQKLDAIRLSD 300
Query: 301 DTVEADDQFGELGAHMRGG 319
+TVEADDQFGELGAHMR G
Sbjct: 301 NTVEADDQFGELGAHMREG 319
>sp|Q54DH7|RPB3_DICDI DNA-directed RNA polymerase II subunit rpb3 OS=Dictyostelium
discoideum GN=polr2c PE=3 SV=1
Length = 302
Score = 282 bits (722), Expect = 2e-75, Method: Compositional matrix adjust.
Identities = 145/292 (49%), Positives = 202/292 (69%), Gaps = 9/292 (3%)
Query: 8 RFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFI 67
R P+++I E+K+D F L +TD S+ANALRRVMIAEVPT+ IDLVE E N+SVL DEFI
Sbjct: 10 RQPELEILEIKNDSIIFILSNTDISVANALRRVMIAEVPTMCIDLVEFESNNSVLCDEFI 69
Query: 68 AHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYS 127
AHRLGLIPL S+ ++RDC D +C+ CSVE L KC ++ DVTS DL S
Sbjct: 70 AHRLGLIPLVSDNIDKFCYTRDCSCSD---RCDQCSVELRLNVKCTENRPRDVTSSDLLS 126
Query: 128 SDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVT 187
+ +V+PV + S++ ++ I IVKLRRGQE++LRAIA+KG+GK+HAKWSP+ T
Sbjct: 127 QNSAVIPVS----SQVTSSNSEQEIPIVKLRRGQEIKLRAIAKKGVGKEHAKWSPSCVAT 182
Query: 188 FMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPN--TGQVYVVDAEAYTYDDEVI 245
+ ++P I +N++ ++ L+ ++K+ WV S PTKV+ P+ T QV + D Y E
Sbjct: 183 YQFQPIIVLNQNRIDELTDQQKEEWVGSCPTKVYSYSPHQSTQQVTIEDPLRCVYCLECK 242
Query: 246 KKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
KKAE+ GKP LV + K+D FIFTVES+GA+K +VL AI+++K+KL ++
Sbjct: 243 KKAESFGKPDLVHLEQKQDKFIFTVESSGALKPEDIVLYAIQIIKRKLTDIQ 294
>sp|Q3T0Q3|RPB3_BOVIN DNA-directed RNA polymerase II subunit RPB3 OS=Bos taurus GN=POLR2C
PE=2 SV=1
Length = 275
Score = 204 bits (520), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 124/293 (42%), Positives = 173/293 (59%), Gaps = 44/293 (15%)
Query: 6 YQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDE 65
Y P V+I EL D+ KF + +TD ++AN++RRV IAEVP IAID V+I+ NSSVL+DE
Sbjct: 3 YANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDE 62
Query: 66 FIAHRLGLIPLTSERAM-SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD 124
FIAHRLGLIPLTS+ + +++SRDC C + C CSVEF L +C+ DQT VTS+D
Sbjct: 63 FIAHRLGLIPLTSDDIVDKLQYSRDC-TC--EEFCPECSVEFTLDVRCNEDQTRHVTSRD 119
Query: 125 LYSSDHSVVPVDF----VDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
L S+ V+PV DP Y +Q I+IVKLR+GQELRLRA A+KG GK+HAKW
Sbjct: 120 LISNSPRVIPVTSRNRDNDPNDY---VEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKW 176
Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
+P A V F Y+P ++ + + + W +S +++
Sbjct: 177 NPTAGVAFEYDP-----DNALRHTVYPKPEEWPKSEYSELD------------------- 212
Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL 293
+DE + GKP + F + VES G+++ +VL+A+ LK+KL
Sbjct: 213 EDESQAPYDPNGKP---------ERFYYNVESCGSLRPETIVLSALSGLKKKL 256
>sp|P16925|CNJC_TETTH Conjugation stage-specific protein OS=Tetrahymena thermophila
GN=CNJC PE=2 SV=1
Length = 310
Score = 202 bits (514), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 113/295 (38%), Positives = 180/295 (61%), Gaps = 13/295 (4%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
K+ + L++ +F L + D S+AN+LRR+++AE+ TIAI V++ N+S L DE+IAHR
Sbjct: 5 KLTLTNLEEFKCEFTLENCDISLANSLRRILLAEIETIAIHNVKVYENTSSLPDEYIAHR 64
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDL----- 125
LGLIPL S + + +C+ G+C+ C++ F LR +++ L+VTS DL
Sbjct: 65 LGLIPLNSAKVDDYNYIWNCNC---QGECDRCTIHFDLRVSNFTNEVLEVTSLDLKQRQD 121
Query: 126 YSSDHSVVPVDFVDPAGYDSTDQQR--GIIIVKLRRGQELRLRAIARKGIGKDHAKWSPA 183
++ + +V P+ V D +R GI I+KL +GQ++ A+KGIGK H+KW+P
Sbjct: 122 HTDEDAVRPIK-VYSILRDEYGNKREVGIPIIKLSKGQQIHFECEAQKGIGKMHSKWNPV 180
Query: 184 ATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDE 243
TF EPEI ++++ ++L +E+K++ V + PTKVF I+P+T + V D Y +E
Sbjct: 181 CISTFSVEPEIIFDQEI-QNLDIEQKKALVNACPTKVFGINPHTNTLEVQDHMKCMYCEE 239
Query: 244 VIKK-AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
+ K AE KP L++I K+D F F VE+TG +K +++ L+QKLD +R
Sbjct: 240 CVYKCAEDFQKPKLIKIDHKKDKFFFKVETTGVMKPVEVLRRGFSTLRQKLDFMR 294
>sp|P19387|RPB3_HUMAN DNA-directed RNA polymerase II subunit RPB3 OS=Homo sapiens
GN=POLR2C PE=1 SV=2
Length = 275
Score = 202 bits (514), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 123/293 (41%), Positives = 172/293 (58%), Gaps = 44/293 (15%)
Query: 6 YQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDE 65
Y P V+I EL D+ KF + +TD ++AN++RRV IAEVP IAID V+I+ NSSVL+DE
Sbjct: 3 YANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDE 62
Query: 66 FIAHRLGLIPLTSERAM-SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD 124
FIAHRLGLIPL S+ + +++SRDC C + C CSVEF L +C+ DQT VTS+D
Sbjct: 63 FIAHRLGLIPLISDDIVDKLQYSRDC-TC--EEFCPECSVEFTLDVRCNEDQTRHVTSRD 119
Query: 125 LYSSDHSVVPVDF----VDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
L S+ V+PV DP Y +Q I+IVKLR+GQELRLRA A+KG GK+HAKW
Sbjct: 120 LISNSPRVIPVTSRNRDNDPNDY---VEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKW 176
Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
+P A V F Y+P ++ + + + W +S +++
Sbjct: 177 NPTAGVAFEYDP-----DNALRHTVYPKPEEWPKSEYSELD------------------- 212
Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL 293
+DE + GKP + F + VES G+++ +VL+A+ LK+KL
Sbjct: 213 EDESQAPYDPNGKP---------ERFYYNVESCGSLRPETIVLSALSGLKKKL 256
>sp|P97760|RPB3_MOUSE DNA-directed RNA polymerase II subunit RPB3 OS=Mus musculus
GN=Polr2c PE=2 SV=1
Length = 275
Score = 191 bits (484), Expect = 7e-48, Method: Compositional matrix adjust.
Identities = 120/293 (40%), Positives = 165/293 (56%), Gaps = 44/293 (15%)
Query: 6 YQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDE 65
Y P V+I EL ++ KF + +TD ++AN++RRV IAEVP IAID V+I+ NSSVL+DE
Sbjct: 3 YANQPTVRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDGNSSVLHDE 62
Query: 66 FIAHRLGLIPLTSERAM-SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD 124
FIAHRLGLIPLTS+ + +++SRDC C + C CSVEF L +C+ DQT VTS+D
Sbjct: 63 FIAHRLGLIPLTSDDIVDKLQYSRDC-TC--EEFCPECSVEFTLDVRCNEDQTRHVTSRD 119
Query: 125 LYSSDHSVVPVDF----VDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
L S+ V+PV DP Y +Q I+IVKLR+GQELRLRA +K GK+HAKW
Sbjct: 120 LISNSPRVIPVTSRNRDNDPNDY---VEQDDILIVKLRKGQELRLRAYVKKRSGKEHAKW 176
Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
+P A V F Y+P+ + + K + E
Sbjct: 177 NPTAGVAFEYDPDNGLRHTVYPKPEEGPKSEYSELD------------------------ 212
Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL 293
+DE + GKP + F + VES G+++ + L+A+ LK+KL
Sbjct: 213 EDESQAPYDPNGKP---------ERFYYNVESCGSLRPETIGLSALSGLKKKL 256
>sp|P16370|RPB3_YEAST DNA-directed RNA polymerase II subunit RPB3 OS=Saccharomyces
cerevisiae (strain ATCC 204508 / S288c) GN=RPB3 PE=1
SV=2
Length = 318
Score = 184 bits (466), Expect = 1e-45, Method: Compositional matrix adjust.
Identities = 115/299 (38%), Positives = 167/299 (55%), Gaps = 38/299 (12%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+VKIRE D F L + D +MAN+LRRVMIAE+PT+AID VE+E N++VL DEFIAH
Sbjct: 6 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPL S + +SRDC D C+ CSV L+A S+ T +V SKDL
Sbjct: 66 RLGLIPLQSMDIEQLEYSRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
+ ++ + P D + G++I KLR+GQEL+L +A+KGI K+HAKW PAA + F
Sbjct: 123 N-LMGRNIGHPIIQDK--EGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFE 179
Query: 190 YEP--EIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
Y+P ++ + E S +E W +S + ++ PN G + A+A
Sbjct: 180 YDPWNKLKHTDYWYEQDSAKE---WPQSKNCE-YEDPPNEGDPFDYKAQA---------- 225
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
D+F VES G+I Q+V+ I+ L++K+ ++ L+ ++ D
Sbjct: 226 ----------------DTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 268
>sp|P37382|RPB3_SCHPO DNA-directed RNA polymerase II subunit RPB3 OS=Schizosaccharomyces
pombe (strain 972 / ATCC 24843) GN=rpb3 PE=1 SV=2
Length = 297
Score = 171 bits (434), Expect = 5e-42, Method: Compositional matrix adjust.
Identities = 102/289 (35%), Positives = 156/289 (53%), Gaps = 46/289 (15%)
Query: 12 VKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRL 71
+ IR + + F L +T ++AN+LRRV++AE+PT+AIDLVEI VN+SV+ DEF+AHRL
Sbjct: 7 ITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRL 66
Query: 72 GLIPLTSER-----AMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLY 126
G+IPL S + + ++R+CD D C CSVE L AKC + T+++ ++DL
Sbjct: 67 GMIPLDSSNIDEPPPVGLEYTRNCDC---DQYCPKCSVELFLNAKCTGEGTMEIYARDLV 123
Query: 127 SSDHSVV--PVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAA 184
S +S + P+ DP + RG +I KLR+ QE+ LR IA+KGI K+HAKWSP +
Sbjct: 124 VSSNSSLGHPI-LADP-------KSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTS 175
Query: 185 TVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEV 244
V F Y+P L+ W E+ DAE +
Sbjct: 176 AVAFEYDP----------WNKLQHTDYWFEND----------------ADAEWPKSKNAD 209
Query: 245 IKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL 293
++ G+P + F VES G+I +++++ + +L++KL
Sbjct: 210 WEEPPREGEP--FNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKL 256
>sp|O94616|RPAC1_SCHPO DNA-directed RNA polymerases I and III subunit RPAC1
OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843)
GN=rpc40 PE=3 SV=1
Length = 348
Score = 140 bits (352), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 101/325 (31%), Positives = 162/325 (49%), Gaps = 42/325 (12%)
Query: 6 YQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDE 65
+++ KV I L + FE+ DAS+ANA RR++IAE+PT+A + V I N+S++ DE
Sbjct: 42 FKKNLKVSITSLDQETMVFEISGIDASIANAFRRILIAEIPTLAFEFVYIINNTSIIQDE 101
Query: 66 FIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD- 124
++HR+GL+P++++ M F + ++ +V F L KC ++ KD
Sbjct: 102 VLSHRIGLVPISADPDMFKWFQHPLPGQEA-THTDYDTVVFSLNKKCEFNKNAATDEKDP 160
Query: 125 --------LYSSD------------HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELR 164
+YS D + P+ V+P I++ KLR GQE+
Sbjct: 161 KRLYVNSEVYSGDLIWKPQGRQEERFADNPIRVVNP----------DIVVAKLRPGQEID 210
Query: 165 LRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDID 224
L A A GIG+DHAK+SP AT ++ P IHI + + E+ + + P V +++
Sbjct: 211 LEAHAILGIGQDHAKFSPVATASYRLLPTIHI----LSPIEGEDAVKFQKCFPKGVIELE 266
Query: 225 --PN-TGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQL 281
P+ Q V D T E ++ E K V++ D ++F+VESTG +K L
Sbjct: 267 EGPDGKKQARVADVRKDTVSRECLRHPEFADK---VQLGRVRDHYLFSVESTGIMKPDVL 323
Query: 282 VLNAIEVLKQKLDAVRLSEDTVEAD 306
+ +I VLK K AV+ S + +D
Sbjct: 324 FIKSIAVLKSKCLAVKSSLQNISSD 348
>sp|Q54SN4|RPAC1_DICDI DNA-directed RNA polymerases I and III subunit rpac1
OS=Dictyostelium discoideum GN=polr1c PE=3 SV=1
Length = 345
Score = 139 bits (350), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 94/280 (33%), Positives = 151/280 (53%), Gaps = 23/280 (8%)
Query: 24 FELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSE-RAM 82
FE+ DA +ANALRR+MI+E+PT+AI+ V I N+S+L DE +AHRLG+IP+ + R
Sbjct: 73 FEMIGIDAPIANALRRIMISEIPTMAIEKVYIINNTSILQDEVLAHRLGMIPIKVDPRKF 132
Query: 83 SMRF-SRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSV-VPVDFVDP 140
+ + +++ A D ++ F L+ KC D + S H + VP +
Sbjct: 133 NFKLPNKEYTAED--------TLIFQLKVKCEKDSVTGKIINETALSKHLIWVPTQDQEE 184
Query: 141 AGYDSTDQQRG----IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHI 196
+ D+ R I I+KLR GQ + ++ K IG++H KWSP T ++ +P I +
Sbjct: 185 MFPNEEDRPRPMEDDIPIMKLRPGQVIDIQCYCEKNIGREHIKWSPVCTASYRLQPVISV 244
Query: 197 NEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGL 256
+ +S+ ++ +E P KVFDI+ ++GQV T E I+ E
Sbjct: 245 D----KSIKGDKANQLLEKCPKKVFDIE-DSGQVVAARPLDCTMCRECIRDPEFEQN--- 296
Query: 257 VEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296
V+I D FIF++ESTGA+K+ ++ AI++ +K + V
Sbjct: 297 VKIERVRDHFIFSIESTGALKSREIFQEAIKIFIEKCNIV 336
>sp|Q2NFZ6|RPOD_METST DNA-directed RNA polymerase subunit D OS=Methanosphaera stadtmanae
(strain DSM 3091) GN=rpoD PE=3 SV=1
Length = 270
Score = 137 bits (346), Expect = 7e-32, Method: Compositional matrix adjust.
Identities = 93/287 (32%), Positives = 151/287 (52%), Gaps = 27/287 (9%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
++IRE D+ A F + D + N +RR+ + E+PT+AI+ V I N + + DE +AHR
Sbjct: 2 NIEIREKDDERAVFVVEGVDDTFINTIRRICLVEIPTLAIEDVNIYKNDAKMFDEVLAHR 61
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKC-HSDQTLDVTSKDLYSSD 129
LGLIP+ ++ + S CD + C+ C V F L+ KC + + V SKDL S D
Sbjct: 62 LGLIPIVTDLDSYVMPSE----CDCESGCQHCRVSFLLKEKCEEGNDSKIVYSKDLKSDD 117
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
+V PV YD+ I IV+LR G+E+ L AIA G+G +HAKW T +
Sbjct: 118 PAVKPV-------YDT------IPIVRLREGEEVELEAIAELGLGSEHAKWQATTTCGYK 164
Query: 190 YEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249
Y P+I I+ + + L + +VE P V I+ +T + V + E + + +E
Sbjct: 165 YYPKIEIDTEKVNDL-----EEYVEECPRNVLQIEDDT--LVVGNIENCSTCRTCQRLSE 217
Query: 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296
+V+ +E +IF +E+ G++K ++ A ++L +K D +
Sbjct: 218 KDDNAIVVDF--EESKYIFKIETDGSLKPFDVLTIACDILSEKADNI 262
>sp|P07703|RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
GN=RPC40 PE=1 SV=1
Length = 335
Score = 137 bits (345), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 95/298 (31%), Positives = 152/298 (51%), Gaps = 20/298 (6%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
+V I L A F+L + D S+ANA RR+MI+EVP++A + V N+SV+ DE +AHR
Sbjct: 41 EVNISSLDAREANFDLINIDTSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHR 100
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTS---KDLYS 127
+GL+PL + M D + D + + ++ L KC + S K+LY+
Sbjct: 101 IGLVPLKVDPDMLTWV--DSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYN 158
Query: 128 SDHSVVPVDFVDPAGYDST--------DQQRGIIIVKLRRGQELRLRAIARKGIGKDHAK 179
+ H +P G ST I++ KLR GQE+ L+A GIG DHAK
Sbjct: 159 NAHVYARDLKFEPQGRQSTTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAK 218
Query: 180 WSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYT 239
+SP +T ++ P+I+I ++ + E + + + P V ID + + YV DA T
Sbjct: 219 FSPVSTASYRLLPQINI----LQPIKGESARRFQKCFPPGVIGIDEGSDEAYVKDARKDT 274
Query: 240 YDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
EV++ E K V++ + FIF VES GA+ ++ ++ +LK K + ++
Sbjct: 275 VSREVLRYEEFADK---VKLGRVRNHFIFNVESAGAMTPEEIFFKSVRILKNKAEYLK 329
>sp|P0CG28|RPOD_METAC DNA-directed RNA polymerase subunit D OS=Methanosarcina acetivorans
(strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) GN=rpoD
PE=3 SV=1
Length = 266
Score = 132 bits (332), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 96/283 (33%), Positives = 138/283 (48%), Gaps = 32/283 (11%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
+V I EL D AKF L + + AN +RR M+A+VPT+AI+ V + N+SVL DE +A R
Sbjct: 4 EVDILELSDRSAKFVLSNVSTAFANGIRRAMVADVPTLAIEYVNLYDNTSVLYDEQLALR 63
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDH 130
L LIPL ++ + +CD C G+G C C V L A + V S+DL SSD
Sbjct: 64 LSLIPLATDIETYLP-QAECDVCGGEG-CPACEVSLTLSA----EGPGTVYSRDLISSDP 117
Query: 131 SVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMY 190
+ P D P IV+L++GQ+L L AIA G G+D KW +
Sbjct: 118 KIQPADPNVP-------------IVELKKGQKLVLEAIAHMGYGRDSVKWQAGVACGYKN 164
Query: 191 EPEIHI-NEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249
P I I N D + E P + ++ ++ AE + + E
Sbjct: 165 MPVITIENCDACGHCAAE--------CPKGIISVEEAGAKI----AEEDIMKCSICRLCE 212
Query: 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQK 292
+ +++ E+SF+FT+ES G+ A LVLNA V+K K
Sbjct: 213 QVCDINAIKVDFYENSFVFTMESDGSYTAKDLVLNAANVIKGK 255
>sp|O28002|RPOD_ARCFU DNA-directed RNA polymerase subunit D OS=Archaeoglobus fulgidus
(strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC
100126) GN=rpoD PE=3 SV=1
Length = 264
Score = 129 bits (325), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 93/287 (32%), Positives = 150/287 (52%), Gaps = 41/287 (14%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+++I E KD KF L++ ++AN+ RR M AEVP +A+D V+I +NSS DE IAH
Sbjct: 3 PEIEILEEKDFKIKFILKNASPALANSFRRAMKAEVPAMAVDYVDIYLNSSYFYDEVIAH 62
Query: 70 RLGLIPLTSERAMSMRFSRDCD-ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSS 128
RL ++P+ + RF+ + +C G+G C C + F L + K +YS
Sbjct: 63 RLAMLPI---KTYLDRFNMQSECSCGGEG-CPNCQISFRLNVE---------GPKVVYSG 109
Query: 129 DHSVVPVDFV--DPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATV 186
DF+ DP + D I +++L GQ+L L A+AR G G++HAK+ P +
Sbjct: 110 -------DFISDDPDVVFAIDN---IPVLELFEGQQLMLEAVARLGTGREHAKFQPVSVC 159
Query: 187 TFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIK 246
+ PEI +NE+ +E+ P VF+ D + +V V + A + E ++
Sbjct: 160 VYKIIPEIVVNENCNGC------GDCIEACPRNVFEKDGD--KVRVKNVMACSMCGECVE 211
Query: 247 KAEAMGKPGLVEIYAKE-DSFIFTVESTGAIKASQLVLNAIEVLKQK 292
E + I E ++F+FTVE TGA+ +++ A+E+L+ K
Sbjct: 212 VCE------MNAISVNETNNFLFTVEGTGALPVREVMKKALEILRSK 252
>sp|Q8PV16|RPOD_METMA DNA-directed RNA polymerase subunit D OS=Methanosarcina mazei
(strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833
/ OCM 88) GN=rpoD PE=3 SV=1
Length = 266
Score = 126 bits (317), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 98/288 (34%), Positives = 140/288 (48%), Gaps = 42/288 (14%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
+V I EL D AKF L + AN +RR MIA+VPT+AI+ V + N+SVL DE +A R
Sbjct: 4 EVDILELSDRSAKFVLSRVSMAFANGVRRAMIADVPTLAIEYVNLYDNTSVLYDEQLALR 63
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDH 130
L LIPL ++ M +C+ C G+G C C V L A + V S+DL SSD
Sbjct: 64 LSLIPLVTDIETYMP-QAECEVCGGEG-CPACEVSLTLSA----EGPGTVYSRDLISSDP 117
Query: 131 SVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMY 190
+ P D I IV+L++GQ+L L AIA G G+D KW +
Sbjct: 118 KIQPAD-------------PNIPIVELKKGQKLVLEAIAHMGYGRDSVKWQAGVACGYKN 164
Query: 191 EPEIHI-NEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKA- 248
P I I N D + E + G + V +A A +D++IK +
Sbjct: 165 VPVITIENCDACGHCAAECPK-----------------GIIRVEEAGARIAEDDLIKCSL 207
Query: 249 ----EAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQK 292
E + +++ E++F+FT+ES G+ A L +NA V+K K
Sbjct: 208 CRLCEQVCDINAIKVDFYENAFVFTMESDGSYTAKDLTINAANVIKGK 255
>sp|Q32L22|RPAC1_BOVIN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Bos taurus
GN=POLR1C PE=2 SV=1
Length = 346
Score = 125 bits (314), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 100/321 (31%), Positives = 163/321 (50%), Gaps = 40/321 (12%)
Query: 2 DGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSV 61
D +++ +V + + ++ +F++ DA++ANA RR+++AEVPT+A++ V + N+S+
Sbjct: 41 DQDRFEKNFRVDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSI 100
Query: 62 LNDEFIAHRLGLIPLTSE-RAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKC-------- 112
+ DE +AHRLGLIP+ ++ R R D +G E +++F L+ +C
Sbjct: 101 VQDEILAHRLGLIPIHADPRLFEYRNQGD------EGGTEIDTLQFRLQVRCTRNPHAAK 154
Query: 113 -HSDQTLDVTSKDLYSSDHSVVPVD-----FVDPAGYDSTDQQRGIIIVKLRRGQELRLR 166
SD + +Y+ + VP+ F + A D I+I +LR GQE+ L
Sbjct: 155 DSSDPNELYVNHRVYTRHMTWVPLGNQADLFPEGAIRPVHDD---ILIAQLRPGQEIDLL 211
Query: 167 AIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPN 226
KGIGKDHAK+SP AT ++ P+I L+E + E + V ++
Sbjct: 212 MHCVKGIGKDHAKFSPVATASYRLLPDI----TLLEPVEGEAAEELSRCFSPGVIEVQEI 267
Query: 227 TGQ--VYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLN 284
G+ V + T+ EV + E + K +V + D FIF+VESTG + LV
Sbjct: 268 QGKKVARVANPRLDTFSREVFRN-EKLKK--VVRLARVRDHFIFSVESTGVLPPDVLVSE 324
Query: 285 AIEVLKQK-------LDAVRL 298
AI+VL K LDAV++
Sbjct: 325 AIKVLMGKCQRFLDELDAVQM 345
>sp|P52432|RPAC1_MOUSE DNA-directed RNA polymerases I and III subunit RPAC1 OS=Mus
musculus GN=Polr1c PE=1 SV=3
Length = 346
Score = 124 bits (312), Expect = 8e-28, Method: Compositional matrix adjust.
Identities = 97/320 (30%), Positives = 162/320 (50%), Gaps = 29/320 (9%)
Query: 2 DGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSV 61
D +++ +V + ++ +D +F++ DA++ANA RR+++AEVPT+A++ V + N+S+
Sbjct: 41 DQNRFEKNFRVDVVQMDEDTLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSI 100
Query: 62 LNDEFIAHRLGLIPLTSE-RAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDV 120
+ DE +AHRLGLIP+ ++ R R + + + D +++F L+ +C +
Sbjct: 101 VQDEILAHRLGLIPILADPRLFEYRNQGEEEGTEID------TLQFRLQVRCTRNPNAAK 154
Query: 121 TSKD---------LYSSDHSVVPVDF---VDPAGYDSTDQQRGIIIVKLRRGQELRLRAI 168
S D +Y+ + VP+ V P G I+I +LR GQE+ L
Sbjct: 155 DSSDPNELYVNHKVYTRHMTWVPLGNQADVFPEGTIRPVHD-DILIAQLRPGQEIDLMMH 213
Query: 169 ARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTG 228
KGIGKDHAK+SP AT ++ P I L+E + E + + V +++ G
Sbjct: 214 CVKGIGKDHAKFSPVATASYRLLPAI----TLLEPVEGEAAEELSQCFSPGVIEVEEVQG 269
Query: 229 Q--VYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAI 286
+ V +A T+ E+ + E + K V + D +IF+VESTG + LV AI
Sbjct: 270 KKVARVANARLDTFSREIFRH-EKLKKA--VRLARVRDHYIFSVESTGVLPPDVLVSEAI 326
Query: 287 EVLKQKLDAVRLSEDTVEAD 306
++L K D VE D
Sbjct: 327 KILMGKCRRFLDELDAVEMD 346
>sp|O26144|RPOD_METTH DNA-directed RNA polymerase subunit D OS=Methanothermobacter
thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM
10044 / NBRC 100330 / Delta H) GN=rpoD PE=3 SV=1
Length = 264
Score = 123 bits (308), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 87/287 (30%), Positives = 139/287 (48%), Gaps = 34/287 (11%)
Query: 12 VKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRL 71
+ ++E D F + NA+RR+ + EVP +AI+ V + N + + DE +AHRL
Sbjct: 3 IALKEKTDTEMVFVVSGVTVPFINAIRRICMMEVPKLAIEYVNMYRNDAKMFDEVLAHRL 62
Query: 72 GLIPLTS--ERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
GL+PL + E A S++ +CD + C CSV LR K V S DL S
Sbjct: 63 GLVPLAADPEFAESLKMPEECDC---EEYCSECSVSLTLRKK----GPGVVYSGDLVSET 115
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
+V PV + D I +VKL EL L A+A+ G+G++HAKW P +
Sbjct: 116 PAVKPV-YPD------------IPLVKLGDDDELELEAVAQLGVGREHAKWEPTTACAYK 162
Query: 190 YEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249
Y P I +ED E L +E+ P V + +G+ VVD E + ++ +
Sbjct: 163 YYPRIEFSEDCDECLEC------IEACPRDV--LGEESGKPVVVDLENCSMCKSCVRACD 214
Query: 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296
+++ +E FIF +E+ G++ ++L A ++L+ K + V
Sbjct: 215 KRA----IDVGYEEGKFIFRIETDGSVDPKDVLLKACDILRDKAEQV 257
>sp|A5UN55|RPOD_METS3 DNA-directed RNA polymerase subunit D OS=Methanobrevibacter smithii
(strain PS / ATCC 35061 / DSM 861) GN=rpoD PE=3 SV=1
Length = 274
Score = 122 bits (306), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 95/302 (31%), Positives = 148/302 (49%), Gaps = 45/302 (14%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
+++++ DD F +RD + NA+RR + VP IAI+ V I N S + +E +AHR
Sbjct: 2 EIEVKSQTDDEIVFIVRDAEVPFINAIRRCAMVNVPKIAIEDVNIMRNDSAMFNEVLAHR 61
Query: 71 LGLIPLTSERAMSMRFSRDCDACDG------DGQCEFCSVEFHLRAKCHSDQTLDVTSKD 124
LGL PL S + DA +G D E SV F L+ + V SKD
Sbjct: 62 LGLTPLVS----------NMDAIEGLPLPGDDDYEENNSVMFSLK----EEGPKVVYSKD 107
Query: 125 LYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAA 184
L SSD + PV YD+ I +VKL+ G++L + A+A+ G GK+HAKW P
Sbjct: 108 LISSDSKIKPV-------YDT------IPLVKLKEGEKLNIEAVAKVGYGKEHAKWMPTT 154
Query: 185 TVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEV 244
+ PEI NED+ + E ++ P V D + ++ ++D E
Sbjct: 155 VCVYKQYPEITFNEDV--GIDYE----CADACPRGVLKSDKRSKEIKILDIEDCAMCKSC 208
Query: 245 ----IKKAEAMGK-PGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDA-VRL 298
I+ A++ GK + + E+ FIF +E+ G++ +++L A + L +K D +R
Sbjct: 209 VRASIRNAQSEGKDESYINVGYHENDFIFRIETDGSMPPKEVLLQACDELGEKADKFIRF 268
Query: 299 SE 300
SE
Sbjct: 269 SE 270
>sp|Q5JJF4|RPOD_PYRKO DNA-directed RNA polymerase subunit D OS=Pyrococcus kodakaraensis
(strain ATCC BAA-918 / JCM 12380 / KOD1) GN=rpoD PE=3
SV=1
Length = 259
Score = 120 bits (301), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 99/282 (35%), Positives = 139/282 (49%), Gaps = 38/282 (13%)
Query: 13 KIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLG 72
KI E + D KF + D ANALRR +++EVPT A+D VE N S L DE IAHRL
Sbjct: 5 KILEKRPDSIKFIVSGVDVPFANALRRTILSEVPTFAVDEVEFLENDSALFDEIIAHRLA 64
Query: 73 LIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSV 132
+IPLT+ RFS DA + D S+E ++ V S DL SSD V
Sbjct: 65 MIPLTTPHE---RFS--LDALELDDYTVTLSLE--------AEGPGMVYSGDLKSSDGDV 111
Query: 133 VPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEP 192
P + I IVKL GQ L A AR G GKDHAKW P V + Y
Sbjct: 112 KPAN-------------PNIPIVKLAEGQRLTFNAYARLGRGKDHAKWQP-GFVYYKYLT 157
Query: 193 EIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMG 252
+IH+++D+ + L+ E + + ++ + ++ + +A+ K E MG
Sbjct: 158 KIHVSKDVPDWEELK------ELAERRGLPVEESDEEIVITTIKAFYLPR---KFEEHMG 208
Query: 253 KPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
K EI SF+FTVE+ G + ++V A+++L +K D
Sbjct: 209 KGIREEIVP--GSFVFTVETNGELPVEEIVSIALKILMRKSD 248
>sp|O15160|RPAC1_HUMAN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Homo
sapiens GN=POLR1C PE=1 SV=1
Length = 346
Score = 120 bits (301), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 94/318 (29%), Positives = 162/318 (50%), Gaps = 34/318 (10%)
Query: 2 DGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSV 61
D +++ +V + + ++ +F++ DA++ANA RR+++AEVPT+A++ V + N+S+
Sbjct: 41 DQDRFEKNFRVDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSI 100
Query: 62 LNDEFIAHRLGLIPLTSE-RAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKC-------- 112
+ DE +AHRLGLIP+ ++ R R D + + D +++F L+ +C
Sbjct: 101 VQDEILAHRLGLIPIHADPRLFEYRNQGDEEGTEID------TLQFRLQVRCTRNPHAAK 154
Query: 113 -HSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQ--QRGIIIVKLRRGQELRLRAIA 169
SD + +Y+ + +P+ + T + I+I +LR GQE+ L
Sbjct: 155 DSSDPNELYVNHKVYTRHMTWIPLGNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHC 214
Query: 170 RKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQ 229
KGIGKDHAK+SP AT ++ P+I L+E + E + V ++ G+
Sbjct: 215 VKGIGKDHAKFSPVATASYRLLPDI----TLLEPVEGEAAEELSRCFSPGVIEVQEVQGK 270
Query: 230 --VYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIE 287
V + T+ E+ + E + K +V + D +IF+VESTG + LV AI+
Sbjct: 271 KVARVANPRLDTFSREIFRN-EKLKK--VVRLARVRDHYIFSVESTGVLPPDVLVSEAIK 327
Query: 288 VLKQK-------LDAVRL 298
VL K LDAV++
Sbjct: 328 VLMGKCRRFLDELDAVQM 345
>sp|Q6KZP5|RPOD_PICTO DNA-directed RNA polymerase subunit D OS=Picrophilus torridus
(strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC
100828) GN=rpoD PE=3 SV=1
Length = 271
Score = 113 bits (283), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 85/295 (28%), Positives = 147/295 (49%), Gaps = 45/295 (15%)
Query: 14 IRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLV------------EIEVNSSV 61
I ELKD+Y KF + ++AN++RR +I ++P +AI+ V + +S
Sbjct: 4 IIELKDNYIKFSISGITPAIANSIRRTLINDIPKLAIENVVFHHGEIRDSEGNVYDSSLP 63
Query: 62 LNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVT 121
L DE +A RLGLIPL ++ + M F C +C+G+G C+ C+V++ + +
Sbjct: 64 LFDEVVALRLGLIPLKTD--LKMNFRDQC-SCNGEG-CDLCTVKYSINK---------LG 110
Query: 122 SKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWS 181
D++SSD ++P++ D D I IVKL++GQ + + A G GKDHAKW
Sbjct: 111 PADVFSSD--LIPINNPDLKPVDPM-----IPIVKLKKGQAMLVTCEAIMGRGKDHAKWQ 163
Query: 182 PAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYD 241
+ V++ Y E IN++ +E+ S + + P V I N ++ D Y
Sbjct: 164 VTSGVSYKYHREFKINKNELENWSF-----YKDKCPKSV--ISENENEITFTDDVECRYL 216
Query: 242 DEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296
++ + V I + FIF E+ G++ A + + A++ LK++ + +
Sbjct: 217 QQLFDEKSG------VTITEDDTKFIFQFETDGSLTAIETLDYALKRLKERFNNL 265
>sp|Q8TVB8|RPOD_METKA DNA-directed RNA polymerase subunit D OS=Methanopyrus kandleri
(strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
GN=rpoD PE=3 SV=1
Length = 275
Score = 112 bits (281), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 88/280 (31%), Positives = 137/280 (48%), Gaps = 37/280 (13%)
Query: 22 AKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERA 81
A F + +T A N +RR + VPT+ I+ V I N + + DE +AHRLGLIPL +
Sbjct: 19 ATFIIEETSAEFVNTIRRALYTLVPTLRIEEVIIYENDTPMYDEMLAHRLGLIPLRVDDI 78
Query: 82 MSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPA 141
CD C G G CE C V RA+ + V ++DL DH V+PA
Sbjct: 79 DQFELPDLCD-CGGKG-CEKCQV----RAELEVEGPTKVYARDL-KFDHP-----DVEPA 126
Query: 142 GYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLM 201
D+ +I ++ Q +RL IA G+G +HAKW P + V + PE+ I+ED
Sbjct: 127 FPDT-------LITEVGEDQRIRLEVIAVPGLGLEHAKWKPVSAVGYKGLPELEIDED-- 177
Query: 202 ESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVD----AEAYTYDDEVIKKAEAMGKPGLV 257
L+EK+ E P + I+ G+V +D E Y K G V
Sbjct: 178 ---KLKEKKITYE-CPQGIIRIE--NGEVVHIDEDRLPECRMY------KEYERETDGAV 225
Query: 258 EIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
+ ++D+F+F VE+ G++ +L A++ ++ KL++++
Sbjct: 226 RVRLRDDAFVFNVETDGSMSLDTAILKALDAIEHKLESLK 265
>sp|C3N8R8|RPOD_SULIY DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain Y.G.57.14 / Yellowstone #1) GN=rpoD PE=3 SV=1
Length = 265
Score = 111 bits (277), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 89/269 (33%), Positives = 138/269 (51%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP ++ID V N+S L DE +AHRL LIP TSE A+ + R+ +C
Sbjct: 24 FVNAIRRATMLYVPVMSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D S+VP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEALNEPKM-LYSKDIKSEDPSIVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L EK +
Sbjct: 128 IPIVLLGANQKISLEARLRLGYGKEHAKFIPVSLAIVRYYPKVEI-------LGNCEKAA 180
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + A T +E ++ GL+ I + ED +I +E
Sbjct: 181 TV--CPEGVFEL--KDGKLSVKNELACTLCEECLRYCN-----GLIRISSIEDKYILELE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>sp|C3NMQ0|RPOD_SULIN DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain Y.N.15.51 / Yellowstone #2) GN=rpoD PE=3 SV=1
Length = 265
Score = 111 bits (277), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 89/269 (33%), Positives = 138/269 (51%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP ++ID V N+S L DE +AHRL LIP TSE A+ + R+ +C
Sbjct: 24 FVNAIRRATMLYVPVMSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D S+VP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEALNEPKM-LYSKDIKSEDPSIVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L EK +
Sbjct: 128 IPIVLLGANQKISLEARLRLGYGKEHAKFIPVSLAIVRYYPKVEI-------LGNCEKAA 180
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + A T +E ++ GL+ I + ED +I +E
Sbjct: 181 TV--CPEGVFEL--KDGKLSVKNELACTLCEECLRYCN-----GLIRISSIEDKYILELE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>sp|C3MJP7|RPOD_SULIL DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain L.S.2.15 / Lassen #1) GN=rpoD PE=3 SV=1
Length = 265
Score = 111 bits (277), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 89/269 (33%), Positives = 138/269 (51%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP ++ID V N+S L DE +AHRL LIP TSE A+ + R+ +C
Sbjct: 24 FVNAIRRATMLYVPVMSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D S+VP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEALNEPKM-LYSKDIKSEDPSIVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L EK +
Sbjct: 128 IPIVLLGANQKISLEARLRLGYGKEHAKFIPVSLAIVRYYPKVEI-------LGNCEKAA 180
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + A T +E ++ GL+ I + ED +I +E
Sbjct: 181 TV--CPEGVFEL--KDGKLSVKNELACTLCEECLRYCN-----GLIRISSIEDKYILELE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>sp|Q8U0E4|RPOD_PYRFU DNA-directed RNA polymerase subunit D OS=Pyrococcus furiosus
(strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=rpoD
PE=3 SV=1
Length = 261
Score = 110 bits (276), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 99/287 (34%), Positives = 138/287 (48%), Gaps = 44/287 (15%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
+V+I E K+D KF L+ S ANALRR ++ EVPT A+D VE N S L DE IAHR
Sbjct: 5 EVQILEKKEDSIKFVLKGVHVSFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 64
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDH 130
L +IPLT+ RF + DA + D S+E ++ V S DL S D
Sbjct: 65 LAMIPLTTPVD---RF--ELDALELDDYTVTLSLE--------AEGPGIVYSGDLKSDDP 111
Query: 131 SVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMY 190
V PV+ I IVKL GQ L A A+ G GKDHAKW P V + Y
Sbjct: 112 DVKPVN-------------PNIPIVKLAEGQRLVFNAYAKLGRGKDHAKWQP-GFVYYKY 157
Query: 191 EPEIHINEDLMESLSLEE--KQSWVESSPTKVFDIDPNTGQVYVV-DAEAYTYDDEVIKK 247
+HI++ + E L++ K+ + T+ + Y+ D E Y
Sbjct: 158 YTIVHISKSIPEWKELKKLAKKRGLPVEETEEEVLVTTIKPFYIPKDFEEYE-------- 209
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
GK EI +++IFTVE+ G + ++V A+++L +K D
Sbjct: 210 ----GKEIWEEIVP--NTYIFTVETNGELPVEEIVSIALKILMRKAD 250
>sp|C3MZ05|RPOD_SULIM DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain M.14.25 / Kamchatka #1) GN=rpoD PE=3 SV=1
Length = 265
Score = 110 bits (276), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 89/269 (33%), Positives = 138/269 (51%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP ++ID V N+S L DE +AHRL LIP TSE A+ + R+ +C
Sbjct: 24 FVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D S+VP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEALNEPKM-LYSKDIKSEDPSIVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L EK +
Sbjct: 128 IPIVLLGANQKISLEARLRLGYGKEHAKFIPVSLAIVRYYPKVEI-------LGNCEKAA 180
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + A T +E ++ GL+ I + ED +I +E
Sbjct: 181 TV--CPEGVFEL--KDGKLSVKNELACTLCEECLRYCN-----GLIRISSIEDKYILELE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>sp|C4KJ93|RPOD_SULIK DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain M.16.4 / Kamchatka #3) GN=rpoD PE=3 SV=1
Length = 265
Score = 110 bits (276), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 89/269 (33%), Positives = 138/269 (51%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP ++ID V N+S L DE +AHRL LIP TSE A+ + R+ +C
Sbjct: 24 FVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D S+VP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEALNEPKM-LYSKDIKSEDPSIVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L EK +
Sbjct: 128 IPIVLLGANQKISLEARLRLGYGKEHAKFIPVSLAIVRYYPKVEI-------LGNCEKAA 180
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + A T +E ++ GL+ I + ED +I +E
Sbjct: 181 TV--CPEGVFEL--KDGKLSVKNELACTLCEECLRYCN-----GLIRISSIEDKYILELE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>sp|C3N054|RPOD_SULIA DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain M.16.27) GN=rpoD PE=3 SV=1
Length = 265
Score = 110 bits (276), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 89/269 (33%), Positives = 138/269 (51%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP ++ID V N+S L DE +AHRL LIP TSE A+ + R+ +C
Sbjct: 24 FVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D S+VP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEALNEPKM-LYSKDIKSEDPSIVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L EK +
Sbjct: 128 IPIVLLGANQKISLEARLRLGYGKEHAKFIPVSLAIVRYYPKVEI-------LGNCEKAA 180
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + A T +E ++ GL+ I + ED +I +E
Sbjct: 181 TV--CPEGVFEL--KDGKLSVKNELACTLCEECLRYCN-----GLIRISSIEDKYILELE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>sp|Q96YW0|RPOD_SULTO DNA-directed RNA polymerase subunit D OS=Sulfolobus tokodaii
(strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=rpoD
PE=3 SV=1
Length = 264
Score = 110 bits (275), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 78/281 (27%), Positives = 137/281 (48%), Gaps = 32/281 (11%)
Query: 18 KDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLT 77
+++ K + + + N++RR I VP +A+D V N+S L DE +AHRL +IP +
Sbjct: 9 ENNSLKLIVGNYPLELVNSIRRASILYVPVMAVDEVYFIENNSPLYDEILAHRLAMIPFS 68
Query: 78 SERAM-SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVD 136
S+ A+ R +C C + C+ C +L + +T+ V S+DL + D ++VP+
Sbjct: 69 SDEALDHYRPPEECAECKEN--CDGCYARVYLDVGANEGETVMVYSRDLKTDDPAIVPI- 125
Query: 137 FVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHI 196
I IV L Q++ L A R G GK+H K+SP + Y P + +
Sbjct: 126 ------------SGNIPIVLLGPKQKVTLEARLRLGYGKEHIKFSPVSIAVVRYYPHVEV 173
Query: 197 NEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGL 256
+ + E P VF ++ G+++V + A T +E IK E
Sbjct: 174 KGNC---------EKAFEVCPEGVFGME--NGKLFVKNEVACTLCEECIKYCENN----- 217
Query: 257 VEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
+ I A E+ +I +ES G++K ++++ A + L +KL+ ++
Sbjct: 218 IFISAVENKYILEIESVGSLKPERILIEAGKSLLRKLNQLK 258
>sp|Q9V198|RPOD_PYRAB DNA-directed RNA polymerase subunit D OS=Pyrococcus abyssi (strain
GE5 / Orsay) GN=rpoD PE=3 SV=1
Length = 259
Score = 108 bits (271), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 97/284 (34%), Positives = 135/284 (47%), Gaps = 38/284 (13%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
++KI + DD F L D + ANALRR ++ EVPT A+D VE N S L DE IAHR
Sbjct: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDH 130
L +IPL + RF + DA + D S+E ++ V S DL S D
Sbjct: 63 LAMIPL---KTPVDRF--ELDALELDDYTVTLSLE--------AEGPGIVYSGDLKSDDP 109
Query: 131 SVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMY 190
V PA D I IVKL +GQ L A A+ G GKDHAKW P T + Y
Sbjct: 110 D------VKPANPD-------IPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTY-YKY 155
Query: 191 EPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEA 250
IHI++++ E +K + P K N +V V + + E E
Sbjct: 156 FTRIHISKEI-EGWEKLKKLAKKRGLPVK-----ENENEVIVETIKPFYIPKEF---EEY 206
Query: 251 MGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
GK EI ++++F VE+ G + ++V A+++L +K D
Sbjct: 207 EGKGIWEEIVP--NTYVFVVETNGELPVEEIVKIALKILMRKAD 248
>sp|O59303|RPOD_PYRHO DNA-directed RNA polymerase subunit D OS=Pyrococcus horikoshii
(strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139
/ OT-3) GN=rpoD PE=3 SV=2
Length = 259
Score = 108 bits (269), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 97/286 (33%), Positives = 134/286 (46%), Gaps = 42/286 (14%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
K+KI + +D F L + ANALRR ++ EVPT A+D VE N S L DE IAHR
Sbjct: 3 KIKILKKTEDSITFILEGVSVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDH 130
L +IPL + + RF + DA + D S+E ++ V S DL S D
Sbjct: 63 LAMIPL---KTPTDRF--ELDALELDDYTVTLSLE--------AEGPGIVYSGDLKSDDP 109
Query: 131 SVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMY 190
V PV I IVKL +GQ L A A+ G GKDHAKW P T + Y
Sbjct: 110 DVKPV-------------TPDIPIVKLAKGQRLVFNAYAKLGRGKDHAKWQPGFTY-YKY 155
Query: 191 EPEIHINEDL--MESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKA 248
+HI++ + E L+ K+ PTK N +V V + + E
Sbjct: 156 FTRVHISKKINGWEKLAKLAKKR---GLPTK-----ENEEEVIVETIKPFYIPKEF---E 204
Query: 249 EAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
E GK EI D+++F VE+ G + ++V A+ +L +K D
Sbjct: 205 EYEGKEIWEEIVP--DTYVFVVETNGELPVEEIVKIALRILMRKAD 248
>sp|Q9HJD9|RPOD_THEAC DNA-directed RNA polymerase subunit D OS=Thermoplasma acidophilum
(strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 /
AMRC-C165) GN=rpoD PE=3 SV=1
Length = 271
Score = 107 bits (268), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 90/298 (30%), Positives = 135/298 (45%), Gaps = 48/298 (16%)
Query: 12 VKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIE-----------VNSS 60
VKI +L D Y +FE+ S ANALRR +I ++P +AI+ V +SS
Sbjct: 3 VKIFKLSDKYIRFEIDGITPSQANALRRTLINDIPKLAIENVTFHHGEIRDSEGNVYDSS 62
Query: 61 V-LNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLD 119
+ L DE +AHRLGLIPL ++ ++M F C +C G G C C+V + + S
Sbjct: 63 LPLFDEMVAHRLGLIPLKTD--LTMNFRDQC-SCGGKG-CSLCTVTYSINKLGPS----T 114
Query: 120 VTSKDLYSSDHS-VVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHA 178
V S DL + H ++PVD P IVKL Q + + A A G K+HA
Sbjct: 115 VFSSDLQAVSHPDLIPVDGEIP-------------IVKLGPKQAILITAEAILGTAKEHA 161
Query: 179 KWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAY 238
KW + V++ Y E H+++ E+ Q + P V D E
Sbjct: 162 KWQVTSGVSYKYHREFHVSKK-----DFEDWQKLKGACPKSVMS---------ETDTEIV 207
Query: 239 TYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296
DD + + V + + FIF E+ G++ A + +L A+ LK + D +
Sbjct: 208 FTDDFGCNDLNVLFESDGVNMIEDDSRFIFQFETDGSLTAKETLLYALNRLKDRWDIL 265
>sp|P95989|RPOD_SULSO DNA-directed RNA polymerase subunit D OS=Sulfolobus solfataricus
(strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) GN=rpoD
PE=1 SV=1
Length = 265
Score = 107 bits (266), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 85/269 (31%), Positives = 133/269 (49%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP +A+D V N+S L DE +AHRL LIP SE A+ + R+ +C
Sbjct: 24 FVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D SVVP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEAPNEPRM-IYSKDIKSEDPSVVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L +
Sbjct: 128 IPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEI---------LANCEK 178
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + + T +E ++ G + I ED +I +E
Sbjct: 179 AVNVCPEGVFEL--KDGKLSVKNELSCTLCEECLRYCN-----GSIRISFVEDKYILEIE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>sp|B1YC30|RPOD_PYRNV DNA-directed RNA polymerase subunit D OS=Pyrobaculum neutrophilum
(strain DSM 2338 / JCM 9278 / V24Sta) GN=rpoD PE=3 SV=1
Length = 262
Score = 105 bits (263), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 70/191 (36%), Positives = 103/191 (53%), Gaps = 19/191 (9%)
Query: 9 FPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIA 68
P VK+ E + K + S+ N+LRRV+I+E+P +AID V + N+SV+ DE +A
Sbjct: 1 MPAVKVVERTPLFLKAVVEGAYPSLVNSLRRVIISELPVMAIDTVIVVNNTSVMYDEMLA 60
Query: 69 HRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSS 128
HRLGLIPLT+ S+ DC++ G C+V F L+ ++D + V S DL S
Sbjct: 61 HRLGLIPLTTP-LQSLPPIEDCES--GLADPSECTVRFTLQV--NADGEVTVYSGDLVSE 115
Query: 129 DHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTF 188
VVPV + I IVKL +GQ + L A A+ G + HAKW AA ++
Sbjct: 116 RPDVVPV-------------HKDIPIVKLVKGQSIVLEAYAKLGRARGHAKWQ-AALASY 161
Query: 189 MYEPEIHINED 199
Y P + + ++
Sbjct: 162 YYYPRVEVRDE 172
>sp|Q8ZYQ3|RPOD_PYRAE DNA-directed RNA polymerase subunit D OS=Pyrobaculum aerophilum
(strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC
100827) GN=rpoD PE=3 SV=1
Length = 260
Score = 105 bits (262), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 87/265 (32%), Positives = 128/265 (48%), Gaps = 48/265 (18%)
Query: 32 SMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCD 91
S+ N+LRRV+I+E+P +AID V + N+SV+ DE +AHRLGLIPLT+ S+ DC
Sbjct: 24 SLVNSLRRVIISELPVMAIDNVVVVNNTSVMYDEMLAHRLGLIPLTTP-LQSLPPYEDC- 81
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
G CS L+ D T + S DL S VVPV +
Sbjct: 82 -VSGLADPSECSTRLTLQVTAEGDTT--IYSGDLASDRPDVVPV-------------YKD 125
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLE---E 208
I IVKL +GQ + L A A+ G+ KDHAKW AAT ++ Y P++ + + + E +
Sbjct: 126 IPIVKLVKGQSIVLEAYAKLGVAKDHAKWQ-AATASYYYYPKVVVKSENCREMCKEICRQ 184
Query: 209 KQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIF 268
++ +E S K A+T D + K GL E+ ++ ++F
Sbjct: 185 LENPIECSFNK-----------------AWTCKD--------LCKEGL-EVTWDKNKYVF 218
Query: 269 TVESTGAIKASQLVLNAIEVLKQKL 293
VES G + + A +LK+K
Sbjct: 219 WVESFGNYDVNTALREAFRILKRKF 243
>sp|P39471|RPOD_SULAC DNA-directed RNA polymerase subunit D OS=Sulfolobus acidocaldarius
(strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 /
NCIMB 11770) GN=rpoD PE=3 SV=2
Length = 264
Score = 103 bits (257), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 80/276 (28%), Positives = 129/276 (46%), Gaps = 33/276 (11%)
Query: 23 KFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM 82
+ L + N++RR I VP +A+D V N+S L DE +AHRL L+P S+ A+
Sbjct: 14 RLVLENYPLEFVNSIRRASILYVPVMAVDEVYFIENNSPLYDEILAHRLALVPFVSDEAL 73
Query: 83 S-MRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPA 141
R +C C + C+ C +L + DQ L + S+DL S D + PV P
Sbjct: 74 EHYRPPEECAECKEN--CDGCYNRVYLDVE-AKDQPLMIYSRDLKSEDQMITPVSGAIP- 129
Query: 142 GYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLM 201
IV L Q++ L A R G GK+H K+SP + Y P++ +
Sbjct: 130 ------------IVLLGSKQKISLEARLRLGYGKEHIKYSPVSVSIVRYYPKVTV----- 172
Query: 202 ESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYA 261
L + VE P VF ++ N ++ V + + +E +K G V I +
Sbjct: 173 ----LGNCEKAVEVCPEGVFAMENN--KLVVKNELSCILCEECLKYCA-----GSVSIES 221
Query: 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
E+ FI +ES G++K ++++ A + L +KL ++
Sbjct: 222 VENKFILEIESVGSLKPERILIEASKSLLRKLSELK 257
>sp|A1RSE3|RPOD_PYRIL DNA-directed RNA polymerase subunit D OS=Pyrobaculum islandicum
(strain DSM 4184 / JCM 9189) GN=rpoD PE=3 SV=1
Length = 262
Score = 103 bits (256), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 70/188 (37%), Positives = 98/188 (52%), Gaps = 19/188 (10%)
Query: 9 FPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIA 68
PK I E + K + S+ N++RRV+I+E+P +AID V I N+SV+ DE +A
Sbjct: 1 MPKATIVEKTPLFLKAVIEGAYPSLVNSIRRVIISELPVMAIDYVVIVSNTSVMYDEMLA 60
Query: 69 HRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSS 128
HRLGL+PLT+ ++ DC+ G C+V L+ SD+ V S DL S
Sbjct: 61 HRLGLVPLTTP-LQALPPIEDCET--GLVDPSECTVRLMLQINAESDKI--VYSGDLVSE 115
Query: 129 DHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTF 188
VVPV + I IVKL +GQ + L A A+ G K+HAKW AA ++
Sbjct: 116 RPDVVPV-------------YKDIPIVKLVKGQSIILEAYAKLGRAKEHAKWQ-AALASY 161
Query: 189 MYEPEIHI 196
Y P I +
Sbjct: 162 YYYPRIKV 169
>sp|Q97B93|RPOD_THEVO DNA-directed RNA polymerase subunit D OS=Thermoplasma volcanium
(strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 /
GSS1) GN=rpoD PE=3 SV=1
Length = 271
Score = 102 bits (255), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 92/295 (31%), Positives = 135/295 (45%), Gaps = 54/295 (18%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIE-----------VNS 59
+VKI +L D Y FE+ S ANALRR +I ++P +AI+ V +S
Sbjct: 2 EVKIFKLSDKYMSFEIDGITPSQANALRRTLINDIPKLAIENVTFHHGEIRDAEGNVYDS 61
Query: 60 SV-LNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTL 118
S+ L DE +AHRLGLIPL ++ +S+ F C +C G G C C+V + + +
Sbjct: 62 SLPLFDEMVAHRLGLIPLKTD--LSLNFRDQC-SCGGKG-CSLCTVTYSINKIGPA---- 113
Query: 119 DVTSKDLYSSDHS-VVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDH 177
V S D+ + H +VPVD I IVKL Q + + A A G K+H
Sbjct: 114 SVMSGDIQAISHPDLVPVD-------------PDIPIVKLGAKQAILITAEAILGTAKEH 160
Query: 178 AKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWV---ESSPTKVFDIDPNTGQVYVVD 234
AKW + V + Y E +N+ L E W E P V D NT +V
Sbjct: 161 AKWQVTSGVAYKYHREFEVNKKLFE--------DWAKIKERCPKSVLSEDENT----IVF 208
Query: 235 AEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVL 289
+ Y +D I + + V+I + FIF E+ G++ A + + A+ L
Sbjct: 209 TDDYGCNDLSI-----LFESDGVQIKEDDSRFIFHFETDGSLTAEETLSYALNRL 258
>sp|A4WNA4|RPOD_PYRAR DNA-directed RNA polymerase subunit D OS=Pyrobaculum arsenaticum
(strain DSM 13514 / JCM 11321) GN=rpoD PE=3 SV=1
Length = 259
Score = 100 bits (250), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 92/288 (31%), Positives = 136/288 (47%), Gaps = 44/288 (15%)
Query: 9 FPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIA 68
P+V I E + K + S+ N+LRRV+I+E+P +AID V + N+SV+ DEF+A
Sbjct: 1 MPRVSIVEKSQLFLKAIVEGVPPSLVNSLRRVIISELPVMAIDTVVVVNNTSVMYDEFLA 60
Query: 69 HRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSS 128
RLGLIPLT+ S+ +C G C L+ D T V S DL S
Sbjct: 61 QRLGLIPLTTP-LHSLPTYEECAT--GVADPTECGTRLVLQVTADGDVT--VYSGDLTSE 115
Query: 129 DHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTF 188
VVPV + I IVKL +GQ + + A A+ GI KDHAKW AAT ++
Sbjct: 116 RPDVVPV-------------YKDIPIVKLVKGQSIVIEAYAKLGIAKDHAKWQ-AATASY 161
Query: 189 MYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNT-GQVYVVDAEAYTYDDEVIKK 247
Y P++ I ++ + E I P+ V +A+T D
Sbjct: 162 YYYPKVIIKDEKCREICKE---------------ICPDLEDPVKCTFNKAWTCKD----- 201
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDA 295
+ K GL ++ +++ ++F VES G + A +LK+K +A
Sbjct: 202 ---LCKGGL-DVEWEKNKYVFWVESFGNYGVDVALKEAFRILKRKFEA 245
>sp|Q9YB53|RPOD_AERPE DNA-directed RNA polymerase subunit D OS=Aeropyrum pernix (strain
ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
GN=rpoD PE=3 SV=2
Length = 286
Score = 93.6 bits (231), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 80/289 (27%), Positives = 133/289 (46%), Gaps = 33/289 (11%)
Query: 12 VKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRL 71
V++ EL + +R NA+RR ++++VPT+A+D I N++ + DE +AHRL
Sbjct: 9 VEVVELDSLRVRLRIRGYPVVFVNAIRRTVLSDVPTMAVDYAYIFDNTTAVYDEMVAHRL 68
Query: 72 GLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLD--VTSKDLYSSD 129
GL+ L S A+ ++ R + + E C VE L A+ ++ +T+ DL SD
Sbjct: 69 GLVVLDSNEAVE-KYRRPEECAGKEPSEEDCFVEVSLEAEVDAEGETGRYITAGDLSISD 127
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
V PV Y T ++ + GQ + ++A AR G GK+H KWSPA+
Sbjct: 128 PQVKPV-------YPETP------LIYVAPGQRIHVQAFARLGRGKEHTKWSPASLSVLR 174
Query: 190 YEPEI-----HINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEV 244
Y P + ++ +E LS + P V + V++ T
Sbjct: 175 YTPILIYDSSKAGDECLECLS---------AYPQVVEALKSGGKGSLVLEGLRRTSG--- 222
Query: 245 IKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL 293
++ G VE+ + VESTGA++ ++V AI L++K+
Sbjct: 223 LRYCAETACRGAVEVRYDSSNLDLEVESTGALRPEKIVELAIRELEEKV 271
>sp|Q3IQT6|RPOD_NATPD DNA-directed RNA polymerase subunit D OS=Natronomonas pharaonis
(strain DSM 2160 / ATCC 35678) GN=rpoD PE=3 SV=1
Length = 247
Score = 92.0 bits (227), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 79/274 (28%), Positives = 127/274 (46%), Gaps = 52/274 (18%)
Query: 22 AKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERA 81
A+F +R + AN LRR MIA+VPT++ID + + NSSV+ DE +A RLGL+PLT+
Sbjct: 17 ARFLVRGVTPAFANGLRRAMIADVPTLSIDTLRVVENSSVMFDEQLALRLGLVPLTT--- 73
Query: 82 MSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPA 141
D + G+ +++ A + S DL SSD V P D
Sbjct: 74 -----PDDYEP----GETVTLAIDVEGPATAY--------SGDLVSSDDKVQPAD----- 111
Query: 142 GYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLM 201
I I++L+ Q+L L A A G GKDHAK V + + + +
Sbjct: 112 --------ENIPIIELKDDQQLELEADATLGRGKDHAKHQGGVAVGYRHLQRVEV----- 158
Query: 202 ESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGL-VEIY 260
+ EK + + P + + G + E +D+++ ++ PG VE+
Sbjct: 159 ----VGEKGEFEDDEPEILRGVIEEDGDLI----ETGEFDNDLSQR-----YPGKEVEVE 205
Query: 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
++F+F VE+ G++ +LVL A E + + D
Sbjct: 206 EVPNAFVFDVETDGSMPVEELVLKAAESIAARAD 239
>sp|A3MXZ5|RPOD_PYRCJ DNA-directed RNA polymerase subunit D OS=Pyrobaculum calidifontis
(strain JCM 11548 / VA1) GN=rpoD PE=3 SV=1
Length = 258
Score = 90.9 bits (224), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 85/286 (29%), Positives = 132/286 (46%), Gaps = 42/286 (14%)
Query: 9 FPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIA 68
PKV I E +AK + S+ N+LRRV+I+E+P +AID V + N+SV+ DE +A
Sbjct: 1 MPKVSIVEKSQFFAKAVVEGVPPSLINSLRRVIISELPVLAIDSVVVVNNTSVMYDEMLA 60
Query: 69 HRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSS 128
HRLGLIPLT+ + DC++ G C+V L+ D V + DL +
Sbjct: 61 HRLGLIPLTTP-LKDLPPIEDCES--GLVDPSECTVRLTLQVNATGDVV--VYAGDLVAD 115
Query: 129 DHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTF 188
V PV + I IVKL GQ + + A A+ G +DHAKW AA ++
Sbjct: 116 RPDVAPV-------------YKDIPIVKLVEGQSVVVEAYAKLGRARDHAKWQ-AALASY 161
Query: 189 MYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKA 248
Y P++ + + + E ++ +P + T++ K
Sbjct: 162 YYYPKVVVKREECREMCKEVCRNL--ENPLEC------------------TFNKATTCKE 201
Query: 249 EAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
G G+V + K D ++F +ES G A + A +LK+K +
Sbjct: 202 MCGG--GIVVEWEK-DKYVFWIESFGNYDAETALREAFRILKKKFE 244
>sp|Q9HQJ4|RPOD_HALSA DNA-directed RNA polymerase subunit D OS=Halobacterium salinarum
(strain ATCC 700922 / JCM 11081 / NRC-1) GN=rpoD PE=3
SV=1
Length = 248
Score = 82.0 bits (201), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 81/291 (27%), Positives = 127/291 (43%), Gaps = 53/291 (18%)
Query: 5 SYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLND 64
S Q F V+ + D A+F +R+ + AN +RR ++ +VPT++ID V NSSV+ D
Sbjct: 2 SSQDF-DVEFVDRDDREARFVVRNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFD 60
Query: 65 EFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD 124
E + RLGL+PLT+ D G+ VE A S D
Sbjct: 61 EQLGLRLGLVPLTTPE----------DYAAGEAVTLALDVEGPGTAY----------SGD 100
Query: 125 LYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAA 184
L S+D V D I I++L+ Q L L A A G G+DHAK
Sbjct: 101 LVSNDPEVEAAD-------------ENIPIIELKDDQRLELEADAVMGHGRDHAKHQGGV 147
Query: 185 TVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEV 244
V + + +H+ D E + + P + + ++ D +D+++
Sbjct: 148 AVGYRHLQRVHVVGDSPE---------YADDDPQMLRGVIEEDDELVPTD----DFDNDL 194
Query: 245 IKKAEAMGKPGL-VEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
+ PG VEI + +F+F VES G++ +LVL A++ L + D
Sbjct: 195 TTR-----YPGKEVEIEDVDGAFVFHVESDGSMPVEELVLRAVDTLVDRAD 240
>sp|B0R4Y2|RPOD_HALS3 DNA-directed RNA polymerase subunit D OS=Halobacterium salinarum
(strain ATCC 29341 / DSM 671 / R1) GN=rpoD PE=3 SV=1
Length = 248
Score = 82.0 bits (201), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 81/291 (27%), Positives = 127/291 (43%), Gaps = 53/291 (18%)
Query: 5 SYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLND 64
S Q F V+ + D A+F +R+ + AN +RR ++ +VPT++ID V NSSV+ D
Sbjct: 2 SSQDF-DVEFVDRDDREARFVVRNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFD 60
Query: 65 EFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD 124
E + RLGL+PLT+ D G+ VE A S D
Sbjct: 61 EQLGLRLGLVPLTTPE----------DYAAGEAVTLALDVEGPGTAY----------SGD 100
Query: 125 LYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAA 184
L S+D V D I I++L+ Q L L A A G G+DHAK
Sbjct: 101 LVSNDPEVEAAD-------------ENIPIIELKDDQRLELEADAVMGHGRDHAKHQGGV 147
Query: 185 TVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEV 244
V + + +H+ D E + + P + + ++ D +D+++
Sbjct: 148 AVGYRHLQRVHVVGDSPE---------YADDDPQMLRGVIEEDDELVPTD----DFDNDL 194
Query: 245 IKKAEAMGKPGL-VEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
+ PG VEI + +F+F VES G++ +LVL A++ L + D
Sbjct: 195 TTR-----YPGKEVEIEDVDGAFVFHVESDGSMPVEELVLRAVDTLVDRAD 240
>sp|Q00813|RPOD_HALMA DNA-directed RNA polymerase subunit D OS=Haloarcula marismortui
(strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
GN=rpoD PE=3 SV=1
Length = 259
Score = 80.5 bits (197), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 83/296 (28%), Positives = 132/296 (44%), Gaps = 50/296 (16%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
+V+ E + A+ +R + AN +RR M+A+VPT +ID V + N+SV+ +E I R
Sbjct: 6 EVEFVERGEREARILVRGITPAFANGIRRAMVADVPTFSIDTVRVIENTSVMFNEQIGLR 65
Query: 71 LGLIPLTSERAMSMRFSRDCDACD-GDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
LGL+PLT+ D D + GD SV D S DL SSD
Sbjct: 66 LGLVPLTT----------DLDDFEIGDEVTLSLSV----------DGPSTAYSSDLVSSD 105
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
V D I I+ L+ GQ L + A A G++HAK V +
Sbjct: 106 PMVEAAD-------------DNIPIIDLKEGQRLEVEADAVLDTGREHAKHQGGVAVGYR 152
Query: 190 YEPEIHINEDLMESLSLEEK--QSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
+ ++ + DL E + + +E + D G++ D +D+++ +
Sbjct: 153 HLQQVEVVGDLGEFEDDDPNILRGVIEEQAAEHAAGDATNGELVATDE----FDNDLRNR 208
Query: 248 AEAMGKPGL-VEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL----DAVRL 298
PG VE+ ++F+F VE+ G+ +LVL A+E L+ + DAV+L
Sbjct: 209 -----YPGKDVEVSDVPNAFVFHVETDGSFTTEELVLRAVETLRDRATELKDAVQL 259
>sp|Q57648|RPOD_METJA DNA-directed RNA polymerase subunit D OS=Methanocaldococcus
jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
10045 / NBRC 100440) GN=rpoD PE=1 SV=1
Length = 191
Score = 79.7 bits (195), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 55/158 (34%), Positives = 76/158 (48%), Gaps = 42/158 (26%)
Query: 32 SMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMS---MRFSR 88
S +NA+RR+MI+EVPT AI+ V I NSS ++DE +AHRLGLIP+ + + + F+
Sbjct: 25 SFSNAIRRIMISEVPTFAIEDVYIYENSSSMDDEILAHRLGLIPIKGKPLLENEVITFT- 83
Query: 89 DCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQ 148
+ +G C V S DL S + V
Sbjct: 84 ----LEKEGPC-------------------TVYSSDLKSENGEVA--------------- 105
Query: 149 QRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATV 186
+ I IVKL +GQ +++ A GIGK HAKW P V
Sbjct: 106 FKNIPIVKLGKGQRIQIECEAIPGIGKVHAKWQPCNAV 143
>sp|A6TWF3|RPOA_ALKMQ DNA-directed RNA polymerase subunit alpha OS=Alkaliphilus
metalliredigens (strain QYMF) GN=rpoA PE=3 SV=1
Length = 315
Score = 37.7 bits (86), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 15/76 (19%)
Query: 10 PKVKIRELKDD--YAKFEL----RDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLN 63
PKV++ E+ DD Y KF + R ++ N+LRR+M++ +P A+ V+I
Sbjct: 7 PKVEVFEISDDSTYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVTSVKI-------- 58
Query: 64 DEFIAHRLGLIPLTSE 79
E I H IP E
Sbjct: 59 -EGILHEFSTIPGVKE 73
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.317 0.134 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 115,402,952
Number of Sequences: 539616
Number of extensions: 4730931
Number of successful extensions: 13146
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 66
Number of HSP's that attempted gapping in prelim test: 12963
Number of HSP's gapped (non-prelim): 153
length of query: 319
length of database: 191,569,459
effective HSP length: 117
effective length of query: 202
effective length of database: 128,434,387
effective search space: 25943746174
effective search space used: 25943746174
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (28.1 bits)