254780142
DNA-directed RNA polymerase subunit beta'
| GeneID in NCBI database: | 8209117 | Locus tag: | CLIBASIA_00105 |
| Protein GI in NCBI database: | 254780142 | Protein Accession: | YP_003064555.1 |
| Gene range: | -(19927, 24123) | Protein Length: | 1398aa |
| Gene description: | DNA-directed RNA polymerase subunit beta' | ||
| COG prediction: | [K] DNA-directed RNA polymerase, beta' subunit/160 kD subunit | ||
| KEGG prediction: | rpoC; DNA-directed RNA polymerase subunit beta' (EC:2.7.7.6); K03046 DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6] | ||
| SEED prediction: | DNA-directed RNA polymerase beta subunit (EC 2.7.7.6) | ||
| Pathway involved in KEGG: | Purine metabolism [PATH:las00230]
Pyrimidine metabolism [PATH:las00240] RNA polymerase [PATH:las03020] | ||
| Subsystem involved in SEED: | RNA polymerase bacterial | ||
| sequence | sequence profile | ||
Prediction of Local Sequence Properties
| Source | Summary | Result |
|---|
|
|
Close Homologs Detected by BLAST or PSI-BLAST
Homolog within the Genome Detected by BLAST
Original result of BLAST against C. L. asiaticus genome
No hits with e-value below 0.05
Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations
Original result of PSI-BLAST first 2 iterations
| Identity | Alignment graph | Length | Definition | Round | E-value |
| Target | 1398 | DNA-directed RNA polymerase subunit beta' [Candidatus L | |||
| 315122744 | 1398 | DNA-directed RNA polymerase subunit beta' [Candidatus L | 1 | 0.0 | |
| 327194526 | 1407 | DNA-directed RNA polymerase protein, beta' subunit [Rhi | 1 | 0.0 | |
| 86357298 | 1402 | DNA-directed RNA polymerase subunit beta' [Rhizobium et | 1 | 0.0 | |
| 190891348 | 1402 | DNA-directed RNA polymerase protein, beta' subunit [Rhi | 1 | 0.0 | |
| 116251533 | 1402 | DNA-directed RNA polymerase subunit beta' [Rhizobium le | 1 | 0.0 | |
| 209548928 | 1402 | DNA-directed RNA polymerase subunit beta' [Rhizobium le | 1 | 0.0 | |
| 241204158 | 1402 | DNA-directed RNA polymerase subunit beta' [Rhizobium le | 1 | 0.0 | |
| 222085669 | 1403 | DNA-directed RNA polymerase, beta' subunit [Agrobacteri | 1 | 0.0 | |
| 159184989 | 1402 | DNA-directed RNA polymerase subunit beta' [Agrobacteriu | 1 | 0.0 | |
| 222148358 | 1403 | DNA-directed RNA polymerase subunit beta' [Agrobacteriu | 1 | 0.0 |
| >gi|315122744|ref|YP_004063233.1| DNA-directed RNA polymerase subunit beta' [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 1398 | Back alignment and organism information |
|---|
Score = 2611 bits (6768), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 1260/1398 (90%), Positives = 1322/1398 (94%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
MQQEVMRFFNPWTDDR FDSVRISIASP KI SLSYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MQQEVMRFFNPWTDDREFDSVRISIASPEKILSLSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLS VRRDRMAHI LASPVAHPWFLKS
Sbjct: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSCVRRDRMAHIQLASPVAHPWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+LRDVERVLYFESYVV+DPGLSSLEKYQILTEEEYVEAV+ FGQDQFIA
Sbjct: 121 LPSRISTLLDMTLRDVERVLYFESYVVIDPGLSSLEKYQILTEEEYVEAVNDFGQDQFIA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
MMGADAI ELLI LDL NLA+TLR QLSKSSSIFRRKKIIKRLKIVDSF+ SGN P WM+
Sbjct: 181 MMGADAIRELLILLDLPNLAITLRGQLSKSSSIFRRKKIIKRLKIVDSFLISGNRPEWMV 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
+ +PVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEII+RNEKRM
Sbjct: 241 MTVIPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIVRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGR+VIVAG
Sbjct: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRTVIVAG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL LHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ
Sbjct: 361 PELLLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVY V+S EAQL
Sbjct: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYVVLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNNLLHPASG PV VPSQDMVLGL YLS +HEGDPGEGM+FAD+ EVYHALE
Sbjct: 481 EARVLMMSTNNLLHPASGVPVVVPSQDMVLGLYYLSIIHEGDPGEGMVFADVDEVYHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
K+VTLHSKIRGRYK++D+ GN +SKIY+TTPGRMI+GEILPRHH ISFDICNQEM+KKN
Sbjct: 541 RKVVTLHSKIRGRYKNIDESGNWVSKIYETTPGRMILGEILPRHHNISFDICNQEMVKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
ISAMVD +YRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDI+VP+SK KIIAEADKM
Sbjct: 601 ISAMVDAVYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIVVPKSKGKIIAEADKM 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMM+ IK+VEFDPETGRQKKMNSIF
Sbjct: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMSLIKQVEFDPETGRQKKMNSIF 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGAR S+HQMRQLGGMRGLIAKPSGEIIESPIRSHFK GL GFEFFQSCVGGRKGL
Sbjct: 721 MMSHSGARSSVHQMRQLGGMRGLIAKPSGEIIESPIRSHFKDGLYGFEFFQSCVGGRKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
LDVVMRTASSGYLSRRLVDVAQNC+VNQVDC T KGL+ITHIVDSGQVVYSLGSRVLGR
Sbjct: 781 LDVVMRTASSGYLSRRLVDVAQNCIVNQVDCGTNKGLSITHIVDSGQVVYSLGSRVLGRI 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI+NP+TN CI+KAG LILESHV EIEK GIRSVRIRSALTCES +GVC LCYGRDL
Sbjct: 841 ALDDIVNPVTNACIIKAGGLILESHVTEIEKSGIRSVRIRSALTCESKKGVCSLCYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSF+ES C+G VKIKNR+
Sbjct: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFLESSCEGTVKIKNRS 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
VCRNS NDLISMGRNTTLQILD+SGQEQ SHRIMYGAKLFVDDG +++ GQR+SEWDPHT
Sbjct: 961 VCRNSANDLISMGRNTTLQILDVSGQEQSSHRIMYGAKLFVDDGDIVKYGQRVSEWDPHT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
FP+ITEVSG V FEDLVDG+SVIES+GESTGIAKRKVIDWRF SR QNLKPAIVV DENG
Sbjct: 1021 FPMITEVSGIVDFEDLVDGLSVIESVGESTGIAKRKVIDWRFTSRGQNLKPAIVVKDENG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
VLK +RGTDARWFLPVDA+LSVSPGQKVS GDVLAR PISSAKTKDITSGLPRVAELFE
Sbjct: 1081 AVLKFSRGTDARWFLPVDAILSVSPGQKVSVGDVLARSPISSAKTKDITSGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPKNHAILAE+SG+I+IKRNYKNKSRV+IEPFE+GVEP EYFIPKNKHFYLQDGD VE
Sbjct: 1141 ARRPKNHAILAEVSGSIKIKRNYKNKSRVLIEPFEEGVEPVEYFIPKNKHFYLQDGDKVE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYIL+GNP P DILRIKG+EALASYLINEVQEVYRLEGV IN KHIEVV+R MLQKVE
Sbjct: 1201 KGDYILEGNPAPHDILRIKGIEALASYLINEVQEVYRLEGVLINDKHIEVVIRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITDPADTEYILGDN+DR+EVEELNRSLAQQGKK VSFSP+LQGITKASLQTKSFISAASF
Sbjct: 1261 ITDPADTEYILGDNIDRVEVEELNRSLAQQGKKQVSFSPVLQGITKASLQTKSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKERSN 1380
QETTKVLTEAAIAGKVD L+G KENVIVGR IPAGTGAILHEKRR+AMNRDQMILK RSN
Sbjct: 1321 QETTKVLTEAAIAGKVDMLEGLKENVIVGRLIPAGTGAILHEKRRIAMNRDQMILKARSN 1380
Query: 1381 FSQNEDLKNTAIQGSIAE 1398
SQ+ D KN IQG IAE
Sbjct: 1381 SSQDSDSKNNQIQGIIAE 1398
|
Species: Candidatus Liberibacter solanacearum Genus: Candidatus Liberibacter Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|327194526|gb|EGE61384.1| DNA-directed RNA polymerase protein, beta' subunit [Rhizobium etli CNPAF512] Length = 1407 | Back alignment and organism information |
|---|
Score = 2101 bits (5444), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 990/1378 (71%), Positives = 1177/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 6 MNQEVMNLFNPQVPAQNFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 65
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 66 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 125
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L+++Q+L+EEEY+ AV ++G+DQF A
Sbjct: 126 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKEHQLLSEEEYMLAVDEYGEDQFTA 185
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYE+L +++L+ +A LR +L+ ++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 186 MIGAEAIYEMLASMNLEKIAGDLRSELADTTSDLKQKKLMKRLKIVENFMESGNRPEWMI 245
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 246 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 305
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 306 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 365
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 366 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 425
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 426 HPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 485
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 486 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSILNQNEPGEGMAFSDLGELHHALE 545
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
+K+VTLH+KIRGR+KSVD+DG SKIY+TTPGR++IGE+LP++ ++ FDICNQEM KKN
Sbjct: 546 SKVVTLHTKIRGRFKSVDEDGKPYSKIYETTPGRLLIGELLPKNGKVPFDICNQEMTKKN 605
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P +K KI+A+ + +
Sbjct: 606 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFAHACRAGISFGKDDMVIPATKAKIVADTENL 665
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFD TGRQK MNSI+
Sbjct: 666 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDENTGRQKPMNSIY 725
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 726 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 785
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+V VDC T+ GLT+T IVD+GQVV SLG+R+LGRT
Sbjct: 786 ADTALKTANSGYLTRRLVDVAQDCIVTHVDCGTETGLTMTAIVDAGQVVASLGARILGRT 845
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 846 ALDDIDHPVTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEIQTGVCSVCYGRDL 905
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG TV+D+SF+E+ +G V+IKNRN
Sbjct: 906 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRN 965
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
V RNS L++MGRN T+QILD G E+ S R+ YG+KL VD+G ++ GQR++EWDP+T
Sbjct: 966 VLRNSEGSLVAMGRNMTVQILDERGVERSSQRVAYGSKLHVDEGDKVKRGQRLAEWDPYT 1025
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV+GTV FEDLVDG+SV+E+ ESTGI KR+VIDWR R +LKPAIV+ D +G
Sbjct: 1026 RPMMTEVAGTVQFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIVIKDASG 1085
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
V K +RG DAR+ L VDA+LSV PG KVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1086 NVAKLSRGGDARFLLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1145
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQDGD++E
Sbjct: 1146 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQDGDYIE 1205
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1206 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1265
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D+ YI+GDNVDRIE+E++N L +QGKK P+L GITKASLQT SFISAASF
Sbjct: 1266 ITDAGDSTYIVGDNVDRIELEDVNDHLIEQGKKPAHGDPVLLGITKASLQTPSFISAASF 1325
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK D L G KENVIVGR IPAGTG + + RR+A +RD++IL+ER
Sbjct: 1326 QETTKVLTEAAIAGKTDGLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDELILEER 1383
|
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|86357298|ref|YP_469190.1| DNA-directed RNA polymerase subunit beta' [Rhizobium etli CFN 42] Length = 1402 | Back alignment and organism information |
|---|
Score = 2100 bits (5441), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 991/1378 (71%), Positives = 1177/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FN + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNGQVPAQNFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L+++Q+LTEEEY+ AV ++G+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKEHQLLTEEEYMLAVDEYGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYE+L +++L+ +A LR +L+ ++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIYEMLASMNLEKIAGDLRSELADTTSDLKQKKLMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSILNQNEPGEGMAFSDLGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
+K+VTLH+KIRGR+KSVD+DG SKIY+TTPGR++IGE+LP++ ++ FDICNQEM KKN
Sbjct: 541 SKVVTLHTKIRGRFKSVDEDGKPYSKIYETTPGRLLIGELLPKNGKVPFDICNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P +K KI+A+ + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACRAGISFGKDDMVIPATKAKIVADTENL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFD TGRQK MNSI+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDENTGRQKPMNSIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+V VDC T+ GLT+T IVD+GQVV SLG+R+LGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVTHVDCGTETGLTMTAIVDAGQVVASLGARILGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDHPVTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEIQTGVCSVCYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG TV+D+SF+E+ +G V+IKNRN
Sbjct: 901 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
V RNS L++MGRN T+QILD G E+ S R+ YG+KL VD+G ++ GQR++EWDP+T
Sbjct: 961 VLRNSEGSLVAMGRNMTVQILDERGVERSSQRVAYGSKLHVDEGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV+GTV FEDLVDG+SV+E+ ESTGI KR+VIDWR R +LKPAIV+ D +G
Sbjct: 1021 RPMMTEVAGTVQFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIVIKDASG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
V K +RG DAR+ L VDA+LSV PG KVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 NVAKLSRGGDARFLLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQDGD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQDGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D+ YI+GDNVDRIE+E++N L +QGKK S P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDAGDSTYIVGDNVDRIELEDVNDHLIEQGKKPASGEPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK D L G KENVIVGR IPAGTG + + RR+A +RD++IL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDGLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDELILEER 1378
|
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|190891348|ref|YP_001977890.1| DNA-directed RNA polymerase protein, beta' subunit [Rhizobium etli CIAT 652] Length = 1402 | Back alignment and organism information |
|---|
Score = 2100 bits (5441), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 990/1378 (71%), Positives = 1177/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNPQVPAQNFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L+++Q+L+EEEY+ AV ++G+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKEHQLLSEEEYMLAVDEYGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYE+L +++L+ +A LR +L+ ++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIYEMLASMNLEKIAGDLRSELADTTSDLKQKKLMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSILNQNEPGEGMAFSDLGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
+K+VTLH+KIRGR+KSVD+DG SKIY+TTPGR++IGE+LP++ ++ FDICNQEM KKN
Sbjct: 541 SKVVTLHTKIRGRFKSVDEDGKPYSKIYETTPGRLLIGELLPKNGKVPFDICNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P +K KI+A+ + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFAHACRAGISFGKDDMVIPATKAKIVADTENL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFD TGRQK MNSI+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDENTGRQKPMNSIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+V VDC T+ GLT+T IVD+GQVV SLG+R+LGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVTHVDCGTETGLTMTAIVDAGQVVASLGARILGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDHPVTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEIQTGVCSVCYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG TV+D+SF+E+ +G V+IKNRN
Sbjct: 901 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
V RNS L++MGRN T+QILD G E+ S R+ YG+KL VD+G ++ GQR++EWDP+T
Sbjct: 961 VLRNSEGSLVAMGRNMTVQILDERGVERSSQRVAYGSKLHVDEGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV+GTV FEDLVDG+SV+E+ ESTGI KR+VIDWR R +LKPAIV+ D +G
Sbjct: 1021 RPMMTEVAGTVQFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIVIKDASG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
V K +RG DAR+ L VDA+LSV PG KVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 NVAKLSRGGDARFLLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQDGD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQDGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D+ YI+GDNVDRIE+E++N L +QGKK P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDAGDSTYIVGDNVDRIELEDVNDHLIEQGKKPAHGDPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK D L G KENVIVGR IPAGTG + + RR+A +RD++IL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDGLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDELILEER 1378
|
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|116251533|ref|YP_767371.1| DNA-directed RNA polymerase subunit beta' [Rhizobium leguminosarum bv. viciae 3841] Length = 1402 | Back alignment and organism information |
|---|
Score = 2098 bits (5435), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 988/1378 (71%), Positives = 1181/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNPQVPAQNFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L+++Q+L+EEEY+ AV ++G+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKEHQLLSEEEYMLAVDEYGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYE+L +++L+ +A LR +L+ ++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIYEMLASMNLEKIAGDLRAELADTTSDLKQKKLMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPILVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSILNQNEPGEGMAFSDLGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
+K+VTLH+KIRGR+KSVD+DG SKIY+TTPGR++IGE+LP++ ++ FDICNQEM KKN
Sbjct: 541 SKVVTLHTKIRGRFKSVDEDGKPYSKIYETTPGRLLIGELLPKNGKVPFDICNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P++K KI+A+ + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFAHACRAGISFGKDDMVIPDAKAKIVADTENL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFD +TGRQK MNSI+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDEKTGRQKPMNSIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+V VDC T+ GLT+T IVD+GQVV S+G+R+LGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVTHVDCGTQTGLTMTAIVDAGQVVASIGARILGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDHPVTGERIVDAGKMILEPDVVEIEKAGIQSIRIRSALTCEIQTGVCSVCYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG TV+D+SF+E+ +G V+IKNRN
Sbjct: 901 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
+ RNS +L++MGRN T+QILD G E+ S R+ YG+KL VD+G ++ GQR++EWDP+T
Sbjct: 961 ILRNSDGNLVAMGRNMTVQILDERGVERSSQRVAYGSKLHVDEGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV+GTV FEDLVDG+SV+E+ ESTGI KR+VIDWR R +LKPAIV+ D +G
Sbjct: 1021 RPMMTEVAGTVQFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIVIKDASG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
+ K +RG DAR+FL VDA+LSV PG KVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 NIAKLSRGGDARFFLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQ+GD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQEGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D+ YI+GDNVDRIE+E++N L +QGKK P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDAGDSTYIVGDNVDRIELEDVNDHLIEQGKKPAYGDPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK D L G KENVIVGR IPAGTG + + RR+A +RD+MIL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDGLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDEMILEER 1378
|
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|209548928|ref|YP_002280845.1| DNA-directed RNA polymerase subunit beta' [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 1402 | Back alignment and organism information |
|---|
Score = 2098 bits (5435), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 987/1378 (71%), Positives = 1179/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNPQVPAQNFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L+++Q+L+EEEY+ AV ++G+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKEHQLLSEEEYMLAVDEYGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYE+L +++L+ +A LR +L+ ++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIYEMLASMNLEKIAGDLRSELADTTSDLKQKKLMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSILNQNEPGEGMAFSDLGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
+K+VTLH+KIRGR+KSVD+DG SKIY+TTPGR++IGE+LP++ ++ FDICNQEM KKN
Sbjct: 541 SKVVTLHTKIRGRFKSVDEDGKPYSKIYETTPGRLLIGELLPKNGKVPFDICNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P++K KI+A+ + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACRAGISFGKDDMVIPDAKAKIVADTETL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFD TGRQK MNSI+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDENTGRQKPMNSIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+V VDC T+ GLT+T IVD+GQVV S+G R+LGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVTHVDCGTETGLTMTAIVDAGQVVASIGVRILGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDHPITGERIVDAGRMILEPDVVEIEKAGIQSIRIRSALTCEIQTGVCAVCYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG TV+D+SF+E+ +G V+IKNRN
Sbjct: 901 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
+ RNS +L++MGRN T+QILD G E+ S R+ YG+KL VD+G ++ GQR++EWDP+T
Sbjct: 961 ILRNSDGNLVAMGRNMTVQILDERGVERSSQRVAYGSKLHVDEGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV+GTV FEDLVDG+SV+E+ ESTGI KR+VIDWR R +LKPAIV+ D +G
Sbjct: 1021 RPMMTEVAGTVQFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIVIKDASG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
V+K +RG DAR+ L VDA+LSV PG KVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 NVMKLSRGGDARFMLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQ+GD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQEGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D+ YI+GDNVDRIE+E++N L +QGKK P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDAGDSTYIVGDNVDRIELEDVNDHLIEQGKKPAYGDPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK D L G KENVIVGR IPAGTG + + RR+A +RD++IL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDGLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDELILEER 1378
|
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|241204158|ref|YP_002975254.1| DNA-directed RNA polymerase subunit beta' [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 1402 | Back alignment and organism information |
|---|
Score = 2097 bits (5434), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 988/1378 (71%), Positives = 1180/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNPQVPAQNFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L+++Q+L+EEEY+ AV ++G+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKEHQLLSEEEYMLAVDEYGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYE+L +++L+ +A LR +L+ ++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIYEMLASMNLEKIAGDLRAELADTTSDLKQKKLMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPILVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSILNQNEPGEGMAFSDLGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
+K+VTLH+KIRGR+KSVD+DG SKIY+TTPGR++IGE+LP++ ++ FDICNQEM KKN
Sbjct: 541 SKVVTLHTKIRGRFKSVDEDGKPYSKIYETTPGRLLIGELLPKNGKVPFDICNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P++K KI+A+ + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFAHACRAGISFGKDDMVIPDAKAKIVADTENL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFD +TGRQK MNSI+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDEKTGRQKPMNSIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+V VDC T+ GLT+T IVD+GQVV S+G R+LGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVTHVDCGTQTGLTMTAIVDAGQVVASIGVRILGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDHPVTGERIVDAGRMILEPDVVEIEKAGIQSIRIRSALTCEIQTGVCSVCYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG TV+D+SF+E+ +G V+IKNRN
Sbjct: 901 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
+ RNS +L++MGRN T+QILD G E+ S R+ YG+KL VD+G ++ GQR++EWDP+T
Sbjct: 961 ILRNSDGNLVAMGRNMTVQILDERGVERSSQRVAYGSKLHVDEGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV+GTV FEDLVDG+SV+E+ ESTGI KR+VIDWR R +LKPAIV+ D +G
Sbjct: 1021 RPMMTEVAGTVQFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIVIKDASG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
+ K +RG DAR+FL VDA+LSV PG KVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 NIAKLSRGGDARFFLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQ+GD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQEGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D+ YI+GDNVDRIE+E++N L +QGKK P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDAGDSTYIVGDNVDRIELEDVNDHLIEQGKKPAYGDPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK D L G KENVIVGR IPAGTG + + RR+A +RD+MIL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDGLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDEMILEER 1378
|
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|222085669|ref|YP_002544199.1| DNA-directed RNA polymerase, beta' subunit [Agrobacterium radiobacter K84] Length = 1403 | Back alignment and organism information |
|---|
Score = 2094 bits (5425), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 983/1378 (71%), Positives = 1178/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNPQVPAQNFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L+++Q+L+EEEY+ AV ++G+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKEHQLLSEEEYMLAVDEYGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYELL +++L+ +A LR +L++++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIYELLASMNLEKIAGDLRAELAETTSDLKQKKLMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSILNQNEPGEGMAFSDLGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
NK+VTLHSKIRGR+KSVD++G SKIY+TTPGR++IGE+LP+H +++FDICNQEM KKN
Sbjct: 541 NKVVTLHSKIRGRFKSVDEEGKPYSKIYETTPGRLLIGELLPKHGKVTFDICNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P++K KI+ + + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVGDTESL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFDP TGRQK MNSI+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDPATGRQKPMNSIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+V VDC T KGLT+T I+D+GQVV S+G R+LGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVTHVDCGTDKGLTMTAIIDAGQVVASIGVRILGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDHPVTGERIVDAGRMILEPDVIEIEKAGIQSIRIRSALTCEIQTGVCSICYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG TV+D+SF+E+ +G V+IKNRN
Sbjct: 901 ARGTPVNLGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
+ RNS L++MGRN +QILD G E+ S R+ YG+K++VD+G ++ GQR++EWDP+T
Sbjct: 961 MLRNSDGILVAMGRNMAVQILDERGVERSSQRVAYGSKIYVDEGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TE++GTV FED++DG+SV+E+ ESTGI KR+VIDWR R +LKPAIV+ D +G
Sbjct: 1021 RPMMTELAGTVQFEDVIDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIVIKDASG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
V K +RG +AR+ L VDA+LSV PGQKVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 NVAKLSRGGEARFLLSVDAILSVEPGQKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQ+GD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQEGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D+ YI+GDNVDRIE+++ N L ++GKK P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDAGDSHYIVGDNVDRIELDDNNDRLIEEGKKPAYGDPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK D L G KENVIVGR IPAGTG + + RR+A RD++IL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDGLQGLKENVIVGRLIPAGTGGTMTQIRRIATARDELILEER 1378
|
Species: Agrobacterium tumefaciens Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|159184989|ref|NP_354930.2| DNA-directed RNA polymerase subunit beta' [Agrobacterium tumefaciens str. C58] Length = 1402 | Back alignment and organism information |
|---|
Score = 2093 bits (5423), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 993/1402 (70%), Positives = 1183/1402 (84%), Gaps = 4/1402 (0%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNPQVPAQHFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL+SL++ Q+L+EEEY+ AV +FG+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTSLKQNQLLSEEEYMIAVDEFGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AIYE+L +++L+ +A LR +L++++S ++KK +KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIYEMLASMNLEKIAGDLRAELAETTSDLKQKKFMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+G P+ VPSQDMVLGL YLS +++ +PGEGM F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGHPIIVPSQDMVLGLYYLSIMNQNEPGEGMAFSDIGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
NK+VTLH+KIRGR+K+VD DG +SKI++TTPGRM+IGE+LP++ + FD CNQEM KKN
Sbjct: 541 NKVVTLHAKIRGRFKTVDADGKPVSKIHETTPGRMLIGELLPKNVNVPFDTCNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGF +AC +GISFGKDD+++P+SK KI+ + + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACRAGISFGKDDMVIPDSKVKIVGDTEAL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV EEMMARIK VEFDPETGRQK MNSI+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEEMMARIKAVEFDPETGRQKPMNSIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+VN VDC T KGLT+T IVD+GQ+V S+G+R+LGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVNSVDCGTDKGLTMTAIVDAGQIVASIGARILGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI NP+T E IVKAG LI E+ V IEK GI+SVRIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDNPVTGENIVKAGTLIDEADVAIIEKAGIQSVRIRSALTCEVQIGVCGVCYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG V+D+SF+E+ +G ++IKNRN
Sbjct: 901 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTANVVDQSFLEASYEGTIQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
+ RNS LI+MGRN ++ ILD G E+ S R+ YG+K+FVDDG ++ GQR++EWDP+T
Sbjct: 961 ILRNSEGVLIAMGRNMSVTILDERGVERSSQRVAYGSKIFVDDGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV GTV FEDLVDG+SV+E+ ESTGI KR+VIDWR R +LKPAI++ D +G
Sbjct: 1021 RPMMTEVEGTVHFEDLVDGLSVLEATDESTGITKRQVIDWRSTPRGSDLKPAIIIKDASG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
V K +RG +AR+ L VDA+LSV PG KVS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 AVAKLSRGGEARFHLSVDAILSVEPGSKVSQGDVLARSPLESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQ+GD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVMIEPAEDGVEPVEYLIPKGKPFHLQEGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KG+YILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGEYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D++YI+GDNVDRIE+E++N L ++GKK P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDAGDSQYIVGDNVDRIEMEDMNDRLIEEGKKPAYGEPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKERSN 1380
QETTKVLTEAAIAGK DTL G KENVIVGR IPAGTG + + RR+A +RD +IL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDDLILEERRK 1380
Query: 1381 ----FSQNEDLKNTAIQGSIAE 1398
S N+ L++ Q AE
Sbjct: 1381 GTGAGSANQMLQDMTDQVPAAE 1402
|
Species: Agrobacterium tumefaciens Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|222148358|ref|YP_002549315.1| DNA-directed RNA polymerase subunit beta' [Agrobacterium vitis S4] Length = 1403 | Back alignment and organism information |
|---|
Score = 2088 bits (5410), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 986/1378 (71%), Positives = 1173/1378 (85%)
Query: 1 MQQEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCA 60
M QEVM FNP + FDS+RISIASP KI S SYGEIKKPETINYRTFKPERDGLFCA
Sbjct: 1 MNQEVMNLFNPQVPAQHFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCA 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
RIFGPIKDYEC+CGKYKRMKYKGIICEKCGVEVTLS VRR+RM HI+LA+PVAH WFLKS
Sbjct: 61 RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIA 180
LPSRISTLL M+L+DVERVLYFE+Y+V +PGL++L++ Q+L+EEEY+ AV ++G+DQF A
Sbjct: 121 LPSRISTLLDMTLKDVERVLYFENYIVTEPGLTALKQNQLLSEEEYMMAVDEYGEDQFTA 180
Query: 181 MMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240
M+GA+AI+E+L +++L+ +A LR L+ ++S ++KK++KRLKIV++F+ SGN P WMI
Sbjct: 181 MIGAEAIFEMLASMNLERIAGELRQDLADTTSDLKQKKLMKRLKIVENFMESGNRPEWMI 240
Query: 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRM 300
++ +PV+PPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP IIIRNEKRM
Sbjct: 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRM 300
Query: 301 LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAG 360
LQESVDALFDNGR RV+TGAN+RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV G
Sbjct: 301 LQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTG 360
Query: 361 PELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQ 420
PEL+LHQCGLPK MALELFKPF+YA+L+ KGY STVKQAKK VEKE+PEVWD+L EV+ +
Sbjct: 361 PELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIRE 420
Query: 421 HVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480
H VLLNRAP+LHRL +QAFEP ++ GKAIQLHPLVC +NADFDGDQMAV+ +S EAQL
Sbjct: 421 HPVLLNRAPTLHRLGIQAFEPILVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Query: 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALE 540
EARVLM+STNN+LHPA+GAP+ VPSQDMVLGL YLS +++ +PGEGM+F+D+GE++HALE
Sbjct: 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSIMNQNEPGEGMVFSDIGELHHALE 540
Query: 541 NKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKN 600
NK+VTLHSKIRGR+K+VD DG +SKI++TTPGRM+IGE+LP++ + FD CNQEM KKN
Sbjct: 541 NKVVTLHSKIRGRFKTVDADGKPVSKIFETTPGRMLIGELLPKNVNVPFDTCNQEMTKKN 600
Query: 601 ISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKM 660
IS M+DT+YRHCGQK TV FCD +M+LGFR+AC +GISFGKDD+++P+SK KI+ + + +
Sbjct: 601 ISKMIDTVYRHCGQKDTVIFCDRIMQLGFRHACKAGISFGKDDMVIPDSKVKIVGDTESL 660
Query: 661 VKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720
VKEYE QYNDGLIT+GEKYNKVVD WGK T+KV E+MMARIK VEFDPETGRQK MN+I+
Sbjct: 661 VKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMARIKAVEFDPETGRQKPMNAIY 720
Query: 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGL 780
MMSHSGARGS +QMRQLGGMRGL+AKPSGEIIE+PI S+FK GL E+F S G RKGL
Sbjct: 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGL 780
Query: 781 LDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRT 840
D ++TA+SGYL+RRLVDVAQ+C+VN VDC T KGLT+T IVD+GQVV S+G RVLGRT
Sbjct: 781 ADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDKGLTMTAIVDAGQVVASIGVRVLGRT 840
Query: 841 ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDL 900
ALDDI +P+T E IV AG++ILE+ V EIEK GI+S+RIRSALTCE GVC +CYGRDL
Sbjct: 841 ALDDIDHPVTGERIVDAGRMILEADVIEIEKAGIQSIRIRSALTCEVQTGVCSICYGRDL 900
Query: 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
ARG+ VN+GEAVGVIAAQSIGEPGTQLTMRTFHLGG V+D+SF+E+ +G ++IKNRN
Sbjct: 901 ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTANVVDQSFLEASYEGTIQIKNRN 960
Query: 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHT 1020
+ RNS ++MGR+ + ILD G E+ S R+ YG+KLFVDDG ++ GQR++EWDP+T
Sbjct: 961 MLRNSDGIYVAMGRSIAVTILDERGVERSSQRVAYGSKLFVDDGDKVKRGQRLAEWDPYT 1020
Query: 1021 FPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENG 1080
P++TEV G V FEDLVDGISV+E+ ESTGI KR+VIDWR R +LKPAIV+ D G
Sbjct: 1021 RPMMTEVEGVVHFEDLVDGISVLEATDESTGITKRQVIDWRSTPRGADLKPAIVIKDTQG 1080
Query: 1081 VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFE 1140
VLK RG +AR+ L VDA+LSV PGQ+VS GDVLAR P+ SAKTKDIT GLPRVAELFE
Sbjct: 1081 NVLKVPRGGEARFQLSVDAILSVEPGQRVSQGDVLARSPMESAKTKDITGGLPRVAELFE 1140
Query: 1141 ARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVE 1200
ARRPK+HAI+AEI GTIR+ R+YKNK RV+IEP EDGVEP EY IPK K F+LQ+GD++E
Sbjct: 1141 ARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQEGDYIE 1200
Query: 1201 KGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
KGDYILDGNP P DIL IKGVEALASYL+NE+QEVYRL+GV IN KHIEV+VR MLQKVE
Sbjct: 1201 KGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVE 1260
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASF 1320
ITD D++YI+GDNVDRIE++E N L ++GKK P+L GITKASLQT SFISAASF
Sbjct: 1261 ITDSGDSQYIVGDNVDRIELDEANERLVEEGKKPAFGDPVLLGITKASLQTPSFISAASF 1320
Query: 1321 QETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILKER 1378
QETTKVLTEAAIAGK DTL G KENVIVGR IPAGTG + + RR+A +RD +IL+ER
Sbjct: 1321 QETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDDLILEER 1378
|
Species: Agrobacterium vitis Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
| Identity | Alignment graph | Length | Definition | E-value |
| Target | 1398 | DNA-directed RNA polymerase subunit beta' [Candidatus L | ||
| CHL00018 | 663 | CHL00018, rpoC1, RNA polymerase beta' subunit | 0.0 | |
| TIGR02387 | 619 | TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gam | 0.0 | |
| PRK00566 | 1156 | PRK00566, PRK00566, DNA-directed RNA polymerase subunit | 0.0 | |
| TIGR02386 | 1140 | TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta | 0.0 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA polym | 0.0 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA polym | 0.0 | |
| PRK14906 | 1460 | PRK14906, PRK14906, DNA-directed RNA polymerase subunit | 0.0 | |
| PRK02625 | 627 | PRK02625, rpoC1, DNA-directed RNA polymerase subunit ga | 0.0 | |
| PRK00566 | 1156 | PRK00566, PRK00566, DNA-directed RNA polymerase subunit | 1e-117 | |
| TIGR02386 | 1140 | TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta | 1e-87 | |
| PRK14906 | 1460 | PRK14906, PRK14906, DNA-directed RNA polymerase subunit | 4e-60 | |
| CHL00117 | 1364 | CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewe | 5e-49 | |
| cd02735 | 309 | cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukar | 3e-04 | |
| smart00663 | 295 | smart00663, RPOLA_N, RNA polymerase I subunit A N-termi | 1e-117 | |
| KOG0262 | 1640 | KOG0262, KOG0262, KOG0262, RNA polymerase I, large subu | 7e-30 | |
| PRK02597 | 1331 | PRK02597, rpoC2, DNA-directed RNA polymerase subunit be | 1e-105 | |
| TIGR02388 | 1227 | TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, bet | 6e-97 | |
| CHL00117 | 1364 | CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewe | 1e-91 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA polym | 5e-84 | |
| pfam04997 | 330 | pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain | 4e-82 | |
| TIGR02390 | 868 | TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase s | 5e-74 | |
| KOG0260 | 1605 | KOG0260, KOG0260, KOG0260, RNA polymerase II, large sub | 3e-54 | |
| PRK08566 | 882 | PRK08566, PRK08566, DNA-directed RNA polymerase subunit | 3e-70 | |
| PRK02597 | 1331 | PRK02597, rpoC2, DNA-directed RNA polymerase subunit be | 4e-69 | |
| TIGR02388 | 1227 | TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, bet | 1e-62 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA polym | 2e-68 | |
| cd02655 | 204 | cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacte | 8e-60 | |
| cd00630 | 158 | cd00630, RNAP_largest_subunit_C, Largest subunit of RNA | 7e-20 | |
| cd06528 | 363 | cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymera | 6e-09 | |
| cd02736 | 300 | cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Euk | 1e-08 | |
| PRK04309 | 383 | PRK04309, PRK04309, DNA-directed RNA polymerase subunit | 1e-08 | |
| PRK14897 | 509 | PRK14897, PRK14897, unknown domain/DNA-directed RNA pol | 2e-08 | |
| PRK14898 | 858 | PRK14898, PRK14898, DNA-directed RNA polymerase subunit | 8e-07 | |
| KOG0261 | 1386 | KOG0261, KOG0261, KOG0261, RNA polymerase III, large su | 1e-05 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA polym | 4e-05 | |
| PRK14906 | 1460 | PRK14906, PRK14906, DNA-directed RNA polymerase subunit | 4e-56 | |
| KOG0261 | 1386 | KOG0261, KOG0261, KOG0261, RNA polymerase III, large su | 1e-55 | |
| pfam00623 | 165 | pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain | 2e-54 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain | 2e-46 | |
| pfam04983 | 158 | pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain | 5e-25 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain | 1e-22 | |
| cd02655 | 204 | cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacte | 3e-17 | |
| PRK04309 | 383 | PRK04309, PRK04309, DNA-directed RNA polymerase subunit | 2e-12 | |
| cd06528 | 363 | cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymera | 8e-12 | |
| cd02735 | 309 | cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukar | 8e-11 | |
| PRK14897 | 509 | PRK14897, PRK14897, unknown domain/DNA-directed RNA pol | 6e-10 | |
| cd00630 | 158 | cd00630, RNAP_largest_subunit_C, Largest subunit of RNA | 2e-09 | |
| cd02584 | 410 | cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Euka | 2e-09 | |
| KOG0262 | 1640 | KOG0262, KOG0262, KOG0262, RNA polymerase I, large subu | 3e-09 | |
| cd02736 | 300 | cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Euk | 1e-08 | |
| KOG0260 | 1605 | KOG0260, KOG0260, KOG0260, RNA polymerase II, large sub | 5e-05 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' subun | 0.001 | |
| PRK14898 | 858 | PRK14898, PRK14898, DNA-directed RNA polymerase subunit | 0.002 | |
| pfam05000 | 108 | pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain | 2e-16 | |
| TIGR02389 | 367 | TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, | 6e-11 | |
| KOG0260 | 1605 | KOG0260, KOG0260, KOG0260, RNA polymerase II, large sub | 1e-07 | |
| KOG0262 | 1640 | KOG0262, KOG0262, KOG0262, RNA polymerase I, large subu | 7e-05 | |
| TIGR02389 | 367 | TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, | 2e-07 | |
| KOG0262 | 1640 | KOG0262, KOG0262, KOG0262, RNA polymerase I, large subu | 7e-07 | |
| cd02584 | 410 | cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Euka | 9e-07 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' subun | 9e-04 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' subun | 0.0 |
| >gnl|CDD|176961 CHL00018, rpoC1, RNA polymerase beta' subunit | Back alignment and domain information |
|---|
Score = 704 bits (1820), Expect = 0.0
Identities = 264/648 (40%), Positives = 374/648 (57%), Gaps = 63/648 (9%)
Query: 14 DDRGFDSVRISIASPAKIASLSY---------GEIKKPETINYRTFKPERDGLFCARIFG 64
D +RI +ASP +I + + GE+ KP TI+Y+T KPE+DGLFC RIFG
Sbjct: 3 DRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFG 62
Query: 65 PIKDYECICGKYKRM---KYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSL 121
PIK C CG Y+ + K CE+CGVE T S VRR RM +I LA PV H W+LK L
Sbjct: 63 PIKSGICACGNYRVIGDEKEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRL 122
Query: 122 PSRISTLLGMSLRDVERVLYFE-SYVVVDPGLSSLEKYQILTEEE---YVEAVSQF---- 173
PS I+ LL L+++E ++Y + S+ + + + L E E + ++ F
Sbjct: 123 PSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRLRGLFEYEIQSWKYSIPLFFSTQ 182
Query: 174 GQDQF----IAMMGADAIYELLIALDLQNLALTLRDQ---LSKSSSIF----------RR 216
G D F I+ GA AI E L LDL+ + + L + S R+
Sbjct: 183 GFDTFRNREIST-GAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKIGRRK 241
Query: 217 KKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIG 276
+++R+K+ FI + P WM++ LPVLPP+LRP++ LD G+ +SDLN+LYRRVI
Sbjct: 242 DFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIY 301
Query: 277 RNNRLMRLKSLH--APEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLK 334
RNN L L + P ++ +K++LQE+VDAL DNG + + + +P KS SD+++
Sbjct: 302 RNNTLTDLLTTSRSTPGELVMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIE 361
Query: 335 GKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVS 394
GK+GRFR NLLGKRVDYSGRSVIV GP L LHQCGLP+ +A+ELF+PF+ L ++ S
Sbjct: 362 GKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLAS 421
Query: 395 TVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPL 454
++ AK + ++ P VW++L EV+ H VLLNRAP+LHRL +QAF+P ++ G+AI LHPL
Sbjct: 422 NIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPL 481
Query: 455 VCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCY 514
VC G+NADFDGDQMAV+ +S EAQ EAR+LM S NLL PA G P++VPSQDM+LGL
Sbjct: 482 VCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYV 541
Query: 515 L-------------STVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDG 561
L + + + + F++ + A K + L S + R++ +
Sbjct: 542 LTIGNRRGIYANRYNPCNRKNSTKEPYFSNSYDALGAYRQKRINLDSPLWLRWRLDQRII 601
Query: 562 NSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIY 609
S R + E+ +I +I K+ + +IY
Sbjct: 602 AS----------REVPIEVQYESLGTYHEIYEHYLIVKSRKKEILSIY 639
|
Length = 663 |
| >gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit | Back alignment and domain information |
|---|
Score = 705 bits (1820), Expect = 0.0
Identities = 322/613 (52%), Positives = 431/613 (70%), Gaps = 50/613 (8%)
Query: 18 FDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKD 68
FD V+I+IASP ++ GE+ KPETINYRT KPE DGLFC +IFGP KD
Sbjct: 2 FDYVKITIASPERVMEWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKD 61
Query: 69 YECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTL 128
+EC CGKYKR++++GI+CE+CGVEVT S VRR RM +I LA+PV H W+LK +PS +S L
Sbjct: 62 WECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSIL 121
Query: 129 LGMSLRDVERVLYFESYVVVDPGLSSLEKY-QILTEEEYVEAVSQ-FGQDQFI-----AM 181
L M LRDVE+++YF +YVV++PG + KY Q+LTE++++E Q + +D +
Sbjct: 122 LDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSELENEEVVG 181
Query: 182 MGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMII 241
+GA+A+ +LL L+L+ +A LR++++ S +R K+IKRL+++D+FI + + P WM++
Sbjct: 182 IGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
Query: 242 RKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRML 301
+PV+PPDLRP+V LD GRFA SDLNDLYRRVI RNNRL RL+ + APEII+RNEKRML
Sbjct: 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRML 300
Query: 302 QESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGP 361
QE+VDAL DNGR R V GAN RPLKSLSD+++GKQGRFR NLLGKRVDYSGRSVIV GP
Sbjct: 301 QEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGP 360
Query: 362 ELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQH 421
+L++HQCGLPK MA+ELF+PF+ +L ++G V+ +K AKK +++ E+W VL EV+ H
Sbjct: 361 KLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADDEIWSVLQEVITGH 420
Query: 422 VVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLE 481
V+LNRAP+LHRL +QAFEP ++ G+AIQLHPLVC +NADFDGDQMAV+ +S EAQ E
Sbjct: 421 PVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
Query: 482 ARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEG-DPGEGMLFADMGEVYHALE 540
AR+LML++NN+L PA+G P+ PSQDMVLG YL+ ++ G + G G F+ + + HA E
Sbjct: 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEKGRGRYFSSLEDAIHAYE 540
Query: 541 NKIVTLHSKI--------------------------------RGRYKSVDKDGNSISKIY 568
+ + LH I R D+DG IS+
Sbjct: 541 DGRIDLHDWIWVRFNGEVETNDPLDEPIKSEDLSDGTRIEQWTYRRDRFDEDGALISQYI 600
Query: 569 DTTPGRMIIGEIL 581
TT GR+I+ +
Sbjct: 601 LTTTGRIIMNHTI 613
|
The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''. Length = 619 |
| >gnl|CDD|179068 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Score = 1716 bits (4448), Expect = 0.0
Identities = 596/1019 (58%), Positives = 731/1019 (71%), Gaps = 50/1019 (4%)
Query: 18 FDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYK 77
FD+++I +ASP KI S SYGE+KKPETINYRT KPERDGLFC RIFGP KDYEC+CGKYK
Sbjct: 7 FDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYK 66
Query: 78 RMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVE 137
R++YKGIICE+CGVEVT S VRR+RM HI+LA+PVAH WF KSLPSRI LL MSL+D+E
Sbjct: 67 RVRYKGIICERCGVEVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLE 126
Query: 138 RVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQ 197
RVLYFESYVV+DPG + LEK Q+LTEEEY EA+ ++G D+F+A MGA+AI ELL +DL+
Sbjct: 127 RVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYG-DEFVAKMGAEAIKELLKNIDLE 185
Query: 198 NLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVAL 257
A LR++L ++ S +RKK +KRLK+V++F SGN P WMI+ LPV+PPDLRPLV L
Sbjct: 186 AEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQL 245
Query: 258 DFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRV 317
D GRFA SDLNDLYRRVI RNNRL RL L APEII+RNEKRMLQE+VDALFDNGR R
Sbjct: 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRP 305
Query: 318 VTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALE 377
VTG N RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV GPEL+LHQCGLPK MALE
Sbjct: 306 VTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALE 365
Query: 378 LFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQ 437
LFKPF+ +L ++G +T+K AKK VE+E PEVWDVL EV+ +H VLLNRAP+LHRL +Q
Sbjct: 366 LFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQ 425
Query: 438 AFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPAS 497
AFEP +I GKAIQLHPLVC +NADFDGDQMAV+ +S EAQ EARVLMLS+NN+L PA+
Sbjct: 426 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAN 485
Query: 498 GAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSV 557
G P+ VPSQDMVLGL YL+ EG GEGM+F+ E A EN V LH++I+ R S
Sbjct: 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITS- 544
Query: 558 DKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKST 617
K+ +TT GR+I EILP + F N+ + KK IS +++ +YR G K T
Sbjct: 545 -------KKLVETTVGRVIFNEILPE--GLPFINVNKPLKKKEISKIINEVYRRYGLKET 595
Query: 618 VAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGE 677
V F D + LGF+YA SGIS G DDI++P K++II EA+K V E E QY GLIT GE
Sbjct: 596 VIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGE 655
Query: 678 KYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQL 737
+YNKV+D+W K TD+V + MM + + Q+ N I+MM+ SGARGS Q+RQL
Sbjct: 656 RYNKVIDIWSKATDEVAKAMMKNLSK--------DQESFNPIYMMADSGARGSASQIRQL 707
Query: 738 GGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRL 797
GMRGL+AKPSGEIIE+PI+S+F+ GL E+F S G RKGL D ++TA SGYL+RRL
Sbjct: 708 AGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL 767
Query: 798 VDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKA 857
VDVAQ+ +V + DC T +G+ +T I++ G+V+ L R+LGR +D+++P T E IV A
Sbjct: 768 VDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPA 827
Query: 858 GQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAA 917
G LI E ++IE+ GI V+IRS LTCE+ GVC CYGRDLA G LVN+GEAVGVIAA
Sbjct: 828 GTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAA 887
Query: 918 QSIGEPGTQLTMRTFHLGG---------------AVTVMDRSFIESPCDGIVKIKNRNVC 962
QSIGEPGTQLTMRTFH GG A + I + DG V
Sbjct: 888 QSIGEPGTQLTMRTFHTGGVDITGGLPRVAELFEARKPKGPAII-AEIDGTVSF------ 940
Query: 963 RNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEW--DPH 1019
+ ++ E+ + I G L V +G +E G ++++ DPH
Sbjct: 941 -------GKETKGKRRIVITPDDGEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPH 992
|
Length = 1156 |
| >gnl|CDD|162830 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
Score = 1335 bits (3458), Expect = 0.0
Identities = 551/1023 (53%), Positives = 707/1023 (69%), Gaps = 56/1023 (5%)
Query: 20 SVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRM 79
+++ISIASP I + SYGE+KKPETINYRT KPE+DGLFC +IFGP KD+EC CGKYK++
Sbjct: 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKI 60
Query: 80 KYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERV 139
+YKG++CE+CGVEVT S VRR+RM HI+LA+PVAH W+ K LPSRI LL ++ +++E V
Sbjct: 61 RYKGVVCERCGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESV 120
Query: 140 LYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNL 199
LYFE+YVV+DPG + L+K ++L E EY E + ++G D F A MGA+AI ELL +DL
Sbjct: 121 LYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYG-DGFRAGMGAEAIKELLEKIDLDKE 179
Query: 200 ALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDF 259
L+ QL +S S +RKK++KRL+IV++F SGN P WM++ +PV+PP+LRP+V LD
Sbjct: 180 IEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDG 239
Query: 260 GRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVT 319
GRFA SDLNDLYRRVI RNNRL RL L APEII+RNEKRMLQE+VDALFDNGR + V
Sbjct: 240 GRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVV 299
Query: 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELF 379
G N RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV GPEL+++QCGLPK MALELF
Sbjct: 300 GKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELF 359
Query: 380 KPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAF 439
KPF+ +L + + +K AKK +E+E PEVWDVL +V+ +H VLLNRAP+LHRL +QAF
Sbjct: 360 KPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAF 419
Query: 440 EPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGA 499
EP ++ GKAI+LHPLVC +NADFDGDQMAV+ +SPEAQ EAR LML++NN+L+P G
Sbjct: 420 EPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGK 479
Query: 500 PVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDK 559
P+ PSQDMVLGL YL+T G GEG +F+++ E A +N V LH+ I R
Sbjct: 480 PIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTS---- 535
Query: 560 DGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVA 619
+I +TT GR+I EILP D N+ + KK IS+++D +Y G + T
Sbjct: 536 -----GEILETTVGRVIFNEILPEGFPYIND--NEPLSKKEISSLIDLLYEVHGIEETAE 588
Query: 620 FCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKY 679
D + LGF+YA SG + DI+VP+ K +I+ EADK V + + YN GLIT E+Y
Sbjct: 589 MLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERY 648
Query: 680 NKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGG 739
KVV +W +T DKVT+ MM +K+ K N IFMM+ SGARG+I Q RQL G
Sbjct: 649 RKVVSIWSETKDKVTDAMMKLLKK--------DTYKFNPIFMMADSGARGNISQFRQLAG 700
Query: 740 MRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVD 799
MRGL+AKPSG+IIE PI+S F+ GL E+F S G RKGL D ++TA SGYL+RRLVD
Sbjct: 701 MRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVD 760
Query: 800 VAQNCVVNQVDCNTKKGLTITHIVD-SGQVVYSLGSRVLGRTALDDIINPLTNECIVKAG 858
VAQ+ VV + DC T++G+ + IV+ +++ SL R++GR + +D+ +P T + I +A
Sbjct: 761 VAQDVVVREEDCGTEEGIEVEAIVEGKDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEAN 820
Query: 859 QLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQ 918
LI E +IE GI V++RS LTCES GVC CYGRDLA G LV +GEAVGVIAAQ
Sbjct: 821 TLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQ 880
Query: 919 SIGEPGTQLTMRTFHLGG--------------------AVTVMDRSFIESPCDGIVKIKN 958
SIGEPGTQLTMRTFH GG A T D++ I + DG V+I
Sbjct: 881 SIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFEARTPKDKAVI-AEVDGTVEIIE 939
Query: 959 RNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE--W 1016
V +N + I D + E+ + I +GA+L V DG + G +++E
Sbjct: 940 DIV-KNKRV----------VVIKDEND-EEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSI 987
Query: 1017 DPH 1019
DPH
Sbjct: 988 DPH 990
|
Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. Length = 1140 |
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
Score = 1596 bits (4133), Expect = 0.0
Identities = 752/1356 (55%), Positives = 995/1356 (73%), Gaps = 10/1356 (0%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
+ F+ V ISIASP I +SYGEI+ T NYRTFK E+ GLFC +IFGP+ D EC+CGK
Sbjct: 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGK 1505
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRD 135
YK+ +++G ICEKCGVEVT S VRR+RM HI+LASPVAH WFLKSLPSRI LL MSLRD
Sbjct: 1506 YKKRRHRGRICEKCGVEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRD 1565
Query: 136 VERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALD 195
+E +LY ++Y+V+DP +S EK +I++E+ Y EA +G D F+AM G +AI ELL LD
Sbjct: 1566 IENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGIDSFVAMQGVEAIRELLTRLD 1625
Query: 196 LQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLV 255
L + LR +L +S RRKKIIKRL+IV++FI SGN P WMI+ +P+LPPDLRPLV
Sbjct: 1626 LHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLV 1685
Query: 256 ALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK 315
+L+ GR A SDLN YR +I RNNRL +L SL+ PEI+IRNEKRMLQE+VD+LFDN R
Sbjct: 1686 SLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRN 1745
Query: 316 RVVTGANRRPL-KSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLM 374
+V A KS+SDMLKGKQGRFR NLLGKRVDYSGRSVIV GP L+L+QCGLPK M
Sbjct: 1746 ALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRM 1805
Query: 375 ALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRL 434
ALELFKPF+Y++L+ G T+K A K + E+PEVWD+L EV+ +H VLLNRAP+LHRL
Sbjct: 1806 ALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEEVIKEHPVLLNRAPTLHRL 1865
Query: 435 SMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494
+QAFEP +I GKAIQLHPLVC +NADFDGDQMAV+ IS EAQLEARVLM+STNN+L
Sbjct: 1866 GIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925
Query: 495 PASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRY 554
P++G P+ VPS+D+VLG+ YL T+ E + F EV H+L + + +HS I+ R
Sbjct: 1926 PSNGRPIIVPSKDIVLGIYYL-TLQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRM 1984
Query: 555 KSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQ 614
+ ++ G + K TTPGR+I+ +I P+H + FD+ NQ + K I+++VD +YR+CGQ
Sbjct: 1985 EYINSSGETHYKTICTTPGRLILWQIFPKHENLGFDLINQVLTVKEITSIVDLVYRNCGQ 2044
Query: 615 KSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLIT 674
+TVAF D LM LGF YA SG+SF + D+++PE+K + A +K++ QY DGLIT
Sbjct: 2045 SATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLIT 2104
Query: 675 RGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQM 734
R E+YNKV+D W K TD + +M+ I + K NS++MM +SGARGS QM
Sbjct: 2105 RSERYNKVIDEWSKCTDMIANDMLKAISIYD------GNSKYNSVYMMVNSGARGSTSQM 2158
Query: 735 RQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLS 794
+QL GMRGL+ KPSGEIIE+PI S+F+ GL FE+F S G RKGL D ++TA+SGYL+
Sbjct: 2159 KQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLT 2218
Query: 795 RRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECI 854
RRLVDV+QNC+V + DC TK GL + V+ +V SL S VLGRTA +DI NP+T E +
Sbjct: 2219 RRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELL 2278
Query: 855 VKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGV 914
VKAG+LI E V +I G+ V+IRS LTCE S GVC LCYGRDLA G +V++GEAVGV
Sbjct: 2279 VKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGV 2338
Query: 915 IAAQSIGEPGTQLTMRTFHLGGAVTV-MDRSFIESPCDGIVKIKNRNVCRNSTNDLISMG 973
IAAQS+GEPGTQLTMRTFH+GG +T ++ S I + + +K+ N N+ + + I +
Sbjct: 2339 IAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIVIS 2398
Query: 974 RNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGF 1033
R+ + ++D G E+ H + YGAKL+VD+GG ++ G +++EWDP+T PIITE +GTV +
Sbjct: 2399 RSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSY 2458
Query: 1034 EDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARW 1093
+DL DGIS+ E + ESTGI+ + V DW+ S NL+P IV+ D+NG V+ A G +A +
Sbjct: 2459 QDLKDGISITEVMDESTGISSKVVKDWKLYSGGANLRPRIVLLDDNGKVMTLASGVEACY 2518
Query: 1094 FLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEI 1153
F+P+ A+L+V GQKV GDV+ R P S KT+DIT GLPRV ELFEARRPK HAI++EI
Sbjct: 2519 FIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEARRPKEHAIVSEI 2578
Query: 1154 SGTIRI-KRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVP 1212
G + +++ + K ++I+P ++ + P EY + ++KH + +GD V KGD ++DG+P
Sbjct: 2579 DGYVAFSEKDRRGKRSILIKPVDEQISPVEYLVSRSKHVIVNEGDFVRKGDLLMDGDPDL 2638
Query: 1213 QDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILG 1272
DILR+ G+EALA Y+I+E+Q+VYRL+GV I++KH+EV+++ MLQKVEITDP DT Y++G
Sbjct: 2639 HDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVG 2698
Query: 1273 DNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAI 1332
+++D++EV+ N +++ GK+ + PILQGIT+ASL+T SFISAASFQETTKVLTEAA
Sbjct: 2699 ESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAF 2758
Query: 1333 AGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAM 1368
GK D L G KENVIVGR IPAGTG I+++ R +++
Sbjct: 2759 CGKSDPLSGLKENVIVGRLIPAGTGLIMNKVRALSL 2794
|
Length = 2836 |
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
Score = 1118 bits (2893), Expect = 0.0
Identities = 504/937 (53%), Positives = 672/937 (71%), Gaps = 30/937 (3%)
Query: 14 DDR--GFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYEC 71
DDR F S ++++ASP KI S SYGE+KKPETINYRT KPERDGLFC +IFGP KDYEC
Sbjct: 1390 DDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYEC 1449
Query: 72 ICGKYKRMKYKGI-ICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLG 130
+CGKYK+ ++K I CEKCGV +T S VRR RM HI+LA+PVAH W++ SLPSRI TLLG
Sbjct: 1450 LCGKYKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLG 1509
Query: 131 MSLRDVERVLYFESYVVVDPGLSSLE--------KYQILTEEEYVEAVSQFGQDQFIAMM 182
+ ++D+ERVLY+E+Y+V +PG ++ + KY IL EE+Y ++ F+A M
Sbjct: 1510 VKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQM 1569
Query: 183 GADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIR 242
G +AI +LL +DL L +L++++ ++S ++KK+IKRLK+V+SF+ SGN P WM++
Sbjct: 1570 GGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLT 1629
Query: 243 KLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQ 302
LPVLPPDLRPLVALD G+FA SD+N+LYRRVI RN RL RL L APEII+RNEKRMLQ
Sbjct: 1630 VLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQ 1689
Query: 303 ESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPE 362
E+VD LFDNGR V GAN+RPLKSLS+++KGKQGRFR NLLGKRVD+SGRSVIV GP
Sbjct: 1690 EAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPN 1749
Query: 363 LQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHV 422
L++ +CGLPK MALELFKP L ++LE++GY +T+KQAK+ +E++ EVW+ L E+ +
Sbjct: 1750 LKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSNEVWECLQEITEGYP 1809
Query: 423 VLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEA 482
VLLNRAP+LH+ S+QAF PK+I GKAIQLHPLVC+ +NADFDGDQMAV+ +S EA E
Sbjct: 1810 VLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAEC 1869
Query: 483 RVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENK 542
+VLMLS+ N+L PASG V +PSQDMVLGL YLS G GE LF+ + E+ A++ K
Sbjct: 1870 KVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTK 1929
Query: 543 IVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNIS 602
+ +H+KIR +D+ I T+ GRMII ILP I D+ N+ M KK+I
Sbjct: 1930 ELDIHAKIR----VLDQ-----GNIIATSAGRMIIKSILPDF--IPTDLWNRPMKKKDIG 1978
Query: 603 AMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVK 662
+VD +++ G T F D+L LGFRYA +GIS +DII P+ K+K++ +A VK
Sbjct: 1979 VLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVK 2038
Query: 663 EYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMM 722
+ + QY+ GL+T E+YNK++D W + DK+++EMM I ++ NSI+MM
Sbjct: 2039 KIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIA--------KDKEGFNSIYMM 2090
Query: 723 SHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLD 782
+ SGARGS Q+RQL MRGL+ KP G IIE+PI S+FK GL E+F S G RKGL D
Sbjct: 2091 ADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLAD 2150
Query: 783 VVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTAL 842
++TA++GYL+R+L+DV+QN V DC T +G+ IT I +++ L R+ GR L
Sbjct: 2151 TALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLL 2210
Query: 843 DDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLAR 902
+D+I+P+TNE ++ A LI E ++ + GI+S+ IR+ +TC++ +GVC CYG +L
Sbjct: 2211 EDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGE 2270
Query: 903 GSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939
G + GEAVGV+AAQSIGEPGTQLT+RTFH+GG +
Sbjct: 2271 GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTAS 2307
|
Length = 2890 |
| >gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional | Back alignment and domain information |
|---|
Score = 829 bits (2142), Expect = 0.0
Identities = 414/908 (45%), Positives = 565/908 (62%), Gaps = 67/908 (7%)
Query: 155 LEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIF 214
+E Q++++E + F MGA+A+ +LL A+DL+ A LR ++
Sbjct: 232 IEPKQLISDEALYREMRLNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQ- 290
Query: 215 RRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRV 274
+R+K +KRLK+VD+F+ SGN+P MI+ +PV+PPDLRP+V LD GRFA SDLNDLYRRV
Sbjct: 291 KREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRV 350
Query: 275 IGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLK 334
I RNNRL RL L APEII+ NEKRMLQE+VD+LFDNGR R VTG RPLKSL+DMLK
Sbjct: 351 INRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLADMLK 410
Query: 335 GKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVS 394
GKQGRFR NLLGKRVDYSGRSVIV GP L+LHQCGLP MALELFKPF+ +L + Y +
Sbjct: 411 GKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAA 470
Query: 395 TVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPL 454
+K AK+ V++ VWDVL EV+ H VLLNRAP+LHRL +QAFEP ++ GKAI+LHPL
Sbjct: 471 NIKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPL 530
Query: 455 VCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCY 514
VC +NADFDGDQMAV+ +S +AQ EARVLMLS+NN+ PA G P+TVP+QDM++G+ Y
Sbjct: 531 VCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYY 590
Query: 515 LSTVHEGDPGEGMLFADMGEVYHALE-NKIVTLHSKI----------RGRYKSVDKDGNS 563
L+T +G GEG FAD + +A + + L +KI RG Y D +
Sbjct: 591 LTTERDGFEGEGRTFADFDDALNAYDARADLDLQAKIVVRLSRDMTVRGSYG--DLEETK 648
Query: 564 ISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDD 623
+ +TT GR+I ++LP + N +M+KK+I +V+ D
Sbjct: 649 AGERIETTVGRIIFNQVLPE----DYPYLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDG 704
Query: 624 LMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVV 683
+ + GF YA +G++ D +P+ K +I+AEAD+ V + Y DG ++ E++ +VV
Sbjct: 705 IKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVV 764
Query: 684 DLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGL 743
D+W + T++V E M+A FD + N I+MM+ SGARG+I Q+RQL GMRGL
Sbjct: 765 DIWTEATEEVGEAMLA-----GFD-------EDNPIYMMADSGARGNIKQIRQLAGMRGL 812
Query: 744 IAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQN 803
+A GEII+ PI+++F+ GL E+F S G RKGL+D +RTA SGYL+RRLVDVAQ+
Sbjct: 813 MADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQD 872
Query: 804 CVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILE 863
+V + DC T +G+T + G V +L +GR L+D+ +P E ++ AG I
Sbjct: 873 VIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDP-NGEVLLSAGDYI-- 925
Query: 864 SHVNEIEK---CGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSI 920
++++++ G+ V+IR+ +TC + GVC CYG DLA VN+G AVG+IAAQSI
Sbjct: 926 ESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSI 985
Query: 921 GEPGTQLTMRTFHLGG--------AVTVMDRSFIESPCDGIVKIKNRNVCRNSTNDL-IS 971
GEPGTQLTMRTFH GG + + F K K V + L I+
Sbjct: 986 GEPGTQLTMRTFHSGGVAGDDITQGLPRVAELF------EARKPKGEAVLAEISGTLQIT 1039
Query: 972 MGRNT-TLQILDMSGQEQ-----YSHRIMYGAKLFVDDGGVIECGQRISEW--DPHTFPI 1023
+ TL I D G + + M G V+DG + GQ+I+ +PH
Sbjct: 1040 GDKTEKTLTIHDQDGNSREYVVSARVQFMPG----VEDGVEVRVGQQITRGSVNPHDLLR 1095
Query: 1024 ITEVSGTV 1031
+T+ + T+
Sbjct: 1096 LTDPNTTL 1103
|
Length = 1460 |
| >gnl|CDD|179452 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; Provisional | Back alignment and domain information |
|---|
Score = 763 bits (1972), Expect = 0.0
Identities = 330/617 (53%), Positives = 431/617 (69%), Gaps = 51/617 (8%)
Query: 10 NPWTDDRGFDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCA 60
N T++R FD V+I +ASP +I GE+ KPETINYRT KPE DGLFC
Sbjct: 2 NLRTENR-FDYVKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCE 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
+IFGP KD+EC CGKYKR++++GI+CE+CGVEVT S VRR RM I LA+PV H W+LK
Sbjct: 61 KIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKG 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKY-QILTEEEYVEAVSQ-FGQDQF 178
+PS ++ LL M LRDVE+++YF YVV+DPG KY Q+LTE++++E Q + +D
Sbjct: 121 IPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSE 180
Query: 179 I-----AMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSG 233
+ +GA+A+ LL L+L+ A LR++++ S +R K+IKRL+++D+FI +G
Sbjct: 181 LEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATG 239
Query: 234 NNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEII 293
+ P WM++ +PV+PPDLRP+V LD GRFA SDLNDLYRRVI RNNRL RL+ + APEII
Sbjct: 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEII 299
Query: 294 IRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSG 353
+RNEKRMLQE+VDAL DNGR R V GAN RPLKSLSD+++GKQGRFR NLLGKRVDYSG
Sbjct: 300 VRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSG 359
Query: 354 RSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDV 413
RSVIV GP+L++HQCGLPK MA+ELF+PF+ +L ++G V+ +K AKK +++ PEVW V
Sbjct: 360 RSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADPEVWQV 419
Query: 414 LAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAV 473
L EV+ H VLLNRAP+LHRL +QAFEP ++ G+AIQLHPLVC +NADFDGDQMAV+
Sbjct: 420 LEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVP 479
Query: 474 ISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDP-GEGMLFADM 532
+S EAQ EAR+LML++NN+L PA+G P+ PSQDMVLG YL+ + G G G FA +
Sbjct: 480 LSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQKGAGRYFASL 539
Query: 533 GEVYHALENKIVTLHSKIRGRYKS--------------------------------VDKD 560
+V A E + LH+ + R+ D+D
Sbjct: 540 EDVIMAFEQGRIDLHAWVWVRFNGEVEDDDEDTEPLKTETLEDGTRIEQYRYRRDRFDED 599
Query: 561 GNSISKIYDTTPGRMII 577
GN IS+ TT GR+I+
Sbjct: 600 GNLISQYILTTVGRVIM 616
|
Length = 627 |
| >gnl|CDD|179068 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Score = 417 bits (1076), Expect = e-117
Identities = 150/246 (60%), Positives = 182/246 (73%), Gaps = 2/246 (0%)
Query: 1127 DITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIP 1186
DIT GLPRVAELFEAR+PK AI+AEI GT+ + K K R+VI P D E EY IP
Sbjct: 908 DITGGLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITP--DDGEEREYLIP 965
Query: 1187 KNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHK 1246
K KH +Q+GDHVE GD + DG+ P DILR+ GVEA+ +YL+NEVQ+VYRL+GV IN K
Sbjct: 966 KGKHLLVQEGDHVEAGDKLTDGSIDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDK 1025
Query: 1247 HIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITK 1306
HIEV+VR ML+KV ITDP DT+++ G+ VDR E EE NR L +GK+ + P+L GITK
Sbjct: 1026 HIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITK 1085
Query: 1307 ASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRV 1366
ASL T+SF+SAASFQETT+VLTEAAI GKVD L G KENVI+GR IPAGTG + +V
Sbjct: 1086 ASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKV 1145
Query: 1367 AMNRDQ 1372
D+
Sbjct: 1146 EPAVDE 1151
|
Length = 1156 |
| >gnl|CDD|162830 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
Score = 321 bits (824), Expect = 1e-87
Identities = 134/244 (54%), Positives = 170/244 (69%), Gaps = 3/244 (1%)
Query: 1121 SSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRN-YKNKSRVVIEPFEDGVE 1179
+ + DIT GLPRV ELFEAR PK+ A++AE+ GT+ I + KNK VVI+ D E
Sbjct: 899 VAGASGDITQGLPRVKELFEARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDEND--E 956
Query: 1180 PAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLE 1239
+Y IP ++DGD V GD + +G+ P D+LRIKG++A+ YL+ EVQ+VYRL+
Sbjct: 957 EKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQ 1016
Query: 1240 GVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSP 1299
GV IN KHIEV+VR ML+KV ITD D+ + G+ +D E E NR L +QGKK S P
Sbjct: 1017 GVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIP 1076
Query: 1300 ILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
L GITKASL T+SF+SAASFQETTKVLT+AAI GKVD L G KENVI+G IPAGTG
Sbjct: 1077 QLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLK 1136
Query: 1360 LHEK 1363
+++
Sbjct: 1137 TYKE 1140
|
Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. Length = 1140 |
| >gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional | Back alignment and domain information |
|---|
Score = 229 bits (586), Expect = 4e-60
Identities = 117/233 (50%), Positives = 155/233 (66%), Gaps = 5/233 (2%)
Query: 1127 DITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIP 1186
DIT GLPRVAELFEAR+PK A+LAEISGT++I + K + + I + EY +
Sbjct: 1006 DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGD-KTEKTLTIHDQDGNSR--EYVVS 1062
Query: 1187 KNKHFY--LQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAIN 1244
F ++DG V G I G+ P D+LR+ Y++++VQ+VY +GV IN
Sbjct: 1063 ARVQFMPGVEDGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDIN 1122
Query: 1245 HKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGI 1304
KHIEV+ R ML+KV +T+P D++Y+ G V+R E E+ +L +GK+ P+L GI
Sbjct: 1123 DKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGI 1182
Query: 1305 TKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTG 1357
TKASL T S++SAASFQETTKVLT+AAI GKVD L G KENVI+G+ IPAGTG
Sbjct: 1183 TKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
|
Length = 1460 |
| >gnl|CDD|177040 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
Score = 192 bits (491), Expect = 5e-49
Identities = 90/262 (34%), Positives = 139/262 (53%), Gaps = 50/262 (19%)
Query: 1099 ALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTI- 1157
A + G+ + GD L L +++ DIT GLP+V +L EAR + IS +
Sbjct: 1102 ATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARS------IDSISMNLE 1155
Query: 1158 -RIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDIL 1216
R++ + +R++ P+ F + + +
Sbjct: 1156 KRLEGWNERITRILGIPW---------------GFLIGAELSIAQ--------------S 1186
Query: 1217 RIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYIL-GDNV 1275
+I L+N++Q+VYR +GV I+ KHIE++VR M KV +++ + L G+ +
Sbjct: 1187 QI--------SLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELI 1238
Query: 1276 DRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGK 1335
+ E +NR+L ++ + + PIL GITKASL T+SFIS ASFQETT+VL +AA+ G+
Sbjct: 1239 GLLRAERINRAL----EEAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGR 1294
Query: 1336 VDTLDGFKENVIVGRSIPAGTG 1357
+D L G KENVI+G IPAGTG
Sbjct: 1295 IDWLKGLKENVILGGLIPAGTG 1316
|
Length = 1364 |
| >gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
Score = 44.1 bits (105), Expect = 3e-04
Identities = 39/212 (18%), Positives = 77/212 (36%), Gaps = 52/212 (24%)
Query: 1148 AILAEISGTIR-IKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206
A++ EI G R + +GV A + + D ++ +
Sbjct: 145 AVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALW---------KFSDILD--VNRI 193
Query: 1207 DGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPAD 1266
N + +L G+EA ++ E+ V+++ G+A++ +H+ ++ +M +
Sbjct: 194 YTNDI-HAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFE-------- 244
Query: 1267 TEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKV 1326
G NR + S SP+ + SF+ T
Sbjct: 245 -----G------GYRPFNRIGMES-----STSPLQK---------------MSFETTLAF 273
Query: 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358
L +A + G +D L ++VG+ + GTG
Sbjct: 274 LKKATLNGDIDNLSSPSSRLVVGKPVNGGTGL 305
|
RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 309 |
| >gnl|CDD|128909 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus | Back alignment and domain information |
|---|
Score = 418 bits (1076), Expect = e-117
Identities = 150/296 (50%), Positives = 186/296 (62%), Gaps = 24/296 (8%)
Query: 238 WMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNE 297
WMI+ LPV PP LRP V+LD GRFA DL L R +I RNNRL RL L APE IIRNE
Sbjct: 2 WMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPEHIIRNE 61
Query: 298 KRMLQESVDALFDNG--RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRS 355
KR+LQE+VD LFDN R +G RPLKSLS LKGK+GRFR NLLGKRVD+S RS
Sbjct: 62 KRLLQEAVDTLFDNEGLPRARQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARS 118
Query: 356 VIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKK------------------GYVSTVK 397
VI P L+L++ G+PK +ALEL P + L G + +K
Sbjct: 119 VITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGPNGAKYIIRGKKTNLK 178
Query: 398 QAKK-FVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVC 456
AK+ + K V V+ VVL NR P+LHR+S+QA +++ GK I+L+PLVC
Sbjct: 179 LAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVC 238
Query: 457 AGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGL 512
+ YNADFDGD+M ++ S EA+ EAR LML NN+L P +G P+ P QDM+LGL
Sbjct: 239 SPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGL 294
|
Length = 295 |
| >gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 128 bits (324), Expect = 7e-30
Identities = 85/338 (25%), Positives = 149/338 (44%), Gaps = 60/338 (17%)
Query: 235 NPGWMI-IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRV------IGRNNRLMRLKSL 287
+P M + L V P RP L + +V I + + M+ K
Sbjct: 323 DPSDMFFLDNLLVPPTRFRPPSMLG-DEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLD 381
Query: 288 HAPEIIIRNEKRM----------LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQ 337
++I+ + + LQ SV+ LFD+ + +R + +L+ K+
Sbjct: 382 EELKLILERLRGIFSKLINAWLQLQASVNVLFDSKMASK----WSRDSPPGIKQILEKKE 437
Query: 338 GRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP-----FLYAQL----- 387
G FR +++GKRV+Y+ RSVI P ++ ++ G+P + A +L P + +L
Sbjct: 438 GLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTPWNVNELRKAVI 497
Query: 388 -------------EKKGYVS-----TVKQ----AKKFVEKERPEVWDVLAEVVHQH---- 421
++ G ++ T +Q A + + + + VH+H
Sbjct: 498 NGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNG 557
Query: 422 -VVLLNRAPSLHRLSMQAFEPKIISG-KAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQ 479
VVL+NR P+LH+ S+ A + +++ G K ++LH C YNADFDGD+M V+ S A+
Sbjct: 558 DVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIAR 617
Query: 480 LEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLST 517
EA + + + L P G P+ QD ++ L+
Sbjct: 618 AEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTM 655
|
Length = 1640 |
| >gnl|CDD|179447 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Score = 377 bits (971), Expect = e-105
Identities = 199/562 (35%), Positives = 300/562 (53%), Gaps = 62/562 (11%)
Query: 592 CNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKE 651
N+ + KK + ++ +++ G T D+L LGFRYA +G+S DD+ VP +K
Sbjct: 4 RNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKR 63
Query: 652 KIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETG 711
++ +A++ + E +Y G IT E++ KV+D W +T +++ +E++ + + DP
Sbjct: 64 DLLEQAEEEITATEERYRRGEITEVERFQKVIDTWNETNERLKDEVVKNFR--QNDP--- 118
Query: 712 RQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQ 771
+NS++MM+ SGARG++ Q+RQL GMRGL+A P GEII+ PI+++F+ GL E+
Sbjct: 119 ----LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTVTEYVI 174
Query: 772 SCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYS 831
S G RKGL+D +RTA SGYL+RRLVDV+Q+ +V + DC T +G+ + + D +V+
Sbjct: 175 SSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIP 234
Query: 832 LGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGV 891
LG R+LGR +D+++P E I + I +IEK G+ V +RS LTCE++R V
Sbjct: 235 LGDRLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSV 293
Query: 892 CVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCD 951
C CYG LA LV++GEAVG+IAAQSIGEPGTQLTMRTFH GG T + SP
Sbjct: 294 CRKCYGWSLAHNHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFA 353
Query: 952 GIV----KIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVI 1007
G V K++ R + + + L + + I G+ LFVDDG +
Sbjct: 354 GTVEFGKKLRTRPYRTRHGVEALQAEVDFDLVLKPSGKGKPQKIEITQGSLLFVDDGQTV 413
Query: 1008 ECGQRISE---------WDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVI 1058
E Q ++E + T +I +++G V F DL+ + G +T A+R +
Sbjct: 414 EADQLLAEVAAGAVKKSTEKATKDVICDLAGEVRFADLIPE-EKTDRQGNTTRKAQRGGL 472
Query: 1059 DWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLA-- 1116
W + NL P A VS G +V GDVLA
Sbjct: 473 LWVLSGDVYNLPP--------------------------GAEPVVSNGDRVEEGDVLAET 506
Query: 1117 ----------RLPISSAKTKDI 1128
RL SS ++++
Sbjct: 507 KLVSEHGGVVRLRESSGDSREV 528
|
Length = 1331 |
| >gnl|CDD|162831 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
Score = 351 bits (903), Expect = 6e-97
Identities = 211/621 (33%), Positives = 312/621 (50%), Gaps = 81/621 (13%)
Query: 593 NQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEK 652
N+ + KK + ++ Y+ G T A D L LGFRYA +G+S DD+ VP +K+
Sbjct: 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQD 63
Query: 653 IIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGR 712
++ A+K ++ E +Y G IT E++ KV+D W T +++ +E++ ++ DP
Sbjct: 64 LLEAAEKEIRATEERYRRGEITEVERFQKVIDTWNGTNEELKDEVVNNFRQT--DP---- 117
Query: 713 QKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQS 772
+NS++MM+ SGARG++ Q+RQL GMRGL+A P GEII+ PI+++F+ GL E+ S
Sbjct: 118 ---LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTVTEYVIS 174
Query: 773 CVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSL 832
G RKGL+D +RTA SGYL+RRLVDV+Q+ +V + DC T++ + + + + + + SL
Sbjct: 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI-SL 233
Query: 833 GSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVC 892
G R+LGR +D+++P E IV I IE GI V +RS LTCE++R VC
Sbjct: 234 GDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVC 292
Query: 893 VLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDG 952
CYG LA LV++GEAVG+IAAQSIGEPGTQLTMRTFH GG T + S DG
Sbjct: 293 RKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDG 352
Query: 953 IV----KIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRI--MYGAKLFVDDGGV 1006
V K++ R D + L I + I G+ LFV+DG
Sbjct: 353 TVEFGKKLRTRGYRTRHGEDAKQVEVAGLLIIKPTGSITNKAQEIEVTQGSLLFVEDGQT 412
Query: 1007 IECGQRISE---------WDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKV 1057
++ GQ ++E + T + ++++G V F D V + G +T IA+R
Sbjct: 413 VDAGQLLAEIALGAVRKSTEKATKDVASDLAGEVKF-DKVVPEEKTDRQGNTTRIAQRGG 471
Query: 1058 IDWRFASRSQNLKP--------------------AIVVTDENGVVLKSARGTDARWFLPV 1097
+ W + NL P + T+ GVV D+R +
Sbjct: 472 LIWVLSGEVYNLPPGAEPVVKNGDRVEQGTVLAETKLSTEHGGVVRLPESVGDSREVEII 531
Query: 1098 DA------------------------------LLSVSPGQKVSTGDVLARLPISSAKTKD 1127
A L +PG KV G V+A L +T
Sbjct: 532 TASVLLDQAKVIEESSQGRELYHIETADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTT- 590
Query: 1128 ITSGLPRVA--ELFEARRPKN 1146
T GL + A E+ + + K
Sbjct: 591 -TGGLLKYAGVEVAKKGKAKQ 610
|
The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. Length = 1227 |
| >gnl|CDD|177040 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
Score = 334 bits (858), Expect = 1e-91
Identities = 145/379 (38%), Positives = 212/379 (55%), Gaps = 18/379 (4%)
Query: 592 CNQEMIKKNISAMVDTIYR---HCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPE 648
N+ + K A+ I H G T D L LGF+ A ++GIS G DD++ P
Sbjct: 10 HNKVIDKT---ALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPP 66
Query: 649 SKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDP 708
SK ++ +A++ E Y+ G + EK + +++W T++ + +EM + DP
Sbjct: 67 SKGWLVQDAEQQSLILEKHYHYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFR--MTDP 124
Query: 709 ETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFE 768
+N ++MMS SGARG+ Q+ QL GMRGL++ P G+II+ PI+S+F+ GL E
Sbjct: 125 -------LNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQSNFREGLSLTE 177
Query: 769 FFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQV 828
+ SC G RKG++D +RTA +GYL+RRLV+V Q+ VV + DC T +G++++ + +
Sbjct: 178 YIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVS-PRNGMMI 236
Query: 829 VYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESS 888
L ++GR DDI + + CI Q I N + + IRS LTC S+
Sbjct: 237 ERILIQTLIGRVLADDIY--IGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRST 294
Query: 889 RGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIES 948
+C LCYG LA G LV +GEAVG+IA QSIGEPGTQLT+RTFH GG T + +
Sbjct: 295 SWICQLCYGWSLAHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQVRA 354
Query: 949 PCDGIVKIKNRNVCRNSTN 967
P +G +K V T
Sbjct: 355 PFNGKIKFNEDLVHPTRTR 373
|
Length = 1364 |
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
Score = 308 bits (791), Expect = 5e-84
Identities = 154/403 (38%), Positives = 241/403 (59%), Gaps = 31/403 (7%)
Query: 980 ILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE-----------WDPHTFPIITEVS 1028
I D +G+E H I G+++ +DD + IS+ WDP+ PII +
Sbjct: 2496 IADDNGREAARHYIARGSEILIDDNSEVSANSVISKPTTNTFKTIATWDPYNTPIIADFK 2555
Query: 1029 GTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARG 1088
G V F D++ G++V E E+TGI V D+ + KP++ + A G
Sbjct: 2556 GKVSFVDIIAGVTVAEKEDENTGITSLVVNDYIPSG----YKPSLFLE--------GANG 2603
Query: 1089 TDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEAR--RPKN 1146
+ R+FL +++S G V +VLA++P ++ K++DIT GLPRV+ELFEAR +PK+
Sbjct: 2604 EEIRYFLEPKTSIAISDGSSVEQAEVLAKIPKATVKSRDITGGLPRVSELFEARKPKPKD 2663
Query: 1147 HAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206
AIL+E+ G + + +NK +++ +DG +YF+ K K + + V G+ +
Sbjct: 2664 VAILSEVDGIVSFGKPIRNKEHIIVTS-KDG-RSMDYFVDKGKQILVHADEFVHAGEAMT 2721
Query: 1207 DGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPAD 1266
DG DILRI G + L Y+++EVQ+VYR +GV+I KHIE++V ML++V I D D
Sbjct: 2722 DGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGD 2781
Query: 1267 TEYILGDNVDRIEVEELN-RSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTK 1325
+++I GD V + +E N R +A +G+ ++ P+L GIT+A++ + S ISAASFQETTK
Sbjct: 2782 SKFIEGDLVSKKLFKEENARVIALKGEPAIA-EPVLLGITRAAIGSDSIISAASFQETTK 2840
Query: 1326 VLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAM 1368
VLTEA+IA K D L+ KENV++GR IP GTG +++ +++ +
Sbjct: 2841 VLTEASIAMKKDFLEDLKENVVLGRMIPVGTG--MYKNKKIVL 2881
|
Length = 2890 |
| >gnl|CDD|147265 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1 | Back alignment and domain information |
|---|
Score = 302 bits (776), Expect = 4e-82
Identities = 132/351 (37%), Positives = 172/351 (49%), Gaps = 44/351 (12%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
+ ++ IASP +I S GE+ KPET NY + KPE GL R+ K
Sbjct: 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGT---------IK 52
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPS--RISTLLGMSL 133
K ICE CGVEVT HI+LA PV H F K + S R L SL
Sbjct: 53 KKS------ICETCGVEVT---ECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSL 103
Query: 134 RDVERVLYFESYVVVDP-GLSSLEKYQILTEEEYVEAVSQFG---------------QDQ 177
E V YF VV+DP G +S ++ + + +++
Sbjct: 104 LLNESVKYFFLKVVIDPKGKNSKKRLKKINNLCKKKSICSKCGEDNGGLKAFEGCGKYQP 163
Query: 178 FIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRR---KKIIKRLKIVDSFITSGN 234
I+ GA+AI LL ++++ L+++L K + KKI K + + F SGN
Sbjct: 164 KISKDGAEAIKALLKNIEIE----ELKEKLRKLNPEKVLQIFKKISKEDEEILGFNPSGN 219
Query: 235 NPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIII 294
P WMI+ LPV PP +RP V LD GRFA DL R +I RNNRL ++ AP II
Sbjct: 220 RPEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLEEGAPSHII 279
Query: 295 RNEKRMLQESVDALFDNG-RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNL 344
R EKR+LQE V LFDN + + RPLKS+S LKGK+GRFR NL
Sbjct: 280 REEKRLLQEHVATLFDNDIPGQPPALQKSGRPLKSISQRLKGKEGRFRGNL 330
|
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand. Length = 330 |
| >gnl|CDD|162833 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
Score = 275 bits (705), Expect = 5e-74
Identities = 241/905 (26%), Positives = 369/905 (40%), Gaps = 198/905 (21%)
Query: 19 DSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKR 78
S++ + SP +I +S E+ +T + + P GL R G I+
Sbjct: 5 GSIKFGLLSPEEIRKMSVVEVVTADTYDDDGY-PIEGGLMDPR-LGVIE----------- 51
Query: 79 MKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVER 138
G+ C+ CG +V HI+LA PV H F K I +L + R R
Sbjct: 52 ---PGLRCKTCGGKV---GECPGHFGHIELARPVVHVGFAKE----IYKILRATCRKCGR 101
Query: 139 VL--------YFESYVVVDPGLSSLEKYQILTEEEYVEAVSQF-----GQDQF-IAMMGA 184
+ Y E + L L E+ EA + G++Q I
Sbjct: 102 ITLTEEEIEQYLEKINKLKEEGGDLAS--TLIEKIVKEAAKRMKCPHCGEEQKKIKFEKP 159
Query: 185 DAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKL 244
YE D++ +R++L K + +++ P WM++ L
Sbjct: 160 TYFYEEGKEGDVKLTPSEIRERLEKIPD--------EDAELL-GINPKVARPEWMVLTVL 210
Query: 245 PVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQES 304
PV P +RP + L+ G + DL +I N RL AP++II + +LQ
Sbjct: 211 PVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYH 270
Query: 305 VDALFDN-------GRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVI 357
V FDN RH+ RPLK+L+ LKGK+GRFR NL GKRV++S R+VI
Sbjct: 271 VATYFDNELPGIPPARHRS------GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVI 324
Query: 358 VAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWD----- 412
P + +++ G+P+ +A EL P + + +++V P+ W
Sbjct: 325 SPDPNISINEVGVPEQIAKELTVPERVTPW-------NIDELREYVLNG-PDSWPGANYV 376
Query: 413 ----------------VLAE------VVHQH-----VVLLNRAPSLHRLSMQAFEPKIIS 445
LAE VV +H +VL NR PSLHR+SM + K++
Sbjct: 377 IRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLP 436
Query: 446 GKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPS 505
GK +L+ VC YNADFDGD+M ++ + EA+ EAR LML ++L P G P+
Sbjct: 437 GKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGI 496
Query: 506 QDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSIS 565
D + G YL T + + EV L Y +
Sbjct: 497 HDYISGA-YLLTHK-----STLFTKE--EVQTILGV----------AGYFGDPPEPAIEK 538
Query: 566 KIYDTTPGRMIIGEILPR----------------------HHEISFDICNQEMI-----K 598
T G+ I LP H+ I N +++ K
Sbjct: 539 PKEYWT-GKQIFSAFLPEDLNFEGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDK 597
Query: 599 KNISA----MVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESK---- 650
K I A ++ I R G ++ F D + RL R+ G + G DDI +P+
Sbjct: 598 KAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEI 657
Query: 651 EKIIAEA----DKMVKEYENQYNDGLITRGEK---YNKVVDLWGKTTDKVTEEMMARIKR 703
E++I +A D +++ Y N + L R + K++++ GK D+ E +
Sbjct: 658 EELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGE-----VAE 712
Query: 704 VEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGM------------RGLIAK----- 746
DPE N +M+ +GARGS+ + Q+ M RG +
Sbjct: 713 KYLDPE-------NHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHF 765
Query: 747 PSGEIIESP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVA 801
G+I +RS FK GL E+F GGR+GL+D +RT+ SGY+ RRL++
Sbjct: 766 KKGDI--GAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINAL 823
Query: 802 QNCVV 806
Q+ V
Sbjct: 824 QDLYV 828
|
This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 868 |
| >gnl|CDD|35481 KOG0260, KOG0260, KOG0260, RNA polymerase II, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 209 bits (534), Expect = 3e-54
Identities = 201/876 (22%), Positives = 328/876 (37%), Gaps = 121/876 (13%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
R SV+ I SP +I +S EI+ PET +P+ GL R+ G
Sbjct: 13 RTVKSVQFGILSPDEIRRMSVAEIEFPET--MEGGRPKLGGLMDPRL-----------GT 59
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTL----LGM 131
R +C+ CG + HI+LA PV HP FLK + + + +
Sbjct: 60 IDRD----SLCQTCGGNMF---ECPGHFGHIELAKPVFHPGFLKKVKKILRCVCFYCSKI 112
Query: 132 SLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELL 191
L + + E D + G
Sbjct: 113 LKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKVVCEGGIDVESDGR-SGCGLKQPSIRR 171
Query: 192 IALDLQN-LALTLRDQLSKSSSIFRR--KKIIKRLKIVDSFITSGN----NPGWMIIRKL 244
+ LDL D + +I KR+ D P WMI+ L
Sbjct: 172 LGLDLWAFWKQGDEDSQESKRKLSAERVLEIFKRISDEDIDQLGFKPKIARPEWMILTVL 231
Query: 245 PVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQES 304
PV PP +RP + + DL +I +N L R + AP II +++LQ
Sbjct: 232 PVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFH 291
Query: 305 VDALFDNG-RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPEL 363
V DN + + RPLKS+S LKGK+GR R NL+GKRVD+S R+VI P L
Sbjct: 292 VATYVDNDIPGQPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNL 351
Query: 364 QLHQCGLPKLMAL-----ELFKPFLYAQLEK-----------KGYVSTVKQAKKFVEKER 407
L + G+P+ +A E PF +L++ Y+ + +
Sbjct: 352 SLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYI-IRDNGDRIDLRYH 410
Query: 408 PEVWDV---LAEVVHQH-----VVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGY 459
D+ V +H VVL NR PSLH++SM A +++ +L+ V + Y
Sbjct: 411 KRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRLNLSVTSPY 470
Query: 460 NADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVH 519
NADFDGD+M ++ S E + E L + ++ P S PV QD + T
Sbjct: 471 NADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTA-VRKMTKR 529
Query: 520 EG--DPGEGMLFADMGEVYHA-------------------LENKIVTLHSKIRGRYKSVD 558
+ + + M + + + I+ + +
Sbjct: 530 DVFLNRAQVMNLLMYVPDWDGPPPAKPAILKPKPLWTGKQIFSLIIPGGINYIRDHSTHP 589
Query: 559 KDGNSISKIYDTTPGRMII--GEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKS 616
+ + DT R++I GE+ + +C + + + +V I+ G K
Sbjct: 590 DSEDELISPGDT---RVLIEGGEL------LIGVLCKKTV-GSSAGGLVHVIFLEKGPKI 639
Query: 617 TVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRG 676
F D + L + G S G D I + +I + + + + R
Sbjct: 640 ARGFFDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNT--IKEAKRDVLA---VIRE 694
Query: 677 EKYNKVVDLWGKTTDKVTEEMMARI-KRVEFDPETGRQK---KMNSIFMMSHSGARGSIH 732
+ N++ G+T + E + R+ + QK + N+ M +G++GS
Sbjct: 695 AQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVVAGSKGSFI 754
Query: 733 QMRQLG---------GMR---GLIAKPSGEIIESP--------IRSHFKGGLCGFEFFQS 772
+ Q+ G R G + + + + + GL EFF
Sbjct: 755 NISQVSACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFH 814
Query: 773 CVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQ 808
+GGR+GL+D ++TA +GY+ RRL+ ++ +V
Sbjct: 815 AMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAY 850
|
Length = 1605 |
| >gnl|CDD|181474 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
Score = 262 bits (673), Expect = 3e-70
Identities = 197/672 (29%), Positives = 293/672 (43%), Gaps = 153/672 (22%)
Query: 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIR 295
P WM++ LPV P +RP + L+ G+ + DL +I N RL AP++II
Sbjct: 206 PEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIE 265
Query: 296 NEKRMLQESVDALFDN-------GRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKR 348
+ +LQ V FDN RH+ RPLK+L+ LKGK+GRFR NL GKR
Sbjct: 266 DLWELLQYHVTTYFDNEIPGIPPARHRS------GRPLKTLAQRLKGKEGRFRGNLSGKR 319
Query: 349 VDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVST--VKQAKKFVEKE 406
V++S R+VI P L +++ G+P+ +A EL P V+ +++ +++V
Sbjct: 320 VNFSARTVISPDPNLSINEVGVPEAIAKELTVPE---------RVTEWNIEELREYVLNG 370
Query: 407 RPEVW---------------------DVLAE------VVHQH-----VVLLNRAPSLHRL 434
PE + LAE +V +H +VL NR PSLHR+
Sbjct: 371 -PEKHPGANYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRM 429
Query: 435 SMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494
S+ A +++ GK +L+ VC YNADFDGD+M ++ + EA+ EAR+LML ++L
Sbjct: 430 SIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILS 489
Query: 495 PASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRY 554
P G P+ QD + G YL T + LF E L
Sbjct: 490 PRYGGPIIGGIQDHISGA-YLLTR------KSTLF-TKEEALDLLR----------AAGI 531
Query: 555 KSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISF--------DICNQEMI--------- 597
+ + +I G+ I LP+ + F D C +E
Sbjct: 532 DELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIK 591
Query: 598 ----------KKNISA----MVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDD 643
KK I A ++D I + G + F D + RL R+ G + G DD
Sbjct: 592 NGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDD 651
Query: 644 I-IVPESKEKI---IAEADKMVKEYENQYNDGLI------TRGEKY-NKVVDLWGKTTDK 692
I E+KE+I I EA+K V+E Y +G + T E K++ + GK D+
Sbjct: 652 EDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDE 711
Query: 693 VTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGG---------M 740
I + N +M+ +GARGS + QM G
Sbjct: 712 A-----GEIAEKYLGLD-------NPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIR 759
Query: 741 RGLIAK-----PSGEIIESP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASS 790
RG + G++ +RS +K GL EFF +GGR+GL+D +RT+ S
Sbjct: 760 RGYRDRTLPHFKPGDL--GAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQS 817
Query: 791 GYLSRRLVDVAQ 802
GY+ RRL++ Q
Sbjct: 818 GYMQRRLINALQ 829
|
Length = 882 |
| >gnl|CDD|179447 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Score = 259 bits (664), Expect = 4e-69
Identities = 133/307 (43%), Positives = 174/307 (56%), Gaps = 24/307 (7%)
Query: 1073 IVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGL 1132
+ V L+ R + + A+L V G V GD LA L AKT DI GL
Sbjct: 928 VEAVSGGSVTLRLGR----PYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGL 983
Query: 1133 PRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRV-VIEPFEDGVEPAEYFIPKNKHF 1191
PR+ EL EAR+PK ILA+ GT++IK V VIE DG EY I ++
Sbjct: 984 PRIEELLEARKPKESCILAKKPGTVQIKYGDDESVDVKVIE--SDGTI-TEYPILPGQNV 1040
Query: 1192 YLQDGDHVEKGDYILDGNPVPQDILRI----------------KGVEALASYLINEVQEV 1235
+ DG V+ G+ + DG P ++L I + ++ L +L+NEVQ V
Sbjct: 1041 MVSDGQQVDAGEPLTDGPINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNV 1100
Query: 1236 YRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLV 1295
Y+ +GV I+ KHIEV+VR M KV I D DT + G+ ++ +VE++N ++A G
Sbjct: 1101 YQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPA 1160
Query: 1296 SFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAG 1355
++P+L GITKASL T SFISAASFQETT+VLTEAAI GK D L G KENVI+GR IPAG
Sbjct: 1161 EYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAG 1220
Query: 1356 TGAILHE 1362
TG E
Sbjct: 1221 TGFSGFE 1227
|
Length = 1331 |
| >gnl|CDD|162831 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
Score = 237 bits (607), Expect = 1e-62
Identities = 129/308 (41%), Positives = 178/308 (57%), Gaps = 21/308 (6%)
Query: 1072 AIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSG 1131
I + V+L+ R + + A+L + G V GD LA L AKT DI G
Sbjct: 925 EIEEVASDYVILRIGR----PYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQG 980
Query: 1132 LPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHF 1191
LPR+ EL EAR+PK ILA+ G +++K ++S V I+ E +EY + ++
Sbjct: 981 LPRIEELLEARKPKEACILAKRPGVVQVKYGTDDES-VSIKVIERDGTISEYPLLPGQNI 1039
Query: 1192 YLQDGDHVEKGDYILDGNPVPQDILRI----------------KGVEALASYLINEVQEV 1235
+ DG V G+ + DG P DIL + + ++ + +L+NEVQ V
Sbjct: 1040 MVSDGQQVTGGEPLTDGPINPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNV 1099
Query: 1236 YRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLV 1295
Y+ +GV I+ KHIEV+VR M KV I D DT + G+ V+ +VE++N ++A G
Sbjct: 1100 YQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPA 1159
Query: 1296 SFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAG 1355
++P+L GITKASL T SFISAASFQETT+VLTEAAI GK D L G KENVI+GR IPAG
Sbjct: 1160 QYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAG 1219
Query: 1356 TGAILHEK 1363
TG +E+
Sbjct: 1220 TGFSSYEE 1227
|
The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. Length = 1227 |
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
Score = 257 bits (657), Expect = 2e-68
Identities = 256/1102 (23%), Positives = 432/1102 (39%), Gaps = 196/1102 (17%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
+ D + + SPA + + EI PE + P + GL R+ G I+
Sbjct: 7 KAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRL-GTIE-------- 56
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRD 135
G C CG L++ HI+LA PV H F+ I LL +
Sbjct: 57 ------PGQKCLTCG---NLAANCPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHK 103
Query: 136 VERVLYFESYVVVDPGLSSLEKY-----QILTEEEYVEAVSQF--------------GQD 176
++ + + V + + ++E +E V G
Sbjct: 104 CAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCGAP 163
Query: 177 QFIAMMGADAIYELLIALDLQN---LALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSG 233
Q + + +++ L + +RD K II + F
Sbjct: 164 QHELEF--EEPTIFIEKTEIEEHRLLPIEIRDIFEK---------IIDDDLELIGFDPKK 212
Query: 234 NNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEII 293
P W +++ V P RP + L+ G + DL + +I N +L K AP +I
Sbjct: 213 ARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLI 272
Query: 294 IRNEKRMLQESVDALFDNG------RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGK 347
+ +E LQ FDN H + + RPLKSL LKGK+GRFR NL+GK
Sbjct: 273 VEDEVDHLQYHTSTFFDNATAGIPQAHHK----GSGRPLKSLFQRLKGKEGRFRGNLIGK 328
Query: 348 RVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP---------------------FLYAQ 386
RVD+S R+VI P + + + G+P+ +A++L P F A
Sbjct: 329 RVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGAN 388
Query: 387 LEKKGYVSTVKQAKKFVEKERPEVWDVLAE------VVHQH-----VVLLNRAPSLHRLS 435
+KG K F+E + + AE +V +H +V+ NR PSLH+LS
Sbjct: 389 AIRKGDG--TKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLS 446
Query: 436 MQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHP 495
+ A K++ G +LHP VC YNADFDGD+M ++ +A+ EA LM +NL+ P
Sbjct: 447 ILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISP 506
Query: 496 ASGAPVTVPSQDMVLGLCYLSTVHEG--DPGEGMLFADMGEVYHALENKIVTLHSKIRGR 553
+G P+ QD + YL T + D E A + + L +
Sbjct: 507 RTGGPIIGALQDFITAA-YLITKDDALFDKNEASNIAMLAGITDPLPEPAIKTKDGPAWT 565
Query: 554 YKS-----VDKDGN--SISKIYDTT------PGRMIIGEILPRHHEISFDICNQEMI--- 597
K + KD N I+K P + G +L + E+ + + +I
Sbjct: 566 GKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGAL 625
Query: 598 KKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEA 657
+ +++D I + G+ + F + ++ + + G S G D+I+P+ ++ I +
Sbjct: 626 VEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIED- 684
Query: 658 DKMVKEYENQYND-GLITRGEKYNKVVDLWGKTTDKVT-----EEMMARIKRVEFDPETG 711
+ + ++ + K + + ++ K +++ EE + E D
Sbjct: 685 -----DIQGMKDEVSDLIDQRKITRKITIY-KGKEELLRGMKEEEALEADIVNELDKARD 738
Query: 712 RQKKM--------NSIFMMSHSGARGSIHQMRQLGG--------MRGLIAKPSGEIIE-- 753
+ N+ +M+ +GARGS+ + Q+ G R G + E
Sbjct: 739 KAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGY 798
Query: 754 -------------SP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSR 795
+P ++++++ GL EFF +GGR+GL+D RT SGY R
Sbjct: 799 KDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQR 858
Query: 796 RLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINP---LTNE 852
RL + ++ + + D + HI+ Q + + + N + +
Sbjct: 859 RLANALEDIRL-EYDETVRD--PHGHII---QFKFGEDGIDPQKLDHGEAFNLERIIEKQ 912
Query: 853 CIVKAGQLILESHVNEIEKCGIRSVRIRSALTCE--------SSRGVCVLCY-GRDLARG 903
I G+ + + E+ K ++ + +C G++
Sbjct: 913 KIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELEAICAEGKEGFEK 972
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGA----VTVMDRSFIE------SPCDGI 953
+ V G+A+G+I+AQSI EPGTQ+T+RTFH G VT FIE P
Sbjct: 973 AKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPT 1032
Query: 954 VKIKNRNVCRNSTNDLISMGRN 975
+ I + C+ I + RN
Sbjct: 1033 MDIYLDDECKEDIEKAIEIARN 1054
|
Length = 1321 |
| >gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
Score = 228 bits (584), Expect = 8e-60
Identities = 92/151 (60%), Positives = 111/151 (73%), Gaps = 2/151 (1%)
Query: 1209 NPVPQDILRIK--GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPAD 1266
P D+LRIK G EA+ YL+ E+Q+VYR +GV IN KHIE++VR M KV+I DP D
Sbjct: 53 KINPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGD 112
Query: 1267 TEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKV 1326
+ ++ G+ VD E EE N+ L GKK + P+L GITKASL T+SFISAASFQETTKV
Sbjct: 113 SGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKV 172
Query: 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTG 1357
LTEAAI GK+D L G KENVI+GR IPAGTG
Sbjct: 173 LTEAAIEGKIDWLRGLKENVILGRLIPAGTG 203
|
Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations. Length = 204 |
| >gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
Score = 95.9 bits (239), Expect = 7e-20
Identities = 42/149 (28%), Positives = 69/149 (46%), Gaps = 42/149 (28%)
Query: 1212 PQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYIL 1271
++L G+EA +I E+Q+V +GV+++ +HIE++ M
Sbjct: 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMT--------------- 94
Query: 1272 GDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASL--QTKSFISAASFQETTKVLTE 1329
+S L+G+T++ S + ASF++TTK L +
Sbjct: 95 -------------------------YSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLLD 129
Query: 1330 AAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358
AA AG+ D L+G EN+I+GR P GTG+
Sbjct: 130 AAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. Length = 158 |
| >gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
Score = 59.6 bits (145), Expect = 6e-09
Identities = 38/151 (25%), Positives = 69/151 (45%), Gaps = 44/151 (29%)
Query: 1212 PQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRH-MLQKVEITDPADTEYI 1270
+I + G+EA + +INE++ +G ++V +RH ML + D
Sbjct: 248 IHEIEEVLGIEAARNAIINEIKRTLEEQG-------LDVDIRHIML----VAD------- 289
Query: 1271 LGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITK--ASLQTKSFISAASFQETTKVLT 1328
++++ ++ I + + + S ++ A+F+ T K L
Sbjct: 290 -----------------------IMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLL 326
Query: 1329 EAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
+AA+ G+VD L G EN+IVG+ IP GTG +
Sbjct: 327 DAAVRGEVDELRGVIENIIVGQPIPLGTGDV 357
|
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. Length = 363 |
| >gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
Score = 58.8 bits (143), Expect = 1e-08
Identities = 40/146 (27%), Positives = 69/146 (47%), Gaps = 38/146 (26%)
Query: 1214 DILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGD 1273
++ ++ G+EA S +INE+Q + G++I+ +HI ++ M K E+ LG
Sbjct: 193 EVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEV---------LG- 242
Query: 1274 NVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIA 1333
+ R GI K +S + ASF++TT L AA+
Sbjct: 243 ---------ITR----------------FGIAKMK---ESVLMLASFEKTTDHLFNAALH 274
Query: 1334 GKVDTLDGFKENVIVGRSIPAGTGAI 1359
G+ D+++G E +I+G+ +P GTG
Sbjct: 275 GRKDSIEGVSECIIMGKPMPIGTGLF 300
|
Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 300 |
| >gnl|CDD|179818 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
Score = 58.3 bits (142), Expect = 1e-08
Identities = 44/146 (30%), Positives = 68/146 (46%), Gaps = 44/146 (30%)
Query: 1215 ILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRH-MLQKVEITDPADTEYILGD 1273
I + G+EA + +I E++ +G ++V +RH ML AD G
Sbjct: 268 IEEVLGIEAARNAIIEEIKNTLEEQG-------LDVDIRHIMLV-------ADMMTWDG- 312
Query: 1274 NVDRIEVEELNRSLAQQGKKLVSFSPILQGIT--KASLQTKSFISAASFQETTKVLTEAA 1331
EV ++ R G++ KAS+ ++ A+F+ T K L +AA
Sbjct: 313 -----EVRQIGR----------------HGVSGEKASV-----LARAAFEVTVKHLLDAA 346
Query: 1332 IAGKVDTLDGFKENVIVGRSIPAGTG 1357
+ G+VD L G EN+IVG+ IP GTG
Sbjct: 347 VRGEVDELKGVTENIIVGQPIPLGTG 372
|
Length = 383 |
| >gnl|CDD|184891 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
Score = 57.9 bits (140), Expect = 2e-08
Identities = 43/149 (28%), Positives = 67/149 (44%), Gaps = 41/149 (27%)
Query: 1214 DILRIK---GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYI 1270
DI+ I G+EA + +I+E + + +G+ ++ +HI +V AD
Sbjct: 388 DIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLV-------------ADMMTF 434
Query: 1271 LGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEA 1330
G V+ + R GI S + S ++ A+F+ T K L A
Sbjct: 435 DG------SVKAIGR----------------HGI---SGEKSSVLARAAFEITGKHLLRA 469
Query: 1331 AIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
I G+VD L G EN+IVG+ I GTGA+
Sbjct: 470 GILGEVDKLAGVAENIIVGQPITLGTGAV 498
|
Length = 509 |
| >gnl|CDD|184892 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
Score = 52.6 bits (126), Expect = 8e-07
Identities = 50/189 (26%), Positives = 87/189 (46%), Gaps = 46/189 (24%)
Query: 1185 IPKNKHFYLQDGDHVEKGDYIL--DGNPVPQDILRIKGVEALASYL--INEVQEVYRLEG 1240
IP + ++ +H +Y+L G+ + +++ +I+GV+ + I E+QEV +E
Sbjct: 688 IPGIERVLVKKEEHENDEEYVLYTQGSNL-REVFKIEGVDTSRTTTNNIIEIQEVLGIEA 746
Query: 1241 V----------AINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQ 1290
+ + +EV +RH++ +I AD E V+ + R
Sbjct: 747 ARNAIINEMMNTLEQQGLEVDIRHLMLVADIMT-ADGE-----------VKPIGR----- 789
Query: 1291 GKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGR 1350
G+ + + S ++ A+F+ET K L +AA G+VD L G ENVIVG+
Sbjct: 790 -----------HGV---AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGK 835
Query: 1351 SIPAGTGAI 1359
I GTG +
Sbjct: 836 PIKLGTGCV 844
|
Length = 858 |
| >gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 48.4 bits (115), Expect = 1e-05
Identities = 33/140 (23%), Positives = 56/140 (40%), Gaps = 42/140 (30%)
Query: 1220 GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279
G+EA + +I+E+ G++I+ +HI ++ M + E+
Sbjct: 1255 GIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVL----------------- 1297
Query: 1280 VEELNRSLAQQGKKLVSFSPILQGITKASLQ--TKSFISAASFQETTKVLTEAAIAGKVD 1337
GIT+ L S + ASF++T L +AA GK D
Sbjct: 1298 -----------------------GITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKD 1334
Query: 1338 TLDGFKENVIVGRSIPAGTG 1357
++G E +I+G + GTG
Sbjct: 1335 AIEGVSECIILGIPMCIGTG 1354
|
Length = 1386 |
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
Score = 46.6 bits (110), Expect = 4e-05
Identities = 28/146 (19%), Positives = 65/146 (44%), Gaps = 32/146 (21%)
Query: 1214 DILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGD 1273
+I G+EA + + NE+ + +G+ +++++I +V M +
Sbjct: 1198 EIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSR--------------G 1243
Query: 1274 NVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIA 1333
++ I ++ G+K S ++ A+F+ TT + AA+
Sbjct: 1244 TIEAIGLQAAGVRHGFAGEK------------------DSPLAKAAFEITTHTIAHAALG 1285
Query: 1334 GKVDTLDGFKENVIVGRSIPAGTGAI 1359
G+++ + G + +I+G++IP G+G +
Sbjct: 1286 GEIEKIKGILDALIMGQNIPIGSGKV 1311
|
Length = 1321 |
| >gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional | Back alignment and domain information |
|---|
Score = 216 bits (551), Expect = 4e-56
Identities = 83/136 (61%), Positives = 109/136 (80%)
Query: 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECIC 73
D FD++RIS+AS I S S+GE+KKPETINYRT KPE+DGLFC +IFGP KD+EC C
Sbjct: 5 DVTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECAC 64
Query: 74 GKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSL 133
GKYKR+++KGI+CE+CGVEVT + VRR+RM HI+LA+PV+H W+ K PSR+ LL +
Sbjct: 65 GKYKRIRFKGIVCERCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKP 124
Query: 134 RDVERVLYFESYVVVD 149
+D+E+VLYF SY++
Sbjct: 125 KDLEKVLYFASYIITS 140
|
Length = 1460 |
| >gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 214 bits (546), Expect = 1e-55
Identities = 203/836 (24%), Positives = 333/836 (39%), Gaps = 161/836 (19%)
Query: 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRR---VIGRNNRLMRLKSLHAPEI 292
P +II ++PV P +RP V + A ++ +DL + +I N+ + + S P
Sbjct: 245 PENLIITRVPVPPVCIRPSVMSEDK--AGTNEDDLTMKLTEIILTNDVIKKHLSKGTPIN 302
Query: 293 IIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYS 352
+I + LQ V ++ + A ++P + LKGKQGRFR NL GKRVD+S
Sbjct: 303 LIMEDWDFLQLQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFS 362
Query: 353 GRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKK----------------GYVSTV 396
GR+VI P L++ + G+P +A L P + + YV
Sbjct: 363 GRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLRQLVRNGPNVHPGANYVVQR 422
Query: 397 K-QAKKFVE-KERPEVWDVLA--EVVHQH-----VVLLNRAPSLHRLSMQAFEPKIISGK 447
K+F++ R ++ D L +VV +H VVL NR PSLH++S+ + K++ +
Sbjct: 423 GEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWR 482
Query: 448 AIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQD 507
+ + VC YNADFDGD+M ++ + EA+ EA VLM NNL+ P +G P+ +QD
Sbjct: 483 TFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQD 542
Query: 508 MVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKI 567
+ G YL T + F D E L S + +D +I K
Sbjct: 543 FITGG-YLLTHKD-------TFLDRAEFSQ--------LCSYMSDAMTHIDLPPPAILKP 586
Query: 568 YDTTPGRMIIGEILPRHHEI-------------------SFDICNQE---MIKKN--ISA 603
+ G+ + ++ + + SF++C + +I+ + IS
Sbjct: 587 VELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLVKGKSFEMCPNDGYVIIRNSELISG 646
Query: 604 MVD--------------TIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDI----I 645
++D + R G + + L +L R+ + G S G DD+ I
Sbjct: 647 VLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGEI 706
Query: 646 VPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVE 705
+ + KE+++ E +YN G + N+ +T + ++ I+
Sbjct: 707 LSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNE-----EETLEAEILSELSTIREEA 761
Query: 706 FDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAK--PSGEIIES-P---- 755
NS +M+ G++GS I QM G + + P G S P
Sbjct: 762 GKICIRELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFER 821
Query: 756 ----------IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDV----- 800
+ + F GL EFF + GR+GL+D ++TA +GY+ RRL+
Sbjct: 822 HSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLS 881
Query: 801 ---------AQNCVV-------------------------------NQVDCNTKKGLTIT 820
+ VV L+
Sbjct: 882 VQYDGTVRNSNGDVVQFTYGGDGLDPAMMEGKDQPVNFNRVFDHAKAIFPHRHDPPLSSE 941
Query: 821 HIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIR 880
+ ++ + G + ++ + + K +L + K +
Sbjct: 942 ELDETLEEELLRKFTEKGDPFVHELREFIAS-LSKKIKKLQDKYGDECGPKFCPDLLYQI 1000
Query: 881 SALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
S LT + C D + V G AVG IAAQSIGEPGTQ+T++TFH G
Sbjct: 1001 SRLTEKQLEKFVERC--LDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAG 1054
|
Length = 1386 |
| >gnl|CDD|144278 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2 | Back alignment and domain information |
|---|
Score = 210 bits (538), Expect = 2e-54
Identities = 73/165 (44%), Positives = 100/165 (60%), Gaps = 22/165 (13%)
Query: 346 GKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKG-------------- 391
GKRVD+SGRSVI P L+L + G+P MALEL KP + +L K
Sbjct: 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPG 60
Query: 392 --YVSTVKQAKKFVEKER---PEVW---DVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKI 443
Y+ +K AK+ +E ++ E+W VL V+ VVLLNR P+LHR+S+ A P++
Sbjct: 61 AKYIKRIKGAKRDLEYKKRIAIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRV 120
Query: 444 ISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLS 488
+ GK I+L+P VC+ YNADFDGD+M ++ S EA+ EAR LML
Sbjct: 121 LEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEARELMLV 165
|
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion. Length = 165 |
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
Score = 184 bits (469), Expect = 2e-46
Identities = 86/309 (27%), Positives = 126/309 (40%), Gaps = 31/309 (10%)
Query: 768 EFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQ 827
EFF +GGR+GL+D ++TA +GYL RRLV ++ VV D G I +
Sbjct: 6 EFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQFLYGED 65
Query: 828 VVYSLGSRVLGRT--------ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRI 879
+ L GR L + ++ + + + + GI S R+
Sbjct: 66 GLDPLKIEGQGRFTIEDSDLKLEKKFKIDLNDVLLLLSEFSLSTLLFEILLRSGIESKRV 125
Query: 880 RSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939
RS LTC S GVC LCYGRD R SLV GEAVG+IAAQSIGEPGTQ+T+ TFH G +
Sbjct: 126 RSELTCNSKAGVCFLCYGRDKYRRSLVEPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVAS 185
Query: 940 VMDRSFIESPCDGIVKIKN-----RNVCRNSTNDLISMGRNTTLQ---ILDMSGQEQYSH 991
+ G+ ++K +N + L+ +
Sbjct: 186 ----KNVTL---GVPRLKEIINVAKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLLK 238
Query: 992 RIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTG 1051
++ ++ DD ++ W F I E + I IG+
Sbjct: 239 KVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPE--------EVAEEVALAIIIIGKRKS 290
Query: 1052 IAKRKVIDW 1060
++K
Sbjct: 291 RKRKKNNLG 299
|
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Length = 447 |
| >gnl|CDD|147253 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3 | Back alignment and domain information |
|---|
Score = 112 bits (283), Expect = 5e-25
Identities = 55/174 (31%), Positives = 73/174 (41%), Gaps = 36/174 (20%)
Query: 491 NLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKI 550
N+L P +G P+ PSQDMVLGL L+ F D EV L IV H I
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLT--RRDT------FFDREEVMQLLMYGIVLPHPAI 52
Query: 551 RGRYKSVDKDGNSISKIYDTTPGRMIIGEILPR-----------HHEISFDICNQEMI-- 597
K T R++ EI P+ ++ I N E+I
Sbjct: 53 LKPIKP--------LWTGKQTFSRLLPNEINPKGKPKTNEETLCENDSYVLINNGELISG 104
Query: 598 -------KKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDI 644
K++ +++ IY+ G + TV F D L +LGFRY SG S G DDI
Sbjct: 105 VIDKKLGGKSLGSLIHIIYKEYGPEETVKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking. Length = 158 |
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
Score = 105 bits (263), Expect = 1e-22
Identities = 51/171 (29%), Positives = 71/171 (41%), Gaps = 4/171 (2%)
Query: 1149 ILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDG 1208
LA I R R K + V + + E + NK + G V+ G + DG
Sbjct: 279 ALAIIIIGKRKSRKRKKNNLGVAKDEK--GLEEEELLLLNKILLVIPGIKVKYGVILTDG 336
Query: 1209 NPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTE 1268
P IL G E L N +Q V RL+GV N K +R ML+K+ I D+
Sbjct: 337 RVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYSNDIREMLKKLGIEAARDSI 396
Query: 1269 YILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQT--KSFISA 1317
+ NV + + +NR L++F L GIT+A L SFI
Sbjct: 397 LLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGLNREKSSFILM 447
|
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Length = 447 |
| >gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
Score = 86.8 bits (216), Expect = 3e-17
Identities = 29/36 (80%), Positives = 31/36 (86%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939
LV +GEAVG+IAAQSIGEPGTQLTMRTFH GG T
Sbjct: 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT 36
|
Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations. Length = 204 |
| >gnl|CDD|179818 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
Score = 71.0 bits (175), Expect = 2e-12
Identities = 27/33 (81%), Positives = 29/33 (87%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SLV GEAVGV+AAQSIGEPGTQ+TMRTFH G
Sbjct: 54 SLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAG 86
|
Length = 383 |
| >gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
Score = 69.2 bits (170), Expect = 8e-12
Identities = 24/33 (72%), Positives = 29/33 (87%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SL+ GEAVG++AAQSIGEPGTQ+T+RTFH G
Sbjct: 35 SLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAG 67
|
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. Length = 363 |
| >gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
Score = 65.7 bits (161), Expect = 8e-11
Identities = 23/33 (69%), Positives = 27/33 (81%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SLV GEAVG++AAQSIGEP TQ+T+ TFH G
Sbjct: 5 SLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 309 |
| >gnl|CDD|184891 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
Score = 62.9 bits (153), Expect = 6e-10
Identities = 23/34 (67%), Positives = 27/34 (79%)
Query: 905 LVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAV 938
V+ EAVG++AAQSIGEPGTQ+TMRTFH G
Sbjct: 178 RVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVA 211
|
Length = 509 |
| >gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
Score = 61.7 bits (150), Expect = 2e-09
Identities = 25/34 (73%), Positives = 29/34 (85%), Gaps = 1/34 (2%)
Query: 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMD 942
GEAVGV+AAQSIGEPGTQ+T+RTFH G V M+
Sbjct: 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAG-VASMN 33
|
RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. Length = 158 |
| >gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
Score = 61.5 bits (150), Expect = 2e-09
Identities = 23/33 (69%), Positives = 26/33 (78%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SLV+ GE VG IAAQSIGEP TQ+T+ TFH G
Sbjct: 22 SLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG 54
|
RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410 |
| >gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 60.4 bits (146), Expect = 3e-09
Identities = 22/33 (66%), Positives = 26/33 (78%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SL + GE VGV+AAQSIGEP TQ+T+ TFH G
Sbjct: 1148 SLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAG 1180
|
Length = 1640 |
| >gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
Score = 58.8 bits (143), Expect = 1e-08
Identities = 21/28 (75%), Positives = 24/28 (85%)
Query: 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
G AVG IAAQSIGEPGTQ+T++TFH G
Sbjct: 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAG 37
|
Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 300 |
| >gnl|CDD|35481 KOG0260, KOG0260, KOG0260, RNA polymerase II, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 46.5 bits (110), Expect = 5e-05
Identities = 18/33 (54%), Positives = 24/33 (72%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
+ + GE VG +AAQS+GEP TQ+T+ TFH G
Sbjct: 1047 AEASPGEMVGALAAQSVGEPATQMTLNTFHYAG 1079
|
Length = 1605 |
| >gnl|CDD|30435 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
Score = 41.8 bits (98), Expect = 0.001
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTV 940
A G AA++ G GTQ+ + T H GG +
Sbjct: 414 VPASGEAAAEARGLMGTQMNILTPHYGGPIVA 445
|
Length = 808 |
| >gnl|CDD|184892 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
Score = 41.0 bits (96), Expect = 0.002
Identities = 17/28 (60%), Positives = 23/28 (82%)
Query: 902 RGSLVNVGEAVGVIAAQSIGEPGTQLTM 929
+LV EAVG++AAQSIGEPGTQ+++
Sbjct: 50 LNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
Length = 858 |
| >gnl|CDD|147268 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4 | Back alignment and domain information |
|---|
Score = 84.0 bits (208), Expect = 2e-16
Identities = 36/109 (33%), Positives = 48/109 (44%), Gaps = 21/109 (19%)
Query: 673 ITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGR-----QKKMNSIFMMSHSGA 727
IT E+Y K+ D+WG T ++V E ++ I DP G NSI+MM+ SGA
Sbjct: 1 ITDAERYGKLEDIWGMTLEEVFEALINNILNKARDP-AGNIASKSLDLNNSIYMMADSGA 59
Query: 728 RGSIHQMRQLGGMRGLIAKPSGEI---------------IESPIRSHFK 761
+GSI + Q+ G RG I IESP F
Sbjct: 60 KGSIINISQIAGCRGQQNVEGKRIPFGFSGRTLPHFKKDIESPESRGFV 108
|
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors. Length = 108 |
| >gnl|CDD|162832 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
Score = 66.2 bits (162), Expect = 6e-11
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 10/79 (12%)
Query: 858 GQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAA 917
+ +L+ ++K I + Y R SL++ GEAVG++AA
Sbjct: 3 PEKLLKELEETVKKREISDKEELDEIIKRVEEE-----YLR-----SLIDPGEAVGIVAA 52
Query: 918 QSIGEPGTQLTMRTFHLGG 936
QSIGEPGTQ+TMRTFH G
Sbjct: 53 QSIGEPGTQMTMRTFHYAG 71
|
This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 367 |
| >gnl|CDD|35481 KOG0260, KOG0260, KOG0260, RNA polymerase II, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 55.4 bits (133), Expect = 1e-07
Identities = 44/205 (21%), Positives = 79/205 (38%), Gaps = 49/205 (23%)
Query: 1161 RNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPV---PQDILR 1217
R + +V + P EDG F P ++ DG ++ + D +P D++
Sbjct: 1253 RGIPDIFKVYMSPTEDG-----EFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVE 1307
Query: 1218 I---KGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDN 1274
I G+EA+ L+ E+ V +G +N++H+ ++ M + + I
Sbjct: 1308 IAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMA------ITRHG 1361
Query: 1275 VDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAG 1334
++R + L R SF+ET +L +AA
Sbjct: 1362 INRQDTGALMRC--------------------------------SFEETVDILMDAAAHA 1389
Query: 1335 KVDTLDGFKENVIVGRSIPAGTGAI 1359
+ D G EN+++G+ P GTG
Sbjct: 1390 EKDPCRGVSENIMLGQLAPMGTGCF 1414
|
Length = 1605 |
| >gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 46.1 bits (109), Expect = 7e-05
Identities = 39/197 (19%), Positives = 76/197 (38%), Gaps = 54/197 (27%)
Query: 1162 NYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGV 1221
+ + V++ +GV F H + D + + D IL GV
Sbjct: 1487 DDVKEKSVLLT---EGVNLPALF----DHADILDVNRLYSNDI--------HAILNTYGV 1531
Query: 1222 EALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVE 1281
EA + ++NEV V+++ G++++ +H+ ++ +M + +
Sbjct: 1532 EAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGY-------------------Q 1572
Query: 1282 ELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDG 1341
NR G+ +S S + SF+ T + L +AA+ G+ D L
Sbjct: 1573 PFNR----------------MGMESSS----SPLQKMSFETTCQFLKQAALFGEEDELSS 1612
Query: 1342 FKENVIVGRSIPAGTGA 1358
++VG + GTG+
Sbjct: 1613 PSARLVVGLPVRGGTGS 1629
|
Length = 1640 |
| >gnl|CDD|162832 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
Score = 54.7 bits (132), Expect = 2e-07
Identities = 32/93 (34%), Positives = 53/93 (56%), Gaps = 13/93 (13%)
Query: 1280 VEELNRSLAQQG-----------KKLVSFSPILQGITKASL--QTKSFISAASFQETTKV 1326
+EE+ R+L +QG L+++ ++ I + + + S ++ A+F+ T K
Sbjct: 270 IEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKH 329
Query: 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
L +AAI G+VD L G EN+IVG+ IP GTG +
Sbjct: 330 LLDAAIRGEVDELAGVIENIIVGQPIPLGTGDV 362
|
This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 367 |
| >gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit [Transcription] | Back alignment and domain information |
|---|
Score = 52.7 bits (126), Expect = 7e-07
Identities = 51/217 (23%), Positives = 85/217 (39%), Gaps = 48/217 (22%)
Query: 624 LMRLGFRYACSSGISFGKDDIIVPES----KEKIIAEA----DKMVKEYENQYNDGLIT- 674
RL Y G + G DD+++ + + +I+ E+ ++ KE D
Sbjct: 786 FSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDE 845
Query: 675 ----------RGEKYNKVVDLWGKT-TDKVTEEMMARIKRVEFDPETGRQKKM--NSIFM 721
+ ++D K+ + T E++ + G KK N++ +
Sbjct: 846 LRSRLEAIYLKDADKLAMLDRVMKSELNGYTSEIVKKCV------PDGLLKKFPENNMQL 899
Query: 722 MSHSGARGSIHQMRQLGGMRGLIAK--------------PSGEIIE-SP-----IRSHFK 761
M SGA+GS Q+ + G PS E SP I F
Sbjct: 900 MIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFL 959
Query: 762 GGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLV 798
G+ E+F C+ GR+GL+D ++T+ SGYL R L+
Sbjct: 960 TGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLI 996
|
Length = 1640 |
| >gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
Score = 52.2 bits (126), Expect = 9e-07
Identities = 19/42 (45%), Positives = 26/42 (61%)
Query: 1318 ASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
SF+ET +L EAA G+ D L G EN+++G+ P GTG
Sbjct: 364 CSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCF 405
|
RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410 |
| >gnl|CDD|30435 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
Score = 42.6 bits (100), Expect = 9e-04
Identities = 27/224 (12%), Positives = 54/224 (24%), Gaps = 29/224 (12%)
Query: 714 KKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSC 773
K + S+ ++ ++ E I+ L E+
Sbjct: 84 KSIPSLL----DMTCRDCERVLYF--EAYVVLGTDLEKIQ---------LLNETEYVYDS 128
Query: 774 VGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLG 833
G + + + R + TK + + + S
Sbjct: 129 FCAHCGAEAIKILLEKPDLETEREEET---------LSPTKVKKLLKRLKVVDAFLLSGN 179
Query: 834 SRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESS-RGVC 892
+ + P I G ES +N++ + I L ++ V
Sbjct: 180 RPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAPIIVR 239
Query: 893 VLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
A +L + + G P L+ R G
Sbjct: 240 NEKRMLQEAVDALFDNR-RPRAVTG---GRPLKSLSQRLKGKQG 279
|
Length = 808 |
| >gnl|CDD|30435 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
Score = 801 bits (2069), Expect = 0.0
Identities = 402/856 (46%), Positives = 502/856 (58%), Gaps = 78/856 (9%)
Query: 20 SVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRM 79
++ +ASP +I S GE+KKPETINYRT KPER GLF RIFGP KDYEC CGKYKR+
Sbjct: 6 DIKFGLASPEEIRS-WSGEVKKPETINYRT-KPERGGLFDERIFGPDKDYECTCGKYKRI 63
Query: 80 KYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERV 139
G HI+LA+PVAH WF KS+PS LL M+ RD ERV
Sbjct: 64 CPGGF-------------------GHIELAAPVAHIWFFKSIPS----LLDMTCRDCERV 100
Query: 140 LYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNL 199
LYFE+YVV+ + LEK Q+L E EYV D F A GA+AI LL DL
Sbjct: 101 LYFEAYVVLG---TDLEKIQLLNETEYVY-------DSFCAHCGAEAIKILLEKPDL--- 147
Query: 200 ALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDF 259
T R++ + S + + KK++KRLK+VD+F+ SGN P WMI+ LPV PPDLRP + LD
Sbjct: 148 -ETEREEETLSPT--KVKKLLKRLKVVDAFLLSGNRPEWMILTVLPVPPPDLRPSIQLDG 204
Query: 260 GRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVT 319
GRFA SDLNDLYRRVI RNNRL RL L AP II+RNEKRMLQE+VDALFDN R R VT
Sbjct: 205 GRFAESDLNDLYRRVINRNNRLKRLLELAAP-IIVRNEKRMLQEAVDALFDNRR-PRAVT 262
Query: 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELF 379
G RPLKSLS LKGKQGRFR NLLGKRVDYSGRSVI GP L+L+QCG+PK MALELF
Sbjct: 263 GG--RPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELF 320
Query: 380 KPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLS-MQA 438
KPF+ +L +G + K AK+ VE+ PEVWDVL EV+ VLLNRAP+LHRLS MQA
Sbjct: 321 KPFVVTELNIEGLRTGAKYAKRMVERRLPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQA 380
Query: 439 FEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASG 498
FEP + GKAI+LHPLVC YNADFDGD+MAV+ S EA EAR LM + N+L P G
Sbjct: 381 FEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYG 440
Query: 499 APVTVPSQDMVLGLCYLSTVH----EGDPGEGML---FADMGEVYHALENKIVTLHSKIR 551
P+ P QD V G L+ V GE L +AD E A+ KI K+
Sbjct: 441 GPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVI 500
Query: 552 GRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRH 611
S D + I TT GR I LP ++ I N ++IK I + TIYR
Sbjct: 501 VSTISPD---LAELSIIVTTDGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYRE 557
Query: 612 CGQ----KSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQ 667
G K+ V D L LG + GI G+ DI + K++I+ EA+ V + Q
Sbjct: 558 YGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQ 617
Query: 668 YNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGA 727
Y +G +TR E+ N V + + + ++ IK + + I M SGA
Sbjct: 618 YEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEE----QGLDFVDIRHMGLSGA 673
Query: 728 RGSIHQMRQLGGMRGLIAKPSGE-------------IIESPIRSHFKGGLCGFEFFQSCV 774
R +I Q+ QL G +G++ + E P S F GL E+F +
Sbjct: 674 RMNISQIVQLIGQQGVMGEKISVLARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPI 733
Query: 775 GGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGS 834
GGR GL+D ++TA SGYL+RRLVDVAQ+ +V + DC T G+ + + G+ L
Sbjct: 734 GGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDCVT-DGIGVVIQFEYGEDGEDLTE 792
Query: 835 RVLGRTALDDIINPLT 850
R+LGR +D++ P+T
Sbjct: 793 RILGRVLEEDVLRPVT 808
|
Length = 808 |
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
| >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=3550.45 Aligned_cols=1337 Identities=54% Similarity=0.888 Sum_probs=1266.3 Q ss_pred EEEEECCCHHHHH-HCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCC Q ss_conf 6898458867885-014489717554254568756887336213685667721566415634--4883567578853047 Q gi|254780142|r 20 SVRISIASPAKIA-SLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMK--YKGIICEKCGVEVTLS 96 (1398) Q Consensus 20 ~i~f~l~spe~I~-~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~--~~g~~C~~Cg~~~~~~ 96 (1398) T Consensus 1 ~I~I~iASpd~Ird~WS~GEVkKPETINYRTLKPEkdGLFcE~IFGPtKDwEC~CGKYK~~rPmyKGvvCerCGVEVT~s 80 (1552) T TIGR02386 1 AIKISIASPDKIRDSWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKVRPMYKGVVCERCGVEVTES 80 (1552) T ss_pred CEEEECCCCCHHHCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCEEEECCCCEEEEE T ss_conf 91753288851310555420218752576556888778754635588876230567532237565751760178179411 Q ss_pred CCCCCCCCCCCCCCCCEEECHHHHHH--HHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHH------HCCCCHHH--- Q ss_conf 75787677200277622013012257--89999809996563013321112321788651043------22369999--- Q gi|254780142|r 97 SVRRDRMAHIDLASPVAHPWFLKSLP--SRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEK------YQILTEEE--- 165 (1398) Q Consensus 97 ~~r~ghfGhIeLa~PV~Hi~f~k~~~--~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~------~~~~~~~~--- 165 (1398) T Consensus 81 kVRRERMGHIELAaPV~HIWy~K~~PSPSRigl~LDi~~k~Le~VlYF~~YvV~d~g~~~~~~~s~f~~k~~L~e~e~k~ 160 (1552) T TIGR02386 81 KVRRERMGHIELAAPVAHIWYFKGLPSPSRIGLLLDITAKELESVLYFEKYVVIDPGDTKLDKKSAFKEKEVLDEKENKR 160 (1552) T ss_pred EEECCCCCCEECCCCCEEEEEECCCCCHHHHHHHHCCCHHHHCCEEEEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCC T ss_conf 64023245321037741453322888743588875788678050477778899878886454202200252026554530 Q ss_pred ---------------------------------HHHHHHHCC--------------CCCEEECCCHHHHHHHHHHCCHHH Q ss_conf ---------------------------------988676358--------------555061155267788877267488 Q gi|254780142|r 166 ---------------------------------YVEAVSQFG--------------QDQFIAMMGADAIYELLIALDLQN 198 (1398) Q Consensus 166 ---------------------------------~~~~~~~~~--------------~~~~~~~~g~~~i~~~l~~~~~~~ 198 (1398) T Consensus 161 ~~~~R~k~~~~~~~~~~~~~~~~~~~dy~~~~~Y~~~~~~yG~PFS~~da~~~I~Ky~~F~a~mGAEAI~~LL~~iDL~~ 240 (1552) T TIGR02386 161 SLKTREKLRRTIRDIIERLIKEKNHEDYRKAKVYREVLERYGVPFSVDDATSYIEKYDGFRAGMGAEAIKELLEKIDLDK 240 (1552) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHHHHHHCCEEEEEECHHHHHHHHHCCCHHH T ss_conf 24225788999999998654100023556656789999840898318999988653385578732489998751378689 Q ss_pred HHHHHHHHHHCCC----CCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHH Q ss_conf 9999998731032----203478864477888666634898511286304507622351388469731310037899999 Q gi|254780142|r 199 LALTLRDQLSKSS----SIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRV 274 (1398) Q Consensus 199 ~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~I 274 (1398) T Consensus 241 e~~~l~~~l~~~~kd~~~~~~~kkllKRLe~~e~F~~Sgn~PeWMvl~~~PVIPPelRPmVQLDGGRFATSDLNDLYRRV 320 (1552) T TIGR02386 241 EIEELKEELRESKKDSKSQQKRKKLLKRLEILEAFKNSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRV 320 (1552) T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCEE T ss_conf 99999999862143456766888888987889999713788753035315758842267764777510122320102302 Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCC Q ss_conf 99869999998739835677769999999888874277678772478765067899861023782000346510045774 Q gi|254780142|r 275 IGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGR 354 (1398) Q Consensus 275 i~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~R 354 (1398) T Consensus 321 INRNNRLKrlL~l~APeIIV~NEKRMLQEAVDALfDNgRR~kPV~G~~nRpLKSLSdmLKGKQGRFRQNLLGKRVDYSGR 400 (1552) T TIGR02386 321 INRNNRLKRLLELKAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGR 400 (1552) T ss_pred EECCHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHCCCEEEECCC T ss_conf 30103788987458886887155335678888874478888631078897754324441266773003206860541552 Q ss_pred EEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHH---------CCCCCCCCCCCCEEECCCCCEEHHHHHHHCCCEEEE Q ss_conf 03412554354620034898776128999999998---------798666300010012248825013266656978997 Q gi|254780142|r 355 SVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEK---------KGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLL 425 (1398) Q Consensus 355 sVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~---------~g~~~~i~~~k~~i~~~~~~v~~v~rhl~~gd~Vl~ 425 (1398) T Consensus 401 SVIVVGPeLKm~QcGLPk~MALeLFKPFIi~~L~~K~DE~GNEI~~~A~NIK~Ak~~ie~~dpeVWdvLE~VIK~hPVLL 480 (1552) T TIGR02386 401 SVIVVGPELKMYQCGLPKKMALELFKPFIIKRLVDKFDELGNEIRELAANIKSAKKMIEQEDPEVWDVLEEVIKEHPVLL 480 (1552) T ss_pred EEEEECCCCCCCCCCCCHHHHHHHCCCEEEHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCC T ss_conf 78998897741136882798875167302322222102367415777776999999987428702368999852488433 Q ss_pred CCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEH Q ss_conf 57631011140123589944954797312254546787754569974689999999999876750542378878204402 Q gi|254780142|r 426 NRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPS 505 (1398) Q Consensus 426 NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~ 505 (1398) T Consensus 481 NRAPTLHRLGIQAFEP~LVEGKAIrLHPLVC~AFNADFDGDQMAVHVPLS~eAq~EAr~LMLa~~NIL~P~dG~Pi~~Ps 560 (1552) T TIGR02386 481 NRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPS 560 (1552) T ss_pred CCCCHHHHCCHHHCCCEEECCCEECCCCHHHHHHCCCCCCCCCEEECCCCHHHHHHHHHHHHCHHHCCCCCCCCEEEECC T ss_conf 67742231003334776441411106821444314788888222802788779999999984433317777885067088 Q ss_pred HHHHHHHHHHHCCC---CCCCCCC-----------------CEECCHHHHHHHHHCC----------------CCCCCCE Q ss_conf 58999999873367---8874468-----------------1417999999999888----------------9867852 Q gi|254780142|r 506 QDMVLGLCYLSTVH---EGDPGEG-----------------MLFADMGEVYHALENK----------------IVTLHSK 549 (1398) Q Consensus 506 QD~i~G~y~lT~~~---~~~~~~~-----------------~~f~~~~~~~~~~~~~----------------~~~~~a~ 549 (1398) T Consensus 561 QDmvLG~YYLT~E~tyf~~~~G~g~makdPtqarvefinnf~~Fs~~~Ev~~Ay~~gGfiddvfGdrrdetGr~~~~~~~ 640 (1552) T TIGR02386 561 QDMVLGLYYLTTEKTYFPGEKGEGLMAKDPTQARVEFINNFKIFSDLEEVIRAYDNGGFIDDVFGDRRDETGRKVHLHAL 640 (1552) T ss_pred CCHHHCCHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCEEECCCE T ss_conf 42200132115454427622478744467024566655421003588999999865880641256541225752001323 Q ss_pred EEEEECCCCCCC-C----CCCEEECCCCCCCCCCEEEECCCCCEEEE-----------------------------ECCH Q ss_conf 365204645667-6----14245217977511220554587510177-----------------------------5110 Q gi|254780142|r 550 IRGRYKSVDKDG-N----SISKIYDTTPGRMIIGEILPRHHEISFDI-----------------------------CNQE 595 (1398) Q Consensus 550 i~~~~~~~~~~~-~----~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~-----------------------------~~~~ 595 (1398) T Consensus 641 I~v~~~A~~n~~F~~~~~rlg~~l~TT~Gr~iFN~iLP~~~py~N~~~N~~~e~e~p~~fi~~~~~~i~~~i~~~~~~~p 720 (1552) T TIGR02386 641 IKVRISAFPNKKFSKENKRLGEILETTVGRVIFNEILPEGFPYINKTKNLYDEKEAPKKFIVEKGEDIKEVIEKIQVVEP 720 (1552) T ss_pred EEEEEECCCCCCCHHHHHHCCCEEEECCCEEEECCCCCCCCCCEECCCCCCHHHCCHHHHHHHCCCCHHHHHHHCCCCCC T ss_conf 78987416873200468752883662256556511157786644554466212203367763158357889974333366 Q ss_pred HCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCH Q ss_conf 02013666999999980817899987558899999998539861321232683699999999978999999886489766 Q gi|254780142|r 596 MIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITR 675 (1398) Q Consensus 596 ~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~ 675 (1398) T Consensus 721 ~~kK~i~~lI~~~Y~~~g~~~t~~~LD~iK~LGF~yaT~~g~t~s~~Di~~p~~K~~~~~~A~~~V~~~~~~Y~~G~iT~ 800 (1552) T TIGR02386 721 LSKKEISELIAKLYEVHGIEETVEMLDKIKDLGFKYATKAGITVSISDIVVPDEKQEILKEADKEVAKIQKDYNKGLITE 800 (1552) T ss_pred CCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 55036789999998760667899999888631000000101506788664387515788899999999999875286011 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC---- Q ss_conf 7888788642346589999999999876115--6543222246883764225555784241120010000246443---- Q gi|254780142|r 676 GEKYNKVVDLWGKTTDKVTEEMMARIKRVEF--DPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG---- 749 (1398) Q Consensus 676 ~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G---- 749 (1398) T Consensus 801 ~ERy~kvv~iWs~~~d~v~~~m~~~l~kd~~ylPdGsvqq~~~NpIf~MadSGARGN~sq~rQLAGMRGLMAkp~GY~~~ 880 (1552) T TIGR02386 801 EERYKKVVSIWSETKDKVTDAMMKLLKKDTYYLPDGSVQQDKFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGYDRK 880 (1552) T ss_pred CCCCCCEEEEECCCCHHHHHHHHHHHHHCCEECCCCCEEECCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCC T ss_conf 11235236653011468899999874012402688644006988279970356643578888876530124688776520 Q ss_pred -------CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEE Q ss_conf -------4445666301110888989764057610322101210156740110154230143277513887666512111 Q gi|254780142|r 750 -------EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHI 822 (1398) Q Consensus 750 -------~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~ 822 (1398) T Consensus 881 N~~g~IK~iIE~PIkssFrEGLtV~EYFiStHGARKGLADTALKTADSGYLTRRLVDv~QdVvv~e~DCGT~~Gi~v~ai 960 (1552) T TIGR02386 881 NNSGVIKDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAI 960 (1552) T ss_pred CCCCCEEEECCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEE T ss_conf 25754232047887343202772453110111200114789987426565521001254448887168788477789999 Q ss_pred EECC----EEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHH Q ss_conf 0088----488650001012211442017789718851786578999999997598402023310003551865788754 Q gi|254780142|r 823 VDSG----QVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGR 898 (1398) Q Consensus 823 ~~~~----~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~ 898 (1398) T Consensus 961 ~~g~~~el~~IesL~DR~vGR~~~edv~~P~~g~~~~~~N~lI~~~~a~~i~~~Gi~~v~iRS~LTC~~~~GVC~kCYG~ 1040 (1552) T TIGR02386 961 VEGKDDELEVIESLKDRIVGRYSAEDVVDPETGKLVAKANTLITEEIAEKIENLGIEKVKIRSVLTCESKHGVCQKCYGR 1040 (1552) T ss_pred EECCCCEEEEEECCCCEEEEEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCEEECCCCCCEEECCCC T ss_conf 84788648898604211673289875312887728871577311799999985796689963421406898823100121 Q ss_pred HCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCC-------------------------- Q ss_conf 201785200010146021111007889877642024543222112202401487-------------------------- Q gi|254780142|r 899 DLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDG-------------------------- 952 (1398) Q Consensus 899 ~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlG-------------------------- 952 (1398) T Consensus 1041 dLat~~~v~~GEAVGvIAAQSIGEPGTQLTMRTFH~GGvA~~~~~~~~~~~~~~gI~N~I~Gl~~~~~~~~~F~R~G~~~ 1120 (1552) T TIGR02386 1041 DLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASSEEESIKVKNGGILNGIEGLIVRVDSGILFSRKGSLK 1120 (1552) T ss_pred CCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHCCCCCCCCCCCCHHECCCCEEEECCCEEEEEECCCEEEEECCEEE T ss_conf 00048521136852378864068467712020110121012332100001003605624340377632745786326078 Q ss_pred EEEE------EEEE------EEECCCCCEEEEECCCCEEEEECCCCEEEE------------EECCCHHCCCCCCCCEEE Q ss_conf 6897------2113------465178877897427604664067760000------------001100001356785532 Q gi|254780142|r 953 IVKI------KNRN------VCRNSTNDLISMGRNTTLQILDMSGQEQYS------------HRIMYGAKLFVDDGGVIE 1008 (1398) Q Consensus 953 VPRl------kEi~------~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~------------~ki~~~~~~~v~~~~~v~ 1008 (1398) T Consensus 1121 i~~~~~~~k~~~~~~~~V~~~Q~V~KG~~l~~~~~Ge~~v~~~~G~~~~~~~~f~i~~ee~~~~V~~G~~i~V~~g~~V~ 1200 (1552) T TIGR02386 1121 ILRYFQELKTVEISELKVLDSQKVIKGENLVVDKKGEEIVVSEEGRIKIEDKKFLIVEEEEVVPVKLGTKILVEDGDAVK 1200 (1552) T ss_pred EEEEECHHHEEECCEEEEECCCEEECCCEEEECCCCCEEEECCCCEEEEECCCEEEECCCEEEECCCCCEEEEECCCCCC T ss_conf 87620010011001256405735533713676588876770788878850585776403215642656688861586205 Q ss_pred CCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHC-CCCCCCCCCEEEECCCCCEEECCC Q ss_conf 2507862135431132024636897531278320012302368602677510110-122123853477427782532247 Q gi|254780142|r 1009 CGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFA-SRSQNLKPAIVVTDENGVVLKSAR 1087 (1398) Q Consensus 1009 ~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~-~~~~~~~~~~~i~d~~~~~~~~~~ 1087 (1398) T Consensus 1201 ~G~~~aefDP~~~PIIse~~Gki~~~D~~~G~~~~~~~~~~Tg~~~l~v~d~~~~~PqGr~L~PrI~i~D~~~~~----- 1275 (1552) T TIGR02386 1201 EGQRIAEFDPYNEPIISEVDGKIKYKDLVEGKSVRKEKDEETGLVELRVIDSRQEKPQGRELEPRIAILDEKGEL----- 1275 (1552) T ss_pred CCCEEEEECCCCCCEEECCCCEEEEEEEECCCCCHHHHCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEECCCCC----- T ss_conf 887578844777452711698578875003762011101424428999985357888987688748998568983----- Q ss_pred CCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCC--CCEECCCCCEEEEE-EECC Q ss_conf 88420213778445413676135484222101320245543367732889887525111--10111347867863-3127 Q gi|254780142|r 1088 GTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKN--HAILAEISGTIRIK-RNYK 1164 (1398) Q Consensus 1088 ~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~--~aiisei~Giv~i~-~~~~ 1164 (1398) T Consensus 1276 --~a~Y~~P~~Aii~V~dG~~v~~GDIlAklp~g~~KT~DITgGLPRv~ELFEar~PK~~e~A~Iae~dG~v~~~~~~~k 1353 (1552) T TIGR02386 1276 --VATYAIPADAIISVEDGQKVKPGDILAKLPKGAEKTKDITGGLPRVKELFEARTPKDFEAAVIAEVDGVVEIIEDDVK 1353 (1552) T ss_pred --CEEEECCCCEEEEECCCCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCEEHCCCEEEEECCCCC T ss_conf --135566301078721587547474788605566455210367612577860168861121100010217885114423 Q ss_pred CCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEEC Q ss_conf 94499998368984026898138965898419877408646438999999987527999999999999999998097006 Q gi|254780142|r 1165 NKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAIN 1244 (1398) Q Consensus 1165 ~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN 1244 (1398) T Consensus 1354 ~~r~~~i~~e~~~~e~~~Y~Ip~~~~L~V~~G~~V~~G~~ltEG~idphd~L~~~Gi~~vq~Yl~~EVQ~VYR~QGV~In 1433 (1552) T TIGR02386 1354 NKRVVVIKDENDDGEEKEYLIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRVKGIQAVQEYLVKEVQKVYRLQGVEIN 1433 (1552) T ss_pred CEEEEEEECCCCCCCEEEEEEECCCEEEEECCCEEECCCEECCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCCEEEC T ss_conf 40899983168885347876506665897218887078520168978789863417789999987523430001886786 Q ss_pred HHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHH Q ss_conf 12560124762861489418864545664106999999999999728987520121000014530231077650402589 Q gi|254780142|r 1245 HKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETT 1324 (1398) Q Consensus 1245 ~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~ 1324 (1398) T Consensus 1434 DKHIEvIvrQMlrKV~itD~GDs~ll~Ge~i~~~~f~E~N~~~~~~Gk~Pa~a~p~l~GItKAsL~t~SFlSAASFQeTT 1513 (1552) T TIGR02386 1434 DKHIEVIVRQMLRKVRITDSGDSDLLPGELIDKHEFNEENKKLLAQGKKPASARPVLLGITKASLNTESFLSAASFQETT 1513 (1552) T ss_pred CEEEEEEEEECCCEEEEEECCCCCCCCCCEECHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHH T ss_conf 71899973010506589836787563674210455688999999827998058788740044125546123320032356 Q ss_pred HHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHHH Q ss_conf 999997452855236653221550730565535466533 Q gi|254780142|r 1325 KVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEK 1363 (1398) Q Consensus 1325 ~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~~ 1363 (1398) T Consensus 1514 kVLTdAai~GK~D~L~GLKENVIiG~lIPAGTGl~~~~~ 1552 (1552) T TIGR02386 1514 KVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKKYKE 1552 (1552) T ss_pred HHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCC T ss_conf 888888644871455466213884562477888754679 |
7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. |
| >PRK01497 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=3310.94 Aligned_cols=1360 Identities=62% Similarity=0.995 Sum_probs=1310.8 Q ss_pred HHHCCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 75135678640536898458867885014489717554254568756887336213685667721566415634488356 Q gi|254780142|r 7 RFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIIC 86 (1398) Q Consensus 7 ~~~~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C 86 (1398) T Consensus 1 ~~~~~~~~~~~~~~i~~~l~spe~Ir~~S~gev~~peTiny~~~kPe~~GLf~~rifg~~~d~ec~cgkyk~~~~~g~~C 80 (1384) T PRK01497 1 NLFKQQTKTEEFDAIKIGLASPEKIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVIC 80 (1384) T ss_pred CCCCCCCCCCCCCEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEC T ss_conf 96567787676454999715889998752589777532137889988887236201486756605156412215598056 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHHH Q ss_conf 75788530477578767720027762201301225789999809996563013321112321788651043223699999 Q gi|254780142|r 87 EKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEY 166 (1398) Q Consensus 87 ~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (1398) T Consensus 81 ~~Cgve~~~~~vrr~rmGHIeLa~Pv~Hi~f~k~~ps~i~~ll~~~~~~l~~v~y~~~~iv~~~~~~~~~~~~~l~~~~~ 160 (1384) T PRK01497 81 EKCGVEVTLSKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIEPGMTPLEKGQLLTEEEY 160 (1384) T ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCEEEEEECCCCHHHHHHHCCCHHHHHHEEEEEEEEEECCCCCCHHHCCCCCHHHH T ss_conf 88887302064023664752436871501441588309898728998885015532126874689885134034669999 Q ss_pred HHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC Q ss_conf 88676358555061155267788877267488999999873103220347886447788866663489851128630450 Q gi|254780142|r 167 VEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPV 246 (1398) Q Consensus 167 ~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV 246 (1398) T Consensus 161 ~~~~~~~~-~~f~~~~g~eai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rl~~~~~f~~~~~rPewmil~vlpV 239 (1384) T PRK01497 161 LDALEEYG-DEFTAKMGAEAIRELLKSIDLDAEAEELREELKETNSETKRKKLLKRLKLVEAFRESGNKPEWMILTVLPV 239 (1384) T ss_pred HHHHHHHC-CCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHEEEECCCC T ss_conf 99998737-63413657899999987478899999999987643317789999999999998875499975134303576 Q ss_pred CCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH Q ss_conf 76223513884697313100378999999986999999873983567776999999988887427767877247876506 Q gi|254780142|r 247 LPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPL 326 (1398) Q Consensus 247 ~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ 326 (1398) T Consensus 240 ~Pp~vRP~v~l~gg~~a~~DL~~l~~~iI~~NnrLk~~~~~~aP~~Ii~ne~~~LQ~~V~tl~dN~~~g~~~~~~~~Rpl 319 (1384) T PRK01497 240 IPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAITGANKRPL 319 (1384) T ss_pred CCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 99888878796899605665358899999987999999876995899998999999999998606787877648899823 Q ss_pred HHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECC Q ss_conf 78998610237820003465100457740341255435462003489877612899999999879866630001001224 Q gi|254780142|r 327 KSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKE 406 (1398) Q Consensus 327 ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~ 406 (1398) T Consensus 320 KSls~rLKGKeGRfR~NLmGKRVDfSaRSVIspDPnL~i~EvGvP~~~A~eL~~Pf~i~~L~~~g~~~~ik~akk~ie~~ 399 (1384) T PRK01497 320 KSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKAAKKMVERE 399 (1384) T ss_pred CHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHCCHHHHHHHHHCCCCCCCCHHHHHHHHC T ss_conf 02898847767511355676620556764751799874554378789999847467799998738766654077887624 Q ss_pred CCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHH Q ss_conf 88250132666569789975763101114012358994495479731225454678775456997468999999999987 Q gi|254780142|r 407 RPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLM 486 (1398) Q Consensus 407 ~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm 486 (1398) T Consensus 400 ~~~v~dile~vi~gd~VLfNRQPTLHrmSimah~~~v~~gkT~Rln~~vc~pYNADFDGDEMNlHvPQS~eAraEa~~Lm 479 (1384) T PRK01497 400 EPEVWDILEEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSLEAQLEARALM 479 (1384) T ss_pred CCHHHHHHHHHHCCCEEEECCCCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHH T ss_conf 86688999877438867882787513010250557872796687261138873688787227850679999999999987 Q ss_pred HHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCC---- Q ss_conf 6750542378878204402589999998733678874468141799999999988898678523652046456676---- Q gi|254780142|r 487 LSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGN---- 562 (1398) Q Consensus 487 ~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~---- 562 (1398) T Consensus 480 ~v~~nilsP~~G~Piig~~QD~l~G~y~lT~~~~~~~~e~~~f~~~~e~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~ 559 (1384) T PRK01497 480 MSTNNILSPANGEPIIVPSQDVVLGLYYLTRERVNAKGEGMVFADVEEVERAYNNGVVELHAKIKVRITEYDKDGDGEFV 559 (1384) T ss_pred HHHCCCCCCCCCCCEEECCHHHHHHHHHHHCCCCCCCCCCEEECCHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCC T ss_conf 43346713789995675008999889998446556667662978999999998669876562489877756666665456 Q ss_pred CCCEEECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 14245217977511220554587510177511002013666999999980817899987558899999998539861321 Q gi|254780142|r 563 SISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKD 642 (1398) Q Consensus 563 ~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~ 642 (1398) T Consensus 560 ~~~~~~~tt~Gr~if~~ilP~~~--~~~~in~~l~Kk~~g~lI~~i~~~~G~~~~~~fld~l~~l~~~~l~~~GfSigi~ 637 (1384) T PRK01497 560 PVTKIVDTTVGRAILNEILPKGL--PFSLVNKPLTKKEISKLINTVYRKCGLKETVIFADQIMYLGFRYATRAGISIGID 637 (1384) T ss_pred CCCEEEECCCHHHHHHHHCCCCC--CCEEEECCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCHH T ss_conf 66337863731888876568999--7146616435531789999999997979999999999999999985077657704 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEE Q ss_conf 23268369999999997899999988648976678887886423465899999999998761156543222246883764 Q gi|254780142|r 643 DIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMM 722 (1398) Q Consensus 643 D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M 722 (1398) T Consensus 638 D~~i~~~k~~ii~~a~~~v~~i~~~y~~G~it~~er~~kvi~~~~~~~~~v~~~~~~~l~~~~~~~-~~~~~~~N~~~~M 716 (1384) T PRK01497 638 DMVIPEEKAEIIEEAEAEVKEIEQQYQSGLITAGERYNKVVDIWSKANDRVAKAMMKNLSKETVIN-EEKQESFNSIYMM 716 (1384) T ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCCCHHHH T ss_conf 514778999999999999999999997388863788999999999989999999999864311433-2124788767541 Q ss_pred ECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHC Q ss_conf 22555578424112001000024644344456663011108889897640576103221012101567401101542301 Q gi|254780142|r 723 SHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQ 802 (1398) Q Consensus 723 ~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~e 802 (1398) T Consensus 717 ~~SGAKGS~~nI~Qm~G~rGlmakp~G~~ie~Pi~s~F~eGL~p~EfFfHamgGREGLiDTAvKTA~SGYLqRRLVkv~e 796 (1384) T PRK01497 717 ADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITSNFREGLNVLEYFISTHGARKGLADTALKTANSGYLTRRLVDVAQ 796 (1384) T ss_pred HHCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHCCCCCHHHHHHCCCCCCCCCHHCCCCCCCCHHHHHHHHHHHC T ss_conf 11257889999998854567652799875567410222059999999870603133102212001000167899998742 Q ss_pred CCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCC Q ss_conf 43277513887666512111008848865000101221144201778971885178657899999999759840202331 Q gi|254780142|r 803 NCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSA 882 (1398) Q Consensus 803 Dl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~ 882 (1398) T Consensus 797 Dv~V~~dDCGT~~g~~i~~~~~g~d~i~~l~eri~gR~~~~dv~~p~~~~~i~~~~~~i~e~~~~~i~~~~i~~v~iRS~ 876 (1384) T PRK01497 797 DLVVTEDDCGTLNGITMTALIEGGEVVEPLRERILGRVAAEDVVDPGTGEVLVPAGTLIDEAWADLIEEAGVDEVKVRSV 876 (1384) T ss_pred CEEEEEECCCCCCCCEEEEEEECCEEEEEHHHHHHCCEEHHHCCCCCCCCEEECCCCCCCHHHHHHHHHCCCCEEEEECC T ss_conf 75999854897577213558738855654034563520174410578875341467614999999999749973774045 Q ss_pred CCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-CEEEECCCCEEEEEEEEE Q ss_conf 0003551865788754201785200010146021111007889877642024543222112-202401487689721134 Q gi|254780142|r 883 LTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDR-SFIESPCDGIVKIKNRNV 961 (1398) Q Consensus 883 lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~-~~iknvTlGVPRlkEi~~ 961 (1398) T Consensus 877 Ltces~~gvc~kcYgrdLa~~~lV~pGEaVGiIAAQSIGEPgTQMTLnTFH~AGVASknvt~~~i~~~~~G~~~v~~lk~ 956 (1384) T PRK01497 877 LTCETRFGVCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIEAKNDGTVKLENLKT 956 (1384) T ss_pred CCHHHHHHHHHHHHCCCHHHCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCEEEECCCCEEEEEEEEE T ss_conf 21230452889874821452781676643004554015885312506665322312333210104623588378501258 Q ss_pred EECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCE Q ss_conf 65178877897427604664067760000001100001356785532250786213543113202463689753127832 Q gi|254780142|r 962 CRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGIS 1041 (1398) Q Consensus 962 ~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~ 1041 (1398) T Consensus 957 v~n~~~~~i~~~~~~~i~i~d~~~~~~~~~~i~~ga~l~v~~~~~v~~~~vi~~~Dp~~~~Ii~e~~g~v~~~d~~~~~t 1036 (1384) T PRK01497 957 VTNSEGKLVVISRNGELAIIDEFGRERERYKVPYGAVLLVKDGDAVKAGQVLAEWDPHTRPIITEVAGTVKFEDLIEGVT 1036 (1384) T ss_pred EECCCCCEEEECCCEEEEEECCCCHHHHHHCCCCCEEEEECCCCEEECCEEEEECCCCCCEEEEECCCEEEEEECCCCCE T ss_conf 86588977886155059952642035665114444189963786774241898505877506870256388864235744 Q ss_pred EHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHH Q ss_conf 00123023686026775101101221238534774277825322478842021377844541367613548422210132 Q gi|254780142|r 1042 VIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPIS 1121 (1398) Q Consensus 1042 ~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~ 1121 (1398) T Consensus 1037 ~~~~~D~~tg~~~~~i~d~~~-~~~~~l~p~i~i~d~~~~~~~~~~~~~~~y~lp~~a~~~v~d~~~v~~gd~l~rip~~ 1115 (1384) T PRK01497 1037 VKEQTDELTGLSSLVVIDRKE-RGGKDLRPAIKIVDANGEDVKIGTDVPAQYFLPVGAILSVEDGQQVKAGDVLARIPQE 1115 (1384) T ss_pred EEEEECCCCCCEEEEEEECCC-CCCCCCCCEEEEECCCCCEEEECCCCCCEEECCCCCEEEECCCCCCCCCCEEEECCHH T ss_conf 677422555624699973323-4556677318998478857750367651363588857872376731368457752413 Q ss_pred HCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEEC Q ss_conf 02455433677328898875251111011134786786331279449999836898402689813896589841987740 Q gi|254780142|r 1122 SAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEK 1201 (1398) Q Consensus 1122 ~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~ 1201 (1398) T Consensus 1116 ~~kt~DItgGLPrV~eLFEar~pk~~aii~ei~G~v~~~~~~k~k~~i~i~~-~~g~~~~~~lv~~~~~l~v~~gd~V~~ 1194 (1384) T PRK01497 1116 SSKTRDITGGLPRVAELFEARRPKDPAILAEIDGTVSFGKETKGKRRLVITP-DDGSEEYEYLIPKGKHLLVFEGDVVEK 1194 (1384) T ss_pred HCCCCCCCCCCCHHHHHHHHHCCCCCCEEEEECCEEEECCCCCCCEEEEEEC-CCCCCEEEEECCCCCEEEEECCCEEEC T ss_conf 2355434478703899887405554103553044687324346743899984-899704899714784689834977732 Q ss_pred CCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHH Q ss_conf 86464389999999875279999999999999999980970061256012476286148941886454566410699999 Q gi|254780142|r 1202 GDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVE 1281 (1398) Q Consensus 1202 gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~ 1281 (1398) T Consensus 1195 g~~lt~g~~~~~eIl~vlGiEA~r~~lv~EIq~Vy~~qGv~In~KHieiivrqMl~Kv~I~~~GDt~~l~Ge~v~~~~~~ 1274 (1384) T PRK01497 1195 GDVISDGPPDPHDILRLLGVEALAEYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKVEITDPGDTTFLEGEQVDRSEFL 1274 (1384) T ss_pred CCEECCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCEECHHHHHHHHHHHHCCEEEEECCCCCCCCCCEEEHHHHH T ss_conf 86604799998999997699999999999999999976964306679999998850637853587655676253398999 Q ss_pred HHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHH Q ss_conf 99999997289875201210000145302310776504025899999974528552366532215507305655354665 Q gi|254780142|r 1282 ELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILH 1361 (1398) Q Consensus 1282 ~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~ 1361 (1398) T Consensus 1275 ~~n~~~~~~g~~pa~~~~~LlGITrasl~t~S~lsaASFeETt~vL~dAAi~gk~D~L~GvkENIIlGqliPaGTG~~~~ 1354 (1384) T PRK01497 1275 EENRRLEAEGKKPATAEPVLLGITKASLQTESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGLAYH 1354 (1384) T ss_pred HHHHHHHHCCCCCCCCCCHHCEEEHHHCCCCCHHHHCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCCCHHHH T ss_conf 99999996688775233210112010013431877601363899999999727987677702263157845677594676 Q ss_pred HHHHHHCCCHH Q ss_conf 33121025102 Q gi|254780142|r 1362 EKRRVAMNRDQ 1372 (1398) Q Consensus 1362 ~~~~~~~~~~~ 1372 (1398) T Consensus 1355 ~~~~~~~~~~~ 1365 (1384) T PRK01497 1355 KDRKVARARAA 1365 (1384) T ss_pred HCCCCCCCCCH T ss_conf 04224567443 |
|
| >PRK09603 DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=3198.86 Aligned_cols=1331 Identities=50% Similarity=0.838 Sum_probs=1254.6
Q ss_pred CCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCC
Q ss_conf 356786405368984588678850144897175542545687568873362136856677215664156344883-5675
Q gi|254780142|r 10 NPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGI-ICEK 88 (1398)
Q Consensus 10 ~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~-~C~~ 88 (1398)
T Consensus 1388 ~~~~~~~~f~~~~i~laspe~i~~ws~gev~kpetinyrt~kpe~dglfc~~ifgp~kd~ec~cgkyk~~~~~g~~vc~~ 1467 (2890)
T PRK09603 1388 KEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIGTCEK 1467 (2890)
T ss_pred CCCCCCCCCCCEEEEECCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEHHHCCCCCCEEECCCCCCCCCCCCCEECCC
T ss_conf 56678788462589505879987503677489875035667887777523154088866355378754302589757587
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCC--------CHHHHCC
Q ss_conf 78853047757876772002776220130122578999980999656301332111232178865--------1043223
Q gi|254780142|r 89 CGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLS--------SLEKYQI 160 (1398)
Q Consensus 89 Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~--------~~~~~~~ 160 (1398)
T Consensus 1468 cgvevt~~~vrr~rmghi~la~pv~hiw~~k~~ps~i~~ll~~~~~~le~v~y~~~~iv~~~~~~~~~~~~~~~~~~~~~ 1547 (2890)
T PRK09603 1468 CGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDI 1547 (2890)
T ss_pred CCCEECCCEEEHHCCCCHHHCCCCEEEEECCCCCHHHHHHHCCCHHHHHHHHCEEEEEEECCCCCCCCCCCCCCHHHHCC
T ss_conf 87286533001203576211386157767178714888884899899776240024899468843233335672065312
Q ss_pred CCHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf 69999988676358555061155267788877267488999999873103220347886447788866663489851128
Q gi|254780142|r 161 LTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240 (1398)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmi 240 (1398)
T Consensus 1548 ~~~~~~~~~~~~~~~~~f~~~~gaeai~~ll~~~dl~~~~~~l~~~~~~~~s~~~~~~~~krl~~v~~f~~s~nrPewMi 1627 (2890)
T PRK09603 1548 LNEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMM 1627 (2890)
T ss_pred CCHHHHHHHHHHHCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHEE
T ss_conf 68999999998717776697567999999998679899999999999865568889999999999999986699975158
Q ss_pred EEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 63045076223513884697313100378999999986999999873983567776999999988887427767877247
Q gi|254780142|r 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTG 320 (1398)
Q Consensus 241 l~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~ 320 (1398)
T Consensus 1628 l~vlPV~Pp~lRP~v~ldggrfatsDlndlyrrvI~rNnrLkrl~~~~aP~~Ii~nekrmLQeaVdal~DN~r~~~~v~~ 1707 (2890)
T PRK09603 1628 LTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG 1707 (2890)
T ss_pred EEEECCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 75432489988754587897532225288899999863999999876996799988899999998897607888878869
Q ss_pred CCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 87650678998610237820003465100457740341255435462003489877612899999999879866630001
Q gi|254780142|r 321 ANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAK 400 (1398)
Q Consensus 321 ~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k 400 (1398)
T Consensus 1708 ~~~RplKSlsd~LKGKqGRFRqNLlGKRVDySgRSVIvvgP~Lkl~QcGlPk~mAleLfkPfi~~~L~~~g~~~~ik~ak 1787 (2890)
T PRK09603 1708 ANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAK 1787 (2890)
T ss_pred CCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCHHHHH
T ss_conf 99881215678647876644566676341538976365798960110578799999866554168887668714477889
Q ss_pred CEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHH
Q ss_conf 00122488250132666569789975763101114012358994495479731225454678775456997468999999
Q gi|254780142|r 401 KFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQL 480 (1398)
Q Consensus 401 ~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAra 480 (1398)
T Consensus 1788 ~~ve~~~~~vw~vl~~vi~~~pVLlNRaPTLHRlsIqaf~p~l~egkairLhplVC~~yNADFDGDqMavHvPlS~EAqa 1867 (2890)
T PRK09603 1788 RMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIA 1867 (2890)
T ss_pred HHHHHCCCCEEEEEHHHHCCCEEEECCCCCHHHCCCCEEEEEEECCCCEECCCCCCCCCCCCCCCHHHHHCCCCCHHHHH
T ss_conf 99985288254311204359916887773422340020466896786602171119842558665432103779999999
Q ss_pred HHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCC
Q ss_conf 99998767505423788782044025899999987336788744681417999999999888986785236520464566
Q gi|254780142|r 481 EARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKD 560 (1398)
Q Consensus 481 Ea~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~ 560 (1398)
T Consensus 1868 Ea~~LMls~~NIlsP~~GkPii~p~QD~vlG~yylT~~~~~~~~e~~~f~~~~e~~~a~~~~~v~l~~~i~~~~~----- 1942 (2890)
T PRK09603 1868 ECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ----- 1942 (2890)
T ss_pred HHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHCCCCEEECEEEEECC-----
T ss_conf 999985121381258999824883118877676610467898776644289999999976799643121688659-----
Q ss_pred CCCCCEEECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 76142452179775112205545875101775110020136669999999808178999875588999999985398613
Q gi|254780142|r 561 GNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFG 640 (1398)
Q Consensus 561 ~~~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSig 640 (1398)
T Consensus 1943 ----~~~~~Tt~Gr~i~~~ilP~~--~~~~~~n~~~~Kk~l~~lI~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sig 2016 (2890)
T PRK09603 1943 ----GNIIATSAGRMIIKSILPDF--IPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISIS 2016 (2890)
T ss_pred ----CCEEEECHHHHHHHHHCCCC--CCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEE
T ss_conf ----93797070488999878476--874210056673149999999999729899999999999999999975767875
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
Q ss_conf 21232683699999999978999999886489766788878864234658999999999987611565432222468837
Q gi|254780142|r 641 KDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIF 720 (1398)
Q Consensus 641 i~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~ 720 (1398)
T Consensus 2017 i~D~~ip~~K~~ii~~a~~~v~~i~~~y~~G~it~~Er~~kvi~~w~~~~d~v~~~~~~~~~~~--------~~~~N~v~ 2088 (2890)
T PRK09603 2017 MEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMSAIAKD--------KEGFNSIY 2088 (2890)
T ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------CCCCCCHH
T ss_conf 6454567589999999999999999997659872068999999999999999999999976643--------55678576
Q ss_pred EEECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHH
Q ss_conf 64225555784241120010000246443444566630111088898976405761032210121015674011015423
Q gi|254780142|r 721 MMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDV 800 (1398)
Q Consensus 721 ~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~ 800 (1398)
T Consensus 2089 mMa~SGARGs~~qirQL~gmrGlmakp~G~iie~PI~sNFreGLtv~EyFist~GaRKGL~DTAlKTAdSGYLTRRLVdv 2168 (2890)
T PRK09603 2089 MMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDV 2168 (2890)
T ss_pred HHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCHHHHHHHHCCCCCCHHHHHEECCCCCEEEHHHHHH
T ss_conf 53113466679998777644374057999803542123431678899998874154213566401135566031367787
Q ss_pred HCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECC
Q ss_conf 01432775138876665121110088488650001012211442017789718851786578999999997598402023
Q gi|254780142|r 801 AQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIR 880 (1398)
Q Consensus 801 ~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~ir 880 (1398)
T Consensus 2169 aQDviV~~ddcgt~~gi~i~~~~~g~d~i~~l~eri~gR~~~~dv~~p~~~~~i~~~~~~i~~~~a~~i~~~gi~~v~iR 2248 (2890)
T PRK09603 2169 SQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIR 2248 (2890)
T ss_pred HCCEEEEECCCCCCCCEEEEEEEECCCCEEEHHHHHHCCHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEC
T ss_conf 52708995267776780588775488207685564641120664127778978971885348999999997799779966
Q ss_pred CCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC-CCEEEECCCCEEEEEEE
Q ss_conf 31000355186578875420178520001014602111100788987764202454322211-22024014876897211
Q gi|254780142|r 881 SALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMD-RSFIESPCDGIVKIKNR 959 (1398)
Q Consensus 881 s~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~-~~~iknvTlGVPRlkEi 959 (1398)
T Consensus 2249 s~ltc~~~~gvc~~cYG~~La~~~~V~~GEAVGiIAAQSIGEPGTQLTmRTFH~gGvas~~~~~~~i~a~~~G~i~f~~~ 2328 (2890)
T PRK09603 2249 TPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGFVRFYNL 2328 (2890)
T ss_pred CCEEEECCCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCEEEECCCCEEEEEEE
T ss_conf 85367666773778839110168887677566654566368751103243000133236642223268356867998533
Q ss_pred EEEECCCCCEEEEECCCC-EE-----------------------------------------------------------
Q ss_conf 346517887789742760-46-----------------------------------------------------------
Q gi|254780142|r 960 NVCRNSTNDLISMGRNTT-LQ----------------------------------------------------------- 979 (1398)
Q Consensus 960 ~~~~n~~~~~i~vs~~~~-~~----------------------------------------------------------- 979 (1398)
T Consensus 2329 ~~~~~~~G~~vv~~~~~~~il~~e~~~~~~~~g~~~~e~~~~ev~~~v~~~~~~~~~~~~~~d~~~~~~l~~~~g~i~g~ 2408 (2890)
T PRK09603 2329 RTYTNKEGKNIIANRRNASILVVEPKIKAPFDGELRIETVYEEVVVSVKNGEQEAKFVLRRSDIVKPSELAGVGGKIEGK 2408 (2890)
T ss_pred EEEECCCCCEEEEECCCCEEEEECCCCCCCCCCCEEEECCCCCEEEEECCCCCCCEEEECCCCCCCCCHHCCCCCCCCCC
T ss_conf 58875889689984145404641353112446612220134303675205643101210245432321001333410130
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780142|r 980 -------------------------------------------------------------------------------- 979 (1398)
Q Consensus 980 -------------------------------------------------------------------------------- 979 (1398)
T Consensus 2409 ~~lp~~~g~~v~~g~~i~~~i~~~~~i~~~i~y~~~l~v~~n~~i~~~i~~~~~giv~~~~l~~~~i~~~~~i~~g~~v~ 2488 (2890)
T PRK09603 2409 VYLPYASGHKVHKGGSIADIIQEGWNVPNRIPYASELLVKDNDPIAQDVYAKEKGIIKYYVLEANHLERTHGIKKGDMVS 2488 (2890)
T ss_pred EEECCCCCCEECCCCCEEEECCCCCCCCCCCCCCCEEEECCCCHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCEEC
T ss_conf 22024665211257601210123322356555542577506860332222113562035431144200012235564001
Q ss_pred -------EEECCCCEEEEEECCCHHCCCCCCCCEEECCE-----------EEEECCCCCCEEEECCCCEEEEEEECCCCE
Q ss_conf -------64067760000001100001356785532250-----------786213543113202463689753127832
Q gi|254780142|r 980 -------ILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQ-----------RISEWDPHTFPIITEVSGTVGFEDLVDGIS 1041 (1398)
Q Consensus 980 -------i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~-----------ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~ 1041 (1398)
T Consensus 2489 ~~~~~~~i~~~~gre~~r~~i~~g~~i~v~d~~~v~~~~~i~~~~~~~~~~i~~~dp~~~pIi~e~~g~v~f~dii~gvt 2568 (2890)
T PRK09603 2489 EKGLFAVIADDNGREAARHYIARGSEILIDDNSEVSANSVISKPTTNTFKTIATWDPYNTPIIADFKGKVSFVDIIAGVT 2568 (2890)
T ss_pred CCCCEEEEECCCCCHHHEEECCCCCEEEECCCCEEECCCEECCCCCCCCEEEECCCCCCCCEEEECCCEEEEEECCCCCE
T ss_conf 35522565235663101132145736884478634126310245654411453027888725760354576343048724
Q ss_pred EHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHH
Q ss_conf 00123023686026775101101221238534774277825322478842021377844541367613548422210132
Q gi|254780142|r 1042 VIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPIS 1121 (1398)
Q Consensus 1042 ~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~ 1121 (1398)
T Consensus 2569 ~~e~~de~tg~~~~~i~~~----~~~~~~p~i~i~~~~g~~~--------~Y~l~~~a~l~V~dG~~V~~GdiLakl~~e 2636 (2890)
T PRK09603 2569 VAEKEDENTGITSLVVNDY----IPSGYKPSLFLEGANGEEI--------RYFLEPKTSIAISDGSSVEQAEVLAKIPKA 2636 (2890)
T ss_pred EEEECCCCCCCEEEEEECC----CCCCCCCEEEEECCCCCEE--------EEECCCCCEEEECCCCEECCCCEEEEECCC
T ss_conf 6651146657157997314----5667784289986899788--------886599978996699996058768971022
Q ss_pred HCCCCCCCCCCCHHHHHHHHH--CCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEE
Q ss_conf 024554336773288988752--511110111347867863312794499998368984026898138965898419877
Q gi|254780142|r 1122 SAKTKDITSGLPRVAELFEAR--RPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHV 1199 (1398)
Q Consensus 1122 ~~k~~DIt~GLPrV~eLFEar--~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V 1199 (1398)
T Consensus 2637 ~~kt~DIt~GLPRV~ELfEAR~~KPK~~ailae~~G~V~~g~~~~~~~~iii~~~-dg-~~~ey~i~~g~~l~V~~Gd~V 2714 (2890)
T PRK09603 2637 TVKSRDITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSK-DG-RSMDYFVDKGKQILVHADEFV 2714 (2890)
T ss_pred CCCCCCCCCCCCCHHHHHHHCCCCCCCCEEEECCCCEEEECCCCCCCEEEEEECC-CC-CEEEEECCCCCEEEECCCCEE
T ss_conf 1567866488860598775134688874389536518995653478526999769-99-477775489987776799887
Q ss_pred ECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHH
Q ss_conf 40864643899999998752799999999999999999809700612560124762861489418864545664106999
Q gi|254780142|r 1200 EKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279 (1398)
Q Consensus 1200 ~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~ 1279 (1398)
T Consensus 2715 ~~Ge~LtdG~inphdIL~i~g~~~lq~yLVnEVQ~VYrsQGV~InDKHIEVIVRQMtsKV~I~d~GDT~fLpGElV~~~~ 2794 (2890)
T PRK09603 2715 HAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKL 2794 (2890)
T ss_pred ECCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCEEEEECCCCCCCCCCCEEEHHH
T ss_conf 06888237999989999840799999999999999999669855362789987513746999568888878856762999
Q ss_pred HHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH
Q ss_conf 99999999972898752012100001453023107765040258999999745285523665322155073056553546
Q gi|254780142|r 1280 VEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398)
Q Consensus 1280 ~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398)
T Consensus 2795 ~e~~N~~~~~~g~~pA~~~PvLLGITKASL~TdSFISAASFQETTRVLTeAAI~GKvD~LrGLKENVIiGrLIPAGTGl~ 2874 (2890)
T PRK09603 2795 FKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMY 2874 (2890)
T ss_pred HHHHHHHHHHCCCCCCEEEEEHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHEEECCCEECCCCCC
T ss_conf 99999999975999862666101151676624068888721308899999996689765788743312058450478837
Q ss_pred HHHHHHHHCCCHHH
Q ss_conf 65331210251022
Q gi|254780142|r 1360 LHEKRRVAMNRDQM 1373 (1398)
Q Consensus 1360 ~~~~~~~~~~~~~~ 1373 (1398)
T Consensus 2875 ~~~~~~~~~~~~~~ 2888 (2890)
T PRK09603 2875 KNKKIVLRTLEDGP 2888 (2890)
T ss_pred CCCEEEEEECCCCC
T ss_conf 04535677446668
|
|
| >PRK05258 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=2985.87 Aligned_cols=1162 Identities=52% Similarity=0.872 Sum_probs=1103.3
Q ss_pred CCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 86405368984588678850144897175542545687568873362136856677215664156344883567578853
Q gi|254780142|r 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEV 93 (1398)
Q Consensus 14 ~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~ 93 (1398)
T Consensus 3 ~~~~f~~i~~~l~spe~Ir~~S~gev~~petiny~~~kPe~~GLf~~rifgp~~d~ec~cgkyk~~~~~g~~C~~Cgve~ 82 (1204)
T PRK05258 3 DVNNFESMQIGLASPEKIRSWSYGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECHCGKYKRVRYKGIVCDRCGVEV 82 (1204)
T ss_pred CCCCCCEEEEEECCHHHHHHHCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 66656649998148899986440897674442588998788982254025978675353776122035985769999864
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHHHHHHHHHC
Q ss_conf 04775787677200277622013012257899998099965630133211123217886510432236999998867635
Q gi|254780142|r 94 TLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQF 173 (1398)
Q Consensus 94 ~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (1398)
T Consensus 83 ~~~~vrr~rmGHIeLa~Pv~Hiw~~k~~~s~i~~~l~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~ 162 (1204)
T PRK05258 83 TRSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVIDPGDTPLEKKQLLTEKEYREYLDKY 162 (1204)
T ss_pred CCCCCCCCCCCCEEECCCEEEEEECCCCHHHHHHHHCCCHHHHHEEEEECCEEEECCCCCCCHHHHHCCHHHHHHHHHHH
T ss_conf 51885588756600167726233206874689998677887750364102248766998741365445899999999984
Q ss_pred CCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCC
Q ss_conf 85550611552677888772674889999998731032203478864477888666634898511286304507622351
Q gi|254780142|r 174 GQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRP 253 (1398)
Q Consensus 174 ~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP 253 (1398)
T Consensus 163 ~-~~~~~~~g~e~i~~ll~~~dl~~~~~~~~~~~~~~-~~~~~~~~~~rl~~~~~f~~~~~rPewmil~vlpV~Pp~~RP 240 (1204)
T PRK05258 163 G-NGFVAKMGAEAIKDLLEEIDLDKEVAELKEELKTA-TGQKRTRAIRRLEVVEAFRKSGNKPEWMILDVLPVIPPDLRP 240 (1204)
T ss_pred C-CCCEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCC
T ss_conf 7-82033557899999998589899999999997522-358888888889999989865999663102127879998871
Q ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 38846973131003789999999869999998739835677769999999888874277678772478765067899861
Q gi|254780142|r 254 LVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDML 333 (1398)
Q Consensus 254 ~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rl 333 (1398)
T Consensus 241 ~V~ldgg~~~~~DLt~~~~~II~~N~rLk~~~~~gap~~ii~~~~~~LQ~~V~~l~dN~~~g~p~~~~~~RplKsl~~rL 320 (1204)
T PRK05258 241 MVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHML 320 (1204)
T ss_pred EEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 28968997457751789999999999999999869948889889999999999987178878876288998610399985
Q ss_pred CCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHH
Q ss_conf 02378200034651004577403412554354620034898776128999999998798666300010012248825013
Q gi|254780142|r 334 KGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDV 413 (1398)
Q Consensus 334 kgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v 413 (1398)
T Consensus 321 KGKeGRfR~NLmGKRVDfSaRSVIspdP~L~i~EvGvP~~~A~~L~~P~~~~~Lv~~g~~~~ik~ak~~i~~~~~~v~~v 400 (1204)
T PRK05258 321 KGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKEMALELFKPFVMKELVERGLAHNIKSAKRKVERVDPEVWDV 400 (1204)
T ss_pred CCCCCEECCCCCCCCCCCCCCEEEECCCCCCCCEECCCHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 66664132456755205567536507998746700386899976278799999997587456278777776069436788
Q ss_pred HHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 26665697899757631011140123589944954797312254546787754569974689999999999876750542
Q gi|254780142|r 414 LAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLL 493 (1398)
Q Consensus 414 ~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~nii 493 (1398)
T Consensus 401 le~vi~~~~VL~NRQPTLHr~SImah~~~v~~gkT~Rln~~vc~pYNADFDGDEMNlHvPQS~eArAEa~~LM~v~~nIl 480 (1204)
T PRK05258 401 LEEVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARLLMLAAHNIL 480 (1204)
T ss_pred HHHHHCCCCEEECCCCCCCCCCCCCCEEEEECCCEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHCHHCCC
T ss_conf 99874278246515863232434451268507835884510167666887762145447899999999999860340547
Q ss_pred CCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEEC---CCCCCCCCCCEEECC
Q ss_conf 37887820440258999999873367887446814179999999998889867852365204---645667614245217
Q gi|254780142|r 494 HPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYK---SVDKDGNSISKIYDT 570 (1398)
Q Consensus 494 sP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~---~~~~~~~~~~~~~~t 570 (1398)
T Consensus 481 sP~~G~PIig~iQD~ilG~y~LT~~d~~~~~eg~~F~~~~e~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~t 560 (1204)
T PRK05258 481 NPKDGKPVVTPSQDMVLGNYYLTMEREGAEGEGMIFKDTDEALMAYQNGYVHLHTRIGVAASSMPNKPFTEEQRSKILVT 560 (1204)
T ss_pred CCCCCCCEEEECHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEC
T ss_conf 68899833650066765638750355455467738778999999997699656873564575678788886547615873
Q ss_pred CCCCCCCCEEEECCCCCE-----------------------------EEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 977511220554587510-----------------------------177511002013666999999980817899987
Q gi|254780142|r 571 TPGRMIIGEILPRHHEIS-----------------------------FDICNQEMIKKNISAMVDTIYRHCGQKSTVAFC 621 (1398)
Q Consensus 571 t~Gr~~~~~ilp~~~~~~-----------------------------~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l 621 (1398)
T Consensus 561 t~Gk~ifs~ilP~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~K~~lg~li~~i~~~~G~~~a~~fl 640 (1204)
T PRK05258 561 TVGKIIFNEIIPEDLPYINEPTNANLEEGTPDKYFLEPGQDIKEYIANLEINFPFKKKFLGNIIAEVFKRFGITETSEML 640 (1204)
T ss_pred CHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCEEEEECCCEEEEEECHHHHHHHHHHHHHHHCHHHHHHHH
T ss_conf 60688898876798875455564444456776400148871489864746630214357899999999997989999999
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 55889999999853986132123268369999999997899999988648976678887886423465899999999998
Q gi|254780142|r 622 DDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARI 701 (1398)
Q Consensus 622 ~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~ 701 (1398)
T Consensus 641 d~l~~l~~~~l~~~GfSiGi~D~~~~~~k~eii~~a~~~v~~i~~~~~~G~~t~~e~~~~v~~~l~~~~d~v~~~~~~~l 720 (1204)
T PRK05258 641 DRMKDLGYKYSTKAGITVGVADIVVLEEKQEILDEAHKKVEKITKQFRRGLITDEERYERVIEIWTDAKDKIQKKLMESL 720 (1204)
T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999999999856964743104670789999999999999999999836674489999999999999999999998536
Q ss_pred HHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHH
Q ss_conf 76115654322224688376422555578424112001000024644344456663011108889897640576103221
Q gi|254780142|r 702 KRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLL 781 (1398)
Q Consensus 702 ~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLi 781 (1398)
T Consensus 721 ------------~~~N~~~~M~~SGAKGS~~Ni~Qm~g~~Gl~~~~~griielPI~~sF~~GLtp~EfFfhamgGReGLi 788 (1204)
T PRK05258 721 ------------DKFNPIFMMADSGARGNISNFTQLAGMRGLMAAPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLA 788 (1204)
T ss_pred ------------CCCCCHHHHHHHCCCCCHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHCCCCHHHHHHCCHHHHCCHH
T ss_conf ------------89985877755137787877999963766024699974676602243448988999980630212202
Q ss_pred CCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCC
Q ss_conf 01210156740110154230143277513887666512111008848865000101221144201778971885178657
Q gi|254780142|r 782 DVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLI 861 (1398)
Q Consensus 782 DTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i 861 (1398)
T Consensus 789 DTAvKTA~SGYLqRRLvkv~eD~~Vr~dDcgt~~g~~v~~i~~g~~~i~~l~~ri~gR~~~~di~~~~~~~~i~~~~~~i 868 (1204)
T PRK05258 789 DTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGLLVSAIKEGNEVIEPLEERLVGRYTRKTVKHPETGEVIVGKNELI 868 (1204)
T ss_pred HCCCCCCCCHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEEEECCCCHHEHHHHHHCCHHHHHHCCCCCCCEEECCCCCC
T ss_conf 22300243038999988875445999715887578068987308710105577674601354423677786765588625
Q ss_pred CHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 89999999975984020233100035518657887542017852000101460211110078898776420245432221
Q gi|254780142|r 862 LESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVM 941 (1398)
Q Consensus 862 ~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~ 941 (1398)
T Consensus 869 ~~~~~~~i~~~gi~~v~iRS~ltc~s~~gvc~kcyg~~Lat~~~VepGEaVGiIAAQSIGEPgTQMTL~TFH~aGvas~- 947 (1204)
T PRK05258 869 TEDIAKKIVDAGIEEVTIRSVFTCNTRHGVCRKCYGRNLATGDAVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGD- 947 (1204)
T ss_pred CHHHHHHHHHCCCCEEEEECHHHHCCHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHCCCCCCCHHHHHHHHHCCCCCCC-
T ss_conf 9999999987278648874211121156499998755332114367776000110113688520142655411552434-
Q ss_pred CCCEEEECCCCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCC
Q ss_conf 12202401487689721134651788778974276046640677600000011000013567855322507862135431
Q gi|254780142|r 942 DRSFIESPCDGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTF 1021 (1398)
Q Consensus 942 ~~~~iknvTlGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~ 1021 (1398)
T Consensus 948 ------nIT~---------------------------------------------------------------------- 951 (1204)
T PRK05258 948 ------DITQ---------------------------------------------------------------------- 951 (1204)
T ss_pred ------CCCC----------------------------------------------------------------------
T ss_conf ------4446----------------------------------------------------------------------
Q ss_pred EEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEE
Q ss_conf 13202463689753127832001230236860267751011012212385347742778253224788420213778445
Q gi|254780142|r 1022 PIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALL 1101 (1398)
Q Consensus 1022 ~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~ 1101 (1398)
T Consensus 952 -------------------------------------------------------------------------------- 951 (1204)
T PRK05258 952 -------------------------------------------------------------------------------- 951 (1204)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred EECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEE
Q ss_conf 41367613548422210132024554336773288988752511110111347867863312794499998368984026
Q gi|254780142|r 1102 SVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPA 1181 (1398)
Q Consensus 1102 ~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~ 1181 (1398)
T Consensus 952 -----------------------------GvPRl~EifeAr~pk~~aiisei~g~v~~i~~~~~~~~~~i~~-~~~~~~~ 1001 (1204)
T PRK05258 952 -----------------------------GLPRVQELFEARNPKGQAVITEVDGTVVAIEEDKADRTKEVTV-KGETETR 1001 (1204)
T ss_pred -----------------------------CCCCHHHHHHCCCCCCCCEEEEECCEEEEEEECCCCEEEEEEE-CCCCEEE
T ss_conf -----------------------------7602899985047788612675145688745426741799997-7996489
Q ss_pred EEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEE
Q ss_conf 89813896589841987740864643899999998752799999999999999999809700612560124762861489
Q gi|254780142|r 1182 EYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEI 1261 (1398)
Q Consensus 1182 e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I 1261 (1398)
T Consensus 1002 ~y~ip~~~~l~v~~gd~V~~G~~l~~g~i~~~~il~v~g~~~~~~yli~Evq~vyr~qGV~i~dKhiEviirqml~kv~i 1081 (1204)
T PRK05258 1002 SYTIPYTARLKVEEGDEVERGDELTEGSIDPKDLLKVKDVLSVETYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKVRV 1081 (1204)
T ss_pred EEECCCCCEEEEECCCEEECCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCEEECCCEEEEEHHHHHHEEEE
T ss_conf 99805775687705999844876257899989976634988999999999999988378764367588636514307899
Q ss_pred ECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCC
Q ss_conf 41886454566410699999999999972898752012100001453023107765040258999999745285523665
Q gi|254780142|r 1262 TDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDG 1341 (1398)
Q Consensus 1262 ~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~G 1341 (1398)
T Consensus 1082 ~~~gdt~~~~g~~vd~~~~~~~n~~~~~~g~~~a~~~~~llGITr~~l~t~S~LsaASFqeTt~vL~dAAi~gk~D~l~G 1161 (1204)
T PRK05258 1082 MDPGDTDLLPGTLMDIFDFTDANKKVLISGGIPATARPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDPLLG 1161 (1204)
T ss_pred EECCCCCCCCCCEEEHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 82787455677685599999999999975997644545887763165233019988526637899999997179862578
Q ss_pred CCEEEECCCCCCCCCCHHHHHHHHHHCCCHHHHHH
Q ss_conf 32215507305655354665331210251022211
Q gi|254780142|r 1342 FKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILK 1376 (1398)
Q Consensus 1342 vSENIIlGqliP~GTG~f~~~~~~~~~~~~~~~~~ 1376 (1398)
T Consensus 1162 lkEnII~G~liP~GTGl~~~~~~~~~~~~~~~~~~ 1196 (1204)
T PRK05258 1162 LKENVIIGKLIPAGTGMARYRNIKPIEDTEEEEVE 1196 (1204)
T ss_pred CCEEEECCCCCCCCCCCHHHCCEEEECCCHHHHHH
T ss_conf 30103517713687585666351432240166654
|
|
| >PRK02173 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=2930.98 Aligned_cols=1169 Identities=41% Similarity=0.703 Sum_probs=1034.3
Q ss_pred CCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCC------
Q ss_conf 786405368984588678850144897175542545687568873362136856677215-6641563448835------
Q gi|254780142|r 13 TDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECI-CGKYKRMKYKGII------ 85 (1398)
Q Consensus 13 ~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~-Cg~~~~~~~~g~~------ 85 (1398)
T Consensus 8 ~~~~~f~~i~i~laspe~Ir~wS~GeV~kpeTinyrt~KPe~~GLfce~Ifgp~kd~eC~~Cgk~~~~~~~~~~c~~~~~ 87 (1438)
T PRK02173 8 ISENKIQKISLALATPEDVLEWSRGEVTKPETINYKTYKPERGGLFDELIFGPLTDYKCPICGRKYKKSNENQLCIATKE 87 (1438)
T ss_pred CCHHCCCEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCEEHHHHCCCCCCCCCHHCCCCCCEEECCEECCCCCC
T ss_conf 37302464899831889999872840289866366889988887622032198635621100771124116855356761
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCH---------HHHHHHHHHCCEEEECCCC-CCH
Q ss_conf 675788530477578767720027762201301225789999809996---------5630133211123217886-510
Q gi|254780142|r 86 CEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSL---------RDVERVLYFESYVVVDPGL-SSL 155 (1398)
Q Consensus 86 C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~---------~~~~~v~y~~~~~~~~~~~-~~~ 155 (1398)
T Consensus 88 C~~~gvev~~~~vrr~rmGHIeLa~PV~Hiwf~K~~ps~i~~lL~l~~~~~~~~~s~k~le~viy~~~~iv~~~~~~~~~ 167 (1438)
T PRK02173 88 CKIEKPEILPKISRRSRMGHIALNAPVVHFWFFKIDHSIISKLLGLKVAESNKTVTKTDLENLIYYKSHIVLETGGLKSL 167 (1438)
T ss_pred CCCCCEEECCCEECCCCCCCCEECCCCEEEEEECCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCEEEEECCCCCCCC
T ss_conf 78888694825450223577002686041003379603999982874434556666878787531201698558875531
Q ss_pred HHHCCCCH----------------------HHHHHHH---------------HHCCCC------------CEEECCCHHH
Q ss_conf 43223699----------------------9998867---------------635855------------5061155267
Q gi|254780142|r 156 EKYQILTE----------------------EEYVEAV---------------SQFGQD------------QFIAMMGADA 186 (1398)
Q Consensus 156 ~~~~~~~~----------------------~~~~~~~---------------~~~~~~------------~~~~~~g~~~ 186 (1398)
T Consensus 168 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gaea 247 (1438)
T PRK02173 168 PKNKIIDISEAALIYKDALEEIIEFYPPGSEEYEAIAETISELADVASSKIGQDYGIDFYELNEIIEEYSSAKIATGSKA 247 (1438)
T ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCHHHH
T ss_conf 01011221244556677889988751233488888888765444443322233305305666677776423442103999
Q ss_pred HHHHHHHCCHHHHHHHHHHHHHC-----------CCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEE
Q ss_conf 78887726748899999987310-----------3220347886447788866663489851128630450762235138
Q gi|254780142|r 187 IYELLIALDLQNLALTLRDQLSK-----------SSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLV 255 (1398)
Q Consensus 187 i~~~l~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v 255 (1398)
T Consensus 248 i~~lL~~~dl~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~~krl~~v~~f~~s~~rPeWMil~vlPV~Pp~lRP~v 327 (1438)
T PRK02173 248 IEYLLKNIDLRAEKEAIEAEIKGINKQIYKNKTSSSKNQKRDKLYKRLQVINAFINSGQDPKSMLIYNLPVIPADLRPLV 327 (1438)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCEE
T ss_conf 99998566879999999999987555432211000135678889999999999986499960588613688999887208
Q ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCCCCHHHHHHHHHC
Q ss_conf 846973131003789999999869999998739835677769999999888874277678-7724787650678998610
Q gi|254780142|r 256 ALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK-RVVTGANRRPLKSLSDMLK 334 (1398)
Q Consensus 256 ~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~-~~~~~~~~rp~ks~~~rlk 334 (1398)
T Consensus 328 ~LdgGrfatsDLn~lyrriI~rNnrLk~l~~~~aP~~Ii~nekrmLQeaVdal~DN~~~g~~~v~~~~~RPLKSLs~rLK 407 (1438)
T PRK02173 328 QLDGGRHSTSDINELYRRIIIRNNRLKKWKEADAPVLIIQNELRMIQEAVDALIDNQRKSPNPVTSKDNRPLKSISDALT 407 (1438)
T ss_pred EECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHC
T ss_conf 96898752665388899999987999999874998889987999999999999727877888773999895543788727
Q ss_pred CCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHHH
Q ss_conf 23782000346510045774034125543546200348987761289999999987986663000100122488250132
Q gi|254780142|r 335 GKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVL 414 (1398)
Q Consensus 335 gK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v~ 414 (1398)
T Consensus 408 GKeGRFR~NLlGKRVDfSgRSVIs~dPnL~l~evGvPk~mA~eLt~P~ii~~L~~~~~~~~ik~akk~ie~~~~~vw~~l 487 (1438)
T PRK02173 408 GKKGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQAGIPREMAAKLFEPWIIKELIQEEKVGSIKMAKKMIEELNPIIWPHV 487 (1438)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEHHHHCCCCCCHHHHHHHHHHCCCCCHHHH
T ss_conf 88763257788666476998715789998530035879999871977456066564774430345556662597112878
Q ss_pred HHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 66656978997576310111401235899449547973122545467877545699746899999999998767505423
Q gi|254780142|r 415 AEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494 (1398)
Q Consensus 415 rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niis 494 (1398)
T Consensus 488 e~vi~gd~VLfNRqPTLHRmSImah~~kl~~gkTfRLhp~VC~pYNADFDGDEMNvHVPQS~EArAEA~~LM~v~~NIls 567 (1438)
T PRK02173 488 AKVIQNKPVLLNRAPTLHRLSIQAFEPVLIRGKAIKLHPLVTTAFNADFDGDQMAVHVPISPEAVREAQELMFANKNILG 567 (1438)
T ss_pred HHHHCCCEEEECCCCCCCCCCCCCCCEEEECCCEEEEEECCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCC
T ss_conf 98746980575277410114333564476417358842001565568888762675167999999999998623047214
Q ss_pred CCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCC--CCCCEEECCCC
Q ss_conf 7887820440258999999873367887446814179999999998889867852365204645667--61424521797
Q gi|254780142|r 495 PASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDG--NSISKIYDTTP 572 (1398)
Q Consensus 495 P~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~--~~~~~~~~tt~ 572 (1398)
T Consensus 568 P~~G~PIig~iQD~IlG~Y~LT~~~~~~~geg~~F~~~~e~~~ay~~~~i~l~~~I~lp~~~I~kp~~l~~~~~~i~TT~ 647 (1438)
T PRK02173 568 PKDGEPIINPSQDMILGLYYLTIEKAGAKGEGKFFSTYEAMLKAYEFKSVSLHARVALPFEQVKKPFIAKTMRGYIISTV 647 (1438)
T ss_pred CCCCCCEEEEHHHHHHHHHHHEECCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEECCHHHCCCCCCCCCCCCEEEECH
T ss_conf 88999547500667546565310244666876365889999999867996333235425553367656677760588471
Q ss_pred CCCCCCEEEECCCCCEEE--------------------------------EECCHHCCHHHHHHHHHHHHHCC-------
Q ss_conf 751122055458751017--------------------------------75110020136669999999808-------
Q gi|254780142|r 573 GRMIIGEILPRHHEISFD--------------------------------ICNQEMIKKNISAMVDTIYRHCG------- 613 (1398)
Q Consensus 573 Gr~~~~~ilp~~~~~~~~--------------------------------~~~~~~~k~~~~~li~~i~~~~G------- 613 (1398)
T Consensus 648 GK~Ifn~ilP~~~~~i~~~~~~~~~~~~~~~~~~~~ip~G~~~~e~i~~~~vn~~~~kk~i~~ii~~i~d~~v~i~~~e~ 727 (1438)
T PRK02173 648 GKFIFNNAFPANFPFIFDDNVDELELNYPSQIKKYVLPYGTNFREYIQNLPVNEPLNKKAIAKIVRQIFDKYVGLLTKED 727 (1438)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCE
T ss_conf 99999876778788544554442112554222221256775300012444344443334577887776641152013430
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780142|r 614 -------------------------------------------------------------------------------- 613 (1398)
Q Consensus 614 -------------------------------------------------------------------------------- 613 (1398)
T Consensus 728 i~gvidk~~~g~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ll~~i~~ 807 (1438)
T PRK02173 728 IASVIDQLNFGNYQNIVLLYAKLKDYKKQKLPVPHLEILSEFTIFEYSKIYKQLQQNGPGESERVWEDHEKAELLEKVWF 807 (1438)
T ss_pred EEEEECCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 10010122335544442011100245554221023445544444321000100002565421110010002334444544
Q ss_pred --HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf --178999875588999999985398613212326836999999999789999998864897667888788642346589
Q gi|254780142|r 614 --QKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTD 691 (1398)
Q Consensus 614 --~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~ 691 (1398)
T Consensus 808 ~~~~~~a~~LD~ik~lGf~~at~sG~SigI~Di~~~~~k~e~I~eae~~v~~l~~~y~~Gllt~~Er~~~~i~~ws~~~d 887 (1438)
T PRK02173 808 KYNNMVASVLDKIKDLGFKFSTLSGTTISISDIKTSPKKKERIKEGENYINKLKTYYAKGLITDDERYVLTIAKWTQIKN 887 (1438)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHCCCEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 11205788888887642577764465011513006716899999999999999999871688377899999999999999
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCC------CCCC-------CCCCCCCC
Q ss_conf 9999999998761156543222246883764225555784241120010000246------4434-------44566630
Q gi|254780142|r 692 KVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAK------PSGE-------IIESPIRS 758 (1398)
Q Consensus 692 ~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gk------p~G~-------~~~~PV~~ 758 (1398)
T Consensus 888 ~v~~~~~k~l~----------~~~~N~i~~Ma~SGAKGS~~NIsQmaGmrG~~~~~gkrl~~~~~~eri~r~~ie~PV~s 957 (1438)
T PRK02173 888 DIQEDLKKIIK----------DNPQNSLFMMMNSGARGNISNFVQLAGMRGLMANNTKALKADAENERVVRSTVEIPVKS 957 (1438)
T ss_pred HHHHHHHHHHH----------CCCCCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99999999864----------28888658877046768899999986463410477764678877664545544467400
Q ss_pred HHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEE--CCEEEEEECCCC
Q ss_conf 111088898976405761032210121015674011015423014327751388766651211100--884886500010
Q gi|254780142|r 759 HFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVD--SGQVVYSLGSRV 836 (1398)
Q Consensus 759 sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~--~~~~~~~l~~~~ 836 (1398)
T Consensus 958 SF~eGLtp~EfFfHtmGGREGLiDTAVKTAeSGYLQRRLVkvleDliV~~dDcgt~~G~~v~di~d~~~~~ii~~L~eri 1037 (1438)
T PRK02173 958 SFLEGLTAYEFYSSTHGARKGLTDTALNTAKSGYLTRRLVDVAQNIVVREEDCGSDFGFVVKDIIDTKTNTIIVPLLERI 1037 (1438)
T ss_pred HHHCCCCHHHHEEECCCCCCCHHHHHHHHHHHCCHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCCCCEEEEHHHHH
T ss_conf 12048973661010223112315534665443225889999741248986357875886866534068983887814522
Q ss_pred CCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHH
Q ss_conf 12211442017789718851786578999999997598402023310003551865788754201785200010146021
Q gi|254780142|r 837 LGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIA 916 (1398)
Q Consensus 837 ~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iA 916 (1398)
T Consensus 1038 ~gR~~~~~i~d~-~~~~i~~~~~li~~~~~~~i~~~~i~~v~irs~ltc~~~~gvc~~cyg~dLa~~~lV~~GEaVGiIA 1116 (1438)
T PRK02173 1038 EGRFLNKDVYDS-RGKLLASAGTLITLETAKKIVAAGIKKVEIRSILSCHTKNGVCKKCYGKDLATNRLVNIGEAVGIIA 1116 (1438)
T ss_pred HCCEEHHHCCCC-CCCEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHCHHHHHCCCCCCCCHHHHHH
T ss_conf 140002320188-8858873887079999999998699789721433311322088998474667389288875678888
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCH
Q ss_conf 11100788987764202454322211220240148768972113465178877897427604664067760000001100
Q gi|254780142|r 917 AQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYG 996 (1398)
Q Consensus 917 AQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~ 996 (1398)
T Consensus 1117 AQSIGEPgTQMTLrTFH~gGvA~~------~dIT~G~pRv~El~ea~--------------------------------- 1157 (1438)
T PRK02173 1117 AQSIGEPGTQLTMRTFHTGGVAGV------EDITGGFGRLIELIDAH--------------------------------- 1157 (1438)
T ss_pred HHHCCCCHHHHHHHHHHCCCCCCC------CCCCCCCCCHHHHHCCC---------------------------------
T ss_conf 882797076676870501423674------44456761376652043---------------------------------
Q ss_pred HCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEE
Q ss_conf 00135678553225078621354311320246368975312783200123023686026775101101221238534774
Q gi|254780142|r 997 AKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVT 1076 (1398)
Q Consensus 997 ~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~ 1076 (1398)
T Consensus 1158 -------------------------------------------------------------------------------- 1157 (1438)
T PRK02173 1158 -------------------------------------------------------------------------------- 1157 (1438)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred CCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCEECCCCC
Q ss_conf 2778253224788420213778445413676135484222101320245543367732889887525111-101113478
Q gi|254780142|r 1077 DENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKN-HAILAEISG 1155 (1398)
Q Consensus 1077 d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~-~aiisei~G 1155 (1398)
T Consensus 1158 -----------------------------------------------------------------~~p~~~~a~i~~~~g 1172 (1438)
T PRK02173 1158 -----------------------------------------------------------------EHPWGRPAKISPYYG 1172 (1438)
T ss_pred -----------------------------------------------------------------CCCCCCCCEEEEECC
T ss_conf -----------------------------------------------------------------688998655774156
Q ss_pred EEEEEEECCCCE--------EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHH
Q ss_conf 678633127944--------999983689840268981389658984198774086464389999999875279999999
Q gi|254780142|r 1156 TIRIKRNYKNKS--------RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASY 1227 (1398)
Q Consensus 1156 iv~i~~~~~~k~--------~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~ 1227 (1398)
T Consensus 1173 ~v~~i~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~v~~gd~v~~G~~l~~G~~~~~~il~~~g~~~~~~y 1252 (1438)
T PRK02173 1173 IITKIKDLKEKNAANKGFLITIEYKTSKNEKATHIIRVEQSQKLRVKVGDKVIPGQKLVEGPIILKELLEVSDARTVQNY 1252 (1438)
T ss_pred EEEEEECCCCCCCCCCCCEEEEEEECCCCCCEEEEEECCCCCEEEECCCCEECCCCCCCCCCCCHHHHHHHCCHHHHHHH
T ss_conf 78786303666554455137898874789824799975479875667999976799847899998999884499999999
Q ss_pred HHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHH
Q ss_conf 99999999998097006125601247628614894188645456641069999999999997289875201210000145
Q gi|254780142|r 1228 LINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKA 1307 (1398)
Q Consensus 1228 Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKa 1307 (1398)
T Consensus 1253 l~~evq~vyr~qGv~i~dKhiEvivrqml~kv~i~~~gds~~~~g~~vd~~~~~~~n~~~~~~g~~~a~~~~~l~Gitka 1332 (1438)
T PRK02173 1253 LLKEIQKIYRMQGISISDKYIEIIIRQMLSKIQIIEPGDSNFFIGSIVDIFDYQEENGQLLSQGKKPAFGKVIIKGAKQI 1332 (1438)
T ss_pred HHHHHHHHHHHCCCEECCCEEEEHHHHHCCEEEEECCCCCCCCCCCEEEHHHHHHHHHHHHHCCCCCCCEEEECCCCCHH
T ss_conf 99999999997597502547885365650722897288877889888459999999999998499875010000232332
Q ss_pred HHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHHHHHHHCCCHHHHHH
Q ss_conf 302310776504025899999974528552366532215507305655354665331210251022211
Q gi|254780142|r 1308 SLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQMILK 1376 (1398)
Q Consensus 1308 sl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~~~~~~~~~~~~~~~ 1376 (1398)
T Consensus 1333 sl~t~S~lsaASFqeTt~vLt~Aai~gk~D~L~GlkENviiG~lIPaGTg~~~~~~~~~~~~~~~~~~~ 1401 (1438)
T PRK02173 1333 PLLSDSFLAAASYQETSKILVHSSISSQIDKLEGLKENIIVGHKIPAGTNSNYEPKSKYDIRNPKSYFR 1401 (1438)
T ss_pred HHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHC
T ss_conf 342346998861214678999998758987678843676426700077782004311245448165514
|
|
| >PRK02995 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=2926.51 Aligned_cols=1157 Identities=51% Similarity=0.847 Sum_probs=1070.6
Q ss_pred CCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 86405368984588678850144897175542545687568873362136856677215664156344883567578853
Q gi|254780142|r 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEV 93 (1398)
Q Consensus 14 ~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~ 93 (1398)
T Consensus 3 ~~~~f~~i~i~laSpe~Ir~wS~geV~kpeTinyrt~kPe~~GLfce~Ifgp~kd~eC~Cgkyk~~~~kg~~C~~Cgvev 82 (1291)
T PRK02995 3 DVNFFDELRIGLATADDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEV 82 (1291)
T ss_pred CCCCCCEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCCCCCCCCCEE
T ss_conf 67765728998148899998618356787652278899988883251422988587671786133246987769998650
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCC-------CH------H----
Q ss_conf 047757876772002776220130122578999980999656301332111232178865-------10------4----
Q gi|254780142|r 94 TLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLS-------SL------E---- 156 (1398)
Q Consensus 94 ~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~-------~~------~---- 156 (1398)
T Consensus 83 t~~~vrr~rmGHIeLa~PV~Hiw~~k~~ps~i~~ll~~~~k~le~viyf~~~iv~~~~~~~~~~~~~~l~~~~~~~~~~~ 162 (1291)
T PRK02995 83 TRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITSVDEEARHNDLPTLEAEMDVEKKQL 162 (1291)
T ss_pred CCCCCCCCCCCCEEECCCCEEECCCCCCCHHHHHHHCCCHHHHHEEEEEECEEECCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 55752325456740178725004127980399998698987821676520326035563211122023444554445554
Q ss_pred --------------------------------------------------------------------HHCCCC-HHHHH
Q ss_conf --------------------------------------------------------------------322369-99998
Q gi|254780142|r 157 --------------------------------------------------------------------KYQILT-EEEYV 167 (1398)
Q Consensus 157 --------------------------------------------------------------------~~~~~~-~~~~~ 167 (1398)
T Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (1291)
T PRK02995 163 EDQRDADIEARAQKLEADLAELEAEGAKADARRKVRDGAEREMRQIRDRAQREIDRLDEVWDTFKKLKPKQLIGDELLYR 242 (1291)
T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHH
T ss_conf 32011256665544323344432101101455542010245677776655555555666655430356322222188999
Q ss_pred HHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf 86763585550611552677888772674889999998731032203478864477888666634898511286304507
Q gi|254780142|r 168 EAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVL 247 (1398)
Q Consensus 168 ~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~ 247 (1398)
T Consensus 243 ~~~~~~~-~~f~~~~gaeai~~ll~~~dl~~~~~~l~~~~~~~~-~~~~~~~~krl~~v~~f~~s~n~Pewmil~vlPV~ 320 (1291)
T PRK02995 243 ELRDRYG-DYFTGGMGAEAIQKRLENFDLDAEAESLRETIRNGK-GQKKLRALKRLKVVAAFLTTGNSPMGMVLDAVPVI 320 (1291)
T ss_pred HHHHHHH-HHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCC
T ss_conf 9998640-233413429999999985799999999999986304-68999999999999999966999440210034779
Q ss_pred CCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHH
Q ss_conf 62235138846973131003789999999869999998739835677769999999888874277678772478765067
Q gi|254780142|r 248 PPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLK 327 (1398)
Q Consensus 248 P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~k 327 (1398)
T Consensus 321 Pp~lRP~v~ldgg~~a~sDLn~ly~~II~~NnrLk~~~~~gaP~~ii~ne~~mLQ~~V~al~DN~~~g~p~~~~~~RpLK 400 (1291)
T PRK02995 321 PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQEAVDALFDNGRRGRPVTGPGNRPLK 400 (1291)
T ss_pred CCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 98787516968986556225889999999889999999769968999889999999999997068888876478999555
Q ss_pred HHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCC
Q ss_conf 89986102378200034651004577403412554354620034898776128999999998798666300010012248
Q gi|254780142|r 328 SLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKER 407 (1398)
Q Consensus 328 s~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~ 407 (1398)
T Consensus 401 Sls~rLKGKeGRFR~NLmGKRVDfSaRSVIspDPnL~i~EvGVP~~mA~eLt~Pfvi~rl~~~~~~~nik~ak~~v~r~~ 480 (1291)
T PRK02995 401 SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQR 480 (1291)
T ss_pred CHHHHHCCCCCEECCCCCCCCCCCCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEHHHHHHCCCCCCHHHHHHHHHHCC
T ss_conf 38998467665120577766526589863617999865502684899987372643575776267566178999988249
Q ss_pred CCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHH
Q ss_conf 82501326665697899757631011140123589944954797312254546787754569974689999999999876
Q gi|254780142|r 408 PEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLML 487 (1398)
Q Consensus 408 ~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~ 487 (1398)
T Consensus 481 ~~v~dvle~vi~~~~VLfNRQPTLHRmSImah~~kv~~gkT~RLn~~vC~pYNADFDGDEMNlHvPQS~eAraEa~~Lm~ 560 (1291)
T PRK02995 481 PQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILML 560 (1291)
T ss_pred CHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEEECCCEEEECHHCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHH
T ss_conf 54778898774277146615752131533551478736845885510067666887773346427799999999999860
Q ss_pred HHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCC-----
Q ss_conf 750542378878204402589999998733678874468141799999999988898678523652046456676-----
Q gi|254780142|r 488 STNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGN----- 562 (1398)
Q Consensus 488 ~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~----- 562 (1398)
T Consensus 561 v~~nilsP~~G~Piig~~QD~ilG~y~LT~~~~~~~~e~~~f~~~~~~~~~~~~~~l~l~~~i~i~~~~~~~~~~~~~~~ 640 (1291)
T PRK02995 561 SSNNILKPADGRPVAMPSQDMVTGLYYLTTVKEGAKGEGRPFSSPAEAIMAFDRGELSLQAKVKIRLTQLRPPAEIEAEL 640 (1291)
T ss_pred CCCCEEECCCCCCEECHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCCC
T ss_conf 33277327999821231189998889875036664456562277999997534386632672799666656776543310
Q ss_pred --------CCCEEECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf --------142452179775112205545875101775110020136669999999808178999875588999999985
Q gi|254780142|r 563 --------SISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACS 634 (1398)
Q Consensus 563 --------~~~~~~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~ 634 (1398)
T Consensus 641 ~~~~~~~~~~~~~~~tt~Gr~ifn~~lp~~~~----~i~g~l~Kk~lg~li~~l~~~yg~~~~~~~ld~l~~l~~~~l~~ 716 (1291)
T PRK02995 641 FGPEGWQPGDAWTAETTLGRVLFNELLPEDYP----FVNEQMDKKVLSAIVNDLAERYPMIVVAQTLDKLKDAGFYWATR 716 (1291)
T ss_pred CCCCCCCCCCCEEECCCCCEEEECCCCCCCCC----EEEEEECCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 47656776763443177674764251478775----35414433148899999999839999999999999999999987
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 39861321232683699999999978999999886489766788878864234658999999999987611565432222
Q gi|254780142|r 635 SGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQK 714 (1398)
Q Consensus 635 ~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 714 (1398)
T Consensus 717 ~GfSiGI~D~~~~~~k~eii~~~~~~~~~i~~~~~~G~lt~~e~~~~l~~il~~a~d~v~~~~~~~l------------~ 784 (1291)
T PRK02995 717 SGVTVAMSDVLVPPEKQEILDGYEAQADKVEKQYERGLLTDDERRQELVEIWTEATDEVAEAMEENF------------P 784 (1291)
T ss_pred CCCEEEHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC------------C
T ss_conf 5865407650687789999999999999999987505565078999999999999999999999657------------8
Q ss_pred CCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEE
Q ss_conf 46883764225555784241120010000246443444566630111088898976405761032210121015674011
Q gi|254780142|r 715 KMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLS 794 (1398)
Q Consensus 715 ~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlq 794 (1398)
T Consensus 785 ~~N~~~~Mv~SGAKGS~~NIsQm~g~rGl~~~~~G~~ip~pI~nsF~~GLtp~EfFfHamgGREGLiDTAVKTA~SGYLq 864 (1291)
T PRK02995 785 DDNPIIMIVDSGARGNMMQIRQLAGMRGLVANPKGEIIPRPIKSSFREGLTVLEYFISTHGARKGLADTALRTADSGYLT 864 (1291)
T ss_pred CCCCHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHCCCCHHHHHHCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf 88859998660576789899998640677668988847763324411169788887616132333100421025412789
Q ss_pred EHHHHHHCCCEEEEECCCCCCCCEEEEEEECCE----EEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHH
Q ss_conf 015423014327751388766651211100884----8865000101221144201778971885178657899999999
Q gi|254780142|r 795 RRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQ----VVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIE 870 (1398)
Q Consensus 795 RrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~----~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~ 870 (1398)
T Consensus 865 RRLVkv~eDv~Vr~dDCgT~~gi~~~~~~~~~~g~~~~~~~~~~~~~~r~l~~d~~~~-~~~vi~~~~~~i~~~~~~~~~ 943 (1291)
T PRK02995 865 RRLVDVSQDVIVREEDCGTERGIVVPIAERDADGTLVRDENVETSVYARTLAADAVDA-DGNVVAEAGTDLGDPLIDALL 943 (1291)
T ss_pred HHHHHHHCCEEEEECCCCCCCCEEEEEEEECCCCCEEECHHHHHHHHHHHHHHHHCCC-CCCEEEECCCCCCHHHHHHHH
T ss_conf 9988875555999726885068043456755887555330235557763438861388-998885488627999999999
Q ss_pred HCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECC
Q ss_conf 75984020233100035518657887542017852000101460211110078898776420245432221122024014
Q gi|254780142|r 871 KCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPC 950 (1398)
Q Consensus 871 ~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvT 950 (1398)
T Consensus 944 ~~gi~~v~iRS~Ltc~s~~gvc~~cYgr~Lat~klVepGEaVGiIAAQSIGEPgTQMTLnTFH~AGvas----------- 1012 (1291)
T PRK02995 944 AAGVEEVKVRSVLTCESKTGVCAKCYGRSLATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVGD----------- 1012 (1291)
T ss_pred HCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHCCCCCC-----------
T ss_conf 759987862143354467889999998877634768888702343103368874203265642155443-----------
Q ss_pred CCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCE
Q ss_conf 87689721134651788778974276046640677600000011000013567855322507862135431132024636
Q gi|254780142|r 951 DGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGT 1030 (1398)
Q Consensus 951 lGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~ 1030 (1398)
T Consensus 1013 -------------------------------------------------------------------------------- 1012 (1291)
T PRK02995 1013 -------------------------------------------------------------------------------- 1012 (1291)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred EEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCC
Q ss_conf 89753127832001230236860267751011012212385347742778253224788420213778445413676135
Q gi|254780142|r 1031 VGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVS 1110 (1398)
Q Consensus 1031 v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~ 1110 (1398)
T Consensus 1013 -------------------------------------------------------------------------------- 1012 (1291)
T PRK02995 1013 -------------------------------------------------------------------------------- 1012 (1291)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred CCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCE
Q ss_conf 48422210132024554336773288988752511110111347867863312794499998368984026898138965
Q gi|254780142|r 1111 TGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKH 1190 (1398)
Q Consensus 1111 ~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~ 1190 (1398)
T Consensus 1013 ----------------nITlGvPRlkEIfeAr~PK~~a~i~e~~g~V~ie~~~~-~~~~~i~~-dd~~~~~~y~i~~~~~ 1074 (1291)
T PRK02995 1013 ----------------DITQGLPRVQELFEARTPKGKAPIAEVAGRVRIEDGER-FRKITIVP-DDGSEEVVYKVSKRQR 1074 (1291)
T ss_pred ----------------CCCCCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCC-CEEEEEEC-CCCCCEEEEECCCCCE
T ss_conf ----------------32367563899985148787763133103899973377-05999977-9998357997257855
Q ss_pred EEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCC
Q ss_conf 89841987740864643899999998752799999999999999999809700612560124762861489418864545
Q gi|254780142|r 1191 FYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYI 1270 (1398)
Q Consensus 1191 l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i 1270 (1398)
T Consensus 1075 l~v~dgd~V~~g~~l~~g~~dp~~iLri~G~~~~~~~lv~evq~Vyr~qGV~I~dKhievIvrqml~kv~i~d~gdt~~l 1154 (1291)
T PRK02995 1075 LRVSDGDHVEVGQQLVEGSADPHEVLRVLGPRAVQVHLVDEVQEVYRSQGVSIHDKHIEVIVRQMLRRVTVIDSGDTEFL 1154 (1291)
T ss_pred EEEECCCEEECCCEECCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCEECCEEHHHHHHHHCEEEEEECCCCCCC
T ss_conf 78735999964875034889989998862999999999999999999659752101007888866207899816866655
Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCC
Q ss_conf 66410699999999999972898752012100001453023107765040258999999745285523665322155073
Q gi|254780142|r 1271 LGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGR 1350 (1398)
Q Consensus 1271 ~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGq 1350 (1398)
T Consensus 1155 ~g~~v~~~~~~~~n~~~~~~~~~~~~~r~~llGITr~~l~t~S~Ls~ASFqeTt~vL~dAAi~gk~D~l~GlkEnIIlG~ 1234 (1291)
T PRK02995 1155 PGELVDRARFEAENRRVVAEGGEPASGRPVLMGITKASLATESWLSAASFQETTRVLTDAAINGRSDKLIGLKENVIIGK 1234 (1291)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCC
T ss_conf 73288799999999999983997113422146640043112219998613516799999998479875778102430478
Q ss_pred CCCCCCCHHHHHHHHHHCCC--HHHHHHHH
Q ss_conf 05655354665331210251--02221112
Q gi|254780142|r 1351 SIPAGTGAILHEKRRVAMNR--DQMILKER 1378 (1398)
Q Consensus 1351 liP~GTG~f~~~~~~~~~~~--~~~~~~~~ 1378 (1398)
T Consensus 1235 liP~GTGl~~y~~~~~~~~~~~~~~~~~~~ 1264 (1291)
T PRK02995 1235 LIPAGTGISRYRNIRVEPTEEARAAAYTIP 1264 (1291)
T ss_pred CCCCCCCHHHHCCCCCCCCHHHHHHHCCCC
T ss_conf 678775938864860565766774426788
|
|
| >PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=2798.08 Aligned_cols=1165 Identities=44% Similarity=0.726 Sum_probs=1039.7 Q ss_pred CCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 86405368984588678850144897175542545687568873362136856677215664156344883567578853 Q gi|254780142|r 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEV 93 (1398) Q Consensus 14 ~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~ 93 (1398) T Consensus 2 ~~k~i~~i~f~l~SPe~Ir~~S~~eV~~peT~n~~~~kP~~~GL~d~rifgp~~d~eC~cgk~k~~~~~g~~C~tCG~~~ 81 (1284) T PRK00566 2 SQKGIKSLTISIASPEQILNWSKGEVTKPETINYKSLKPEPNGLFDEAIFGPVKDYECACGKYKKIKHRGKICERCGVEI 81 (1284) T ss_pred CCCEECEEEEEECCHHHHHHHHCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCC T ss_conf 97630549999429999987605587277740088998789997477346978676342676254455985899999874 Q ss_pred CCCCCCCCCCCCCCCCCCCEEECHHHHH--HHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHH------ Q ss_conf 0477578767720027762201301225--78999980999656301332111232178865104322369999------ Q gi|254780142|r 94 TLSSVRRDRMAHIDLASPVAHPWFLKSL--PSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEE------ 165 (1398) Q Consensus 94 ~~~~~r~ghfGhIeLa~PV~Hi~f~k~~--~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~------ 165 (1398) T Consensus 82 ~~~~vr~ghfGHIeLa~PV~Higf~k~i~~ps~i~~lL~~~~k~le~v~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (1284) T PRK00566 82 TESIVRRERMGHIELAAPVAHIWMTKELPSPSKISLVLDISYKEVEQVVYFVNYIVLDEGNNKYDKKSIFNFKEVLDLTS 161 (1284) T ss_pred CCCCCCCCCCCCCCCCCCEEECCEECCCCCHHHHHHHHCCCHHHHHHHHHCCCEEEECCCCCCCCHHCHHHHHHHHHHHH T ss_conf 50786899612513888645274635888725899986889999876640025799547876550002156899986540 Q ss_pred ---------------------------------HHHH------HHH----C----------CCCCEEECCCHHHHHHHHH Q ss_conf ---------------------------------9886------763----5----------8555061155267788877 Q gi|254780142|r 166 ---------------------------------YVEA------VSQ----F----------GQDQFIAMMGADAIYELLI 192 (1398) Q Consensus 166 ---------------------------------~~~~------~~~----~----------~~~~~~~~~g~~~i~~~l~ 192 (1398) T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~e~i~~~l~ 241 (1284) T PRK00566 162 PKGSIRTRNKLRRTLRNIQERIEKELSHEQDFDYRLAVTYYQMLKDSNLPFSVKDVFNFIEKHTGVRFGIGAEAILELLE 241 (1284) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHH T ss_conf 22013578999999999888766530231156665556676543002466422456654430145213777899999987 Q ss_pred HCCHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHH Q ss_conf 267488999999873103--220347886447788866663489851128630450762235138846973131003789 Q gi|254780142|r 193 ALDLQNLALTLRDQLSKS--SSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDL 270 (1398) Q Consensus 193 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~ 270 (1398) T Consensus 242 ~idl~~~~~~~~~~~~~~~~~~~~~~~~~~krl~~~~~~~~~~~rPewmiltvlpVpPp~vRPsv~ldgg~~~~dDLt~~ 321 (1284) T PRK00566 242 KIDLEEEHEKINQALRKSDNAEDQKTKRLLRRLETIRWIKDSGSKPEWMILTRIPVTPPDTRPIIQLDGGRFTTSDINNF 321 (1284) T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEEEECCCCCCCCCCHHH T ss_conf 69989999999999742676367899999988999997762699971689842478999873459968997664321889 Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCC Q ss_conf 99999986999999873983567776999999988887427767877247876506789986102378200034651004 Q gi|254780142|r 271 YRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVD 350 (1398) Q Consensus 271 ~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVd 350 (1398) T Consensus 322 l~~Ii~~N~~Lk~~~~~gap~~ii~~~~~lLQ~~V~tl~dN~~~~~p~~~~s~RplKsl~qrLKGKeGRfR~NLmGKRVD 401 (1284) T PRK00566 322 YRKIIIRNERLKRIQETDAPSILLNNEKRLLQEAVDALFDNNSRKKPVLGKDKRPLKSLSDHLKGKQGLFRQNLLGKRVD 401 (1284) T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCC T ss_conf 99999999999999875998899999999999999998707787887758899834019988466554013566766205 Q ss_pred CCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHH----HHHCC-----CCCCCCCCCCEEECCCCCEEHHHHHHHCCC Q ss_conf 577403412554354620034898776128999999----99879-----866630001001224882501326665697 Q gi|254780142|r 351 YSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQ----LEKKG-----YVSTVKQAKKFVEKERPEVWDVLAEVVHQH 421 (1398) Q Consensus 351 fs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~----L~~~g-----~~~~i~~~k~~i~~~~~~v~~v~rhl~~gd 421 (1398) T Consensus 402 fSaRSVIspDPnL~i~EvGVP~~~A~~Lt~P~~V~ell~~~v~nGp~~~p~a~~ik~~~~~~~~~~~~~~~i~e~~i~~~ 481 (1284) T PRK00566 402 YSGRSVIVVGPELKMYEVGIPALMILKLFKPFIIHELIRKFDENGNEIQPIAANIKLAEQMILNQDDEIWPIVEKVIKQR 481 (1284) T ss_pred CCCCEEEECCCCCCHHHCCCHHHHHHHCCCCEEHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCC T ss_conf 67870562699765111277088887708847799999987406986675302357778998733741457799875388 Q ss_pred EEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCE Q ss_conf 89975763101114012358994495479731225454678775456997468999999999987675054237887820 Q gi|254780142|r 422 VVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPV 501 (1398) Q Consensus 422 ~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi 501 (1398) T Consensus 482 ~VLfNRQPSLHkmSiMahrvkv~~gkTfRLn~~vc~pYNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~nilsP~~G~Pi 561 (1284) T PRK00566 482 PVLLNRAPTLHRLGIQAFEPKIVDGKAIRLHPLVTTAFNADFDGDQMAVHVPLSKEAVAEARAILLASWHILGPKDGKPI 561 (1284) T ss_pred EEEECCCCCCCCCEEEEEEEEEECCCEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCE T ss_conf 14653776212043213577983684477334456655578887424521668999999999986244157137899953 Q ss_pred EEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCEEE Q ss_conf 44025899999987336788744681417999999999888986785236520464566761424521797751122055 Q gi|254780142|r 502 TVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEIL 581 (1398) Q Consensus 502 ~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~~~tt~Gr~~~~~il 581 (1398) T Consensus 562 ig~iQD~i~G~y~LT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~i~~~~~~~p~~~~~~~~~~~tt~Gk~ifs~~l 641 (1284) T PRK00566 562 ITPTQDMVLGNYYLTTEKFPQPGEGMIFSTVDEAIRAYELKKVHIHAIIGISTKAFPNKTFSKQGILITTVGKIIFNDVL 641 (1284) T ss_pred EECCHHHHHCCHHHCCCCCCCCCCCEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHC T ss_conf 40323354212211014467766532726899999998739842375123131337777656774498454331198765 Q ss_pred ECCCCCE----------------------EE----EECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 4587510----------------------17----751100201366699999998081789998755889999999853 Q gi|254780142|r 582 PRHHEIS----------------------FD----ICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSS 635 (1398) Q Consensus 582 p~~~~~~----------------------~~----~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~ 635 (1398) T Consensus 642 p~~~~~~~~~~~~~~~~~~~ii~~~~~~~~~i~~~~~~~~~~kk~~~~li~~l~~~~g~~~~~~~ld~i~~l~~~~~~~~ 721 (1284) T PRK00566 642 PENFPYINDGKNLYGLNQFEIVGMGEDIRDYLKAYNLKEPFTKKTLSKVIDYLYKVSEIEVVPQTMDKIKALGFKYSTIS 721 (1284) T ss_pred CCCCCCCCCCCCCCCCCCCEEEECCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 89988655764334588753872698337888520650454642299999999998389999999999999999999756 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98613212326836999999999789999998864897667888788642346589999999999876115654322224 Q gi|254780142|r 636 GISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKK 715 (1398) Q Consensus 636 GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 715 (1398) T Consensus 722 g~sigi~Di~~~~~k~~~i~~a~~~v~~~~~~~~~g~lt~~e~~~~v~~~l~~~~~~v~~~~~~~~~~--------~~~~ 793 (1284) T PRK00566 722 ATTISAFDIPSYDNKQEYFKETDELVAKLKEFYLKGLLTDDERYTKVVQAWSQVKDKVSHDIEKLINS--------PEYK 793 (1284) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------CCCC T ss_conf 87511134567257899999999999999999864688530789999999999999999999998730--------3256 Q ss_pred CCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC-----------CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCC Q ss_conf 6883764225555784241120010000246443-----------44456663011108889897640576103221012 Q gi|254780142|r 716 MNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG-----------EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVV 784 (1398) Q Consensus 716 ~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G-----------~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTA 784 (1398) T Consensus 794 ~N~~~iM~~SGAKGS~~NisQm~G~~G~~~~~~~~~~~~~~~~~~~~~e~pV~nsF~~GLtP~EfFFHaMgGREGLIDTA 873 (1284) T PRK00566 794 DNSIVIMADSGARGNISNFTQLFGMRGLMSKSYNYDQKNNSKVIKDTIEVPIKHSFIEGLTVSEYFNSSYGARKGMTDTA 873 (1284) T ss_pred CCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHCCCCCCCCHHHCC T ss_conf 77368986167766899999987423651467787667777766665550000110249973664220654233014410 Q ss_pred CCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEEC--CEEEEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCC Q ss_conf 10156740110154230143277513887666512111008--8488650001012211442017789718851786578 Q gi|254780142|r 785 MRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDS--GQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLIL 862 (1398) Q Consensus 785 vKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~--~~~~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~ 862 (1398) T Consensus 874 VKTAeSGYlQRRLVKalEDl~V~ydd~~t~~g~~v~~~~~~~d~~~ie~l~~~~~~r~~~~~i~~~~~~~~~~~~~~~i~ 953 (1284) T PRK00566 874 MKTAKSGYMTRKLVDATQEVIINDDDCGTKKGIIVEEIRNTKDNSSIESLKDRIVNRYSINPIYDPKTKKLIVEADKLIT 953 (1284) T ss_pred HHCCCCCCCHHHHHHHHCCEEEEECCCCCCCCEEEEEEEECCCCCEEEEHHHHHHCCEEHHHHCCCCCCEEEECCCCCCC T ss_conf 22000146287888764647987314777788189998866997520123544415052445168566706520454002 Q ss_pred HHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 99999999759840202331000355186578875420178520001014602111100788987764202454322211 Q gi|254780142|r 863 ESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMD 942 (1398) Q Consensus 863 ~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~ 942 (1398) T Consensus 954 ~~~~~~i~~~~i~~~~irs~l~~~~~~~~~~kc~g~dl~~~~lvepGEaVG~IAAQSIGEPgTQMTLnTFH~AGVas~-- 1031 (1284) T PRK00566 954 SELANQIQNSGIREVEVRSPLHCESENGVCQKCFGLDLSTNKLVETGTAIGVIAAQSIGEPGTQLTMRTFHTGGVAGE-- 1031 (1284) T ss_pred HHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHCHHHHHCCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCCCC-- T ss_conf 999999998199789853731342154199998566556078677777210000023688622032766543433566-- Q ss_pred CCEEEECCCCEEEEEEEEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCE Q ss_conf 22024014876897211346517887789742760466406776000000110000135678553225078621354311 Q gi|254780142|r 943 RSFIESPCDGIVKIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFP 1022 (1398) Q Consensus 943 ~~~iknvTlGVPRlkEi~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~ 1022 (1398) T Consensus 1032 ----~NVTlGvPRlkEIin~~~pk~~---------------------------------------------------~~~ 1056 (1284) T PRK00566 1032 ----TNITQGFERLKQLFDVIQPKEN---------------------------------------------------EKA 1056 (1284) T ss_pred ----CCCCCCCHHHHHHHHHCCCCCC---------------------------------------------------CCE T ss_conf ----7624675357988872488986---------------------------------------------------644 Q ss_pred EEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEE Q ss_conf 32024636897531278320012302368602677510110122123853477427782532247884202137784454 Q gi|254780142|r 1023 IITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLS 1102 (1398) Q Consensus 1023 i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~ 1102 (1398) T Consensus 1057 ~i~~v~g~------------------------------------------------------------------------ 1064 (1284) T PRK00566 1057 VISEVKGT------------------------------------------------------------------------ 1064 (1284) T ss_pred EEEECCEE------------------------------------------------------------------------ T ss_conf 66752729------------------------------------------------------------------------ Q ss_pred ECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCC-CEEEEEEECCCCCCEE Q ss_conf 136761354842221013202455433677328898875251111011134786786331279-4499998368984026 Q gi|254780142|r 1103 VSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKN-KSRVVIEPFEDGVEPA 1181 (1398) Q Consensus 1103 v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~-k~~~vi~~~~~g~~~~ 1181 (1398) T Consensus 1065 ------------------------------------------------------i~~i~~~~~~~~~~~v~-~~~~~~~~ 1089 (1284) T PRK00566 1065 ------------------------------------------------------VESITKDSNANGYNVVI-IKNKDNEV 1089 (1284) T ss_pred ------------------------------------------------------EEEEEECCCCCCEEEEE-ECCCCCEE T ss_conf ------------------------------------------------------99999705887248999-56997179 Q ss_pred EEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEE Q ss_conf 89813896589841987740864643899999998752799999999999999999809700612560124762861489 Q gi|254780142|r 1182 EYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEI 1261 (1398) Q Consensus 1182 e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I 1261 (1398) T Consensus 1090 ~~~i~~~~~l~v~~~d~v~~g~~lt~g~i~~~~ll~v~Gi~~~~~~~i~evq~Vy~~qGv~i~dk~ievi~rqm~~~~~i 1169 (1284) T PRK00566 1090 NYPTPFNAVLRVKTGDEVIPGSKITEGSIDVKDLLKVAGIENVRQYIIKEVQKVYRMQGIEIADKYIEVIIRQLTNKLQI 1169 (1284) T ss_pred EEECCCCCEEEECCCCEEECCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEECCEEEHHHHHHCCEEEE T ss_conf 99746787788636998946986458999989987556999999999999999988448656256635267664246599 Q ss_pred ECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCC Q ss_conf 41886454566410699999999999972898752012100001453023107765040258999999745285523665 Q gi|254780142|r 1262 TDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDG 1341 (1398) Q Consensus 1262 ~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~G 1341 (1398) T Consensus 1170 ~~~gd~~~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~GIt~~~~~~~S~L~~ASFeeT~~vL~dAA~~g~~D~l~G 1249 (1284) T PRK00566 1170 TDPGDSGLFVGQTISINEFTEVNQSMLLNKKKPPSAINQVFGLDEAPSKSGSFLSAASFQDTKKILTDAAVKSQKDYLIG 1249 (1284) T ss_pred EECCCCCCCCCCEEEHHHHHHHHHHHHHCCCCCCEEECHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 95798664575375399999999999977998823221103623033554329998311316689999998479885778 Q ss_pred CCEEEECCCCCCCCCCHHHHHHHHHHCCC Q ss_conf 32215507305655354665331210251 Q gi|254780142|r 1342 FKENVIVGRSIPAGTGAILHEKRRVAMNR 1370 (1398) Q Consensus 1342 vSENIIlGqliP~GTG~f~~~~~~~~~~~ 1370 (1398) T Consensus 1250 vsEnII~G~~iP~GTG~~~~~~~~~~~~~ 1278 (1284) T PRK00566 1250 LKENVILGNLIPAGTGFKDVEEVIAYGEE 1278 (1284) T ss_pred CCHHHCCCCCCCCCCCCCHHHEEEECCHH T ss_conf 00353038976877687413216864587 |
|
| >KOG0260 consensus | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=2101.98 Aligned_cols=1211 Identities=25% Similarity=0.320 Sum_probs=888.6 Q ss_pred CCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 35678640536898458867885014489717554254568756887336213685667721566415634488356757 Q gi|254780142|r 10 NPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKC 89 (1398) Q Consensus 10 ~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~C 89 (1398) T Consensus 7 ~~~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~--e~~~pk~ggl~D~RlG~idr~~---------------~CqTC 69 (1605) T KOG0260 7 FSQAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETM--EGGRPKLGGLMDPRLGTIDRDS---------------LCQTC 69 (1605) T ss_pred CCCCCCEEEEEEEEECCCHHHHHCCEEEEEECCCCC--CCCCCCCCCCCCCCCCCCCCCC---------------HHHHH T ss_conf 323742145688750468566420224775334201--3677776774663347777641---------------10433 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEECHHHH---HHHHHHHHHCCCHHHHHHHHHHCCEEEEC-CCCCCHHHHCCCCHHH Q ss_conf 8853047757876772002776220130122---57899998099965630133211123217-8865104322369999 Q gi|254780142|r 90 GVEVTLSSVRRDRMAHIDLASPVAHPWFLKS---LPSRISTLLGMSLRDVERVLYFESYVVVD-PGLSSLEKYQILTEEE 165 (1398) Q Consensus 90 g~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~---~~~~i~~~l~~~~~~~~~v~y~~~~~~~~-~~~~~~~~~~~~~~~~ 165 (1398) T Consensus 70 ~g~~~~Cp---GHFGhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~~k~rl~~v~~vck~k~ 146 (1605) T KOG0260 70 GGNMFECP---GHFGHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKV 146 (1605) T ss_pred CCCCCCCC---CCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCHHEEECCCCCCHHHHHHHHCCCCCHHHHHHHHHCCCE T ss_conf 35533278---655526504432238999999999988510102302044683044556640487413899987633310 Q ss_pred HHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHC------CCCCHHHHHHHHHH----HHHHHHHHCCCC Q ss_conf 98867635855506115526778887726748899999987310------32203478864477----888666634898 Q gi|254780142|r 166 YVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSK------SSSIFRRKKIIKRL----KIVDSFITSGNN 235 (1398) Q Consensus 166 ~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~----~~~~~f~~~~~~ 235 (1398) T Consensus 147 ~ce~g~~~e~~----g~sgcg~kqP~i~r~gl~l~a~~k~~~e~~~e~k~~ls~e~V~~i~k~Isded~~~lg~~~~~ar 222 (1605) T KOG0260 147 VCEGGIDVESD----GRSGCGLKQPSIRRLGLDLWAFWKQGDEDSQESKRKLSAERVLEIFKRISDEDIDQLGFKPKIAR 222 (1605) T ss_pred EEECCCCCCCC----CCCCCCCCCCCEECCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHCCCCCCCC T ss_conf 44045201456----65543446872342574054432115766771002475999999998613445666357877688 Q ss_pred CCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 51128630450762235138846973131003789999999869999998739835677769999999888874277678 Q gi|254780142|r 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK 315 (1398) Q Consensus 236 Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~ 315 (1398) T Consensus 223 pewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~n~~l~r~e~~ga~~H~i~e~~~LlqfhVat~~Dn~~pg 302 (1605) T KOG0260 223 PEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFHVATYVDNDIPG 302 (1605) T ss_pred CCEEEEEEECCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHEECCCCCC T ss_conf 76258888437987666504532543576333789999999878875323228704668887767640131101466667 Q ss_pred CCC-CCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHH-----HHHHHH-- Q ss_conf 772-478765067899861023782000346510045774034125543546200348987761289-----999999-- Q gi|254780142|r 316 RVV-TGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP-----FLYAQL-- 387 (1398) Q Consensus 316 ~~~-~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P-----~~~~~L-- 387 (1398) T Consensus 303 qp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqe 382 (1605) T KOG0260 303 QPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQE 382 (1605) T ss_pred CCCCCCCCCCCCCCHHHHHCCCCCHHHHCCCCCCCCCCEEEEECCCCCCCHHCCCCCHHHHHHCCCCCEECCCCHHHHHH T ss_conf 75000236985200565521421022321002345764025664899865010368699996466743015203899999 Q ss_pred -HHCCCCCCCCCCCCEEEC-----------------CCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEE Q ss_conf -987986663000100122-----------------48825013266656978997576310111401235899449547 Q gi|254780142|r 388 -EKKGYVSTVKQAKKFVEK-----------------ERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAI 449 (1398) Q Consensus 388 -~~~g~~~~i~~~k~~i~~-----------------~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~ 449 (1398) T Consensus 383 LV~~g~~~~--pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTf 460 (1605) T KOG0260 383 LVRRGLLEH--PGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTF 460 (1605) T ss_pred HHHCCCCCC--CCCCEEEECCCCEEEEEECCCCCCCCCCCCCEEEEEECCCCEEEECCCCCHHHHHHHHCEEEECCCCEE T ss_conf 850787779--775135514785788863477566546666678886315988997489717776545307897057518 Q ss_pred EEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEE Q ss_conf 97312254546787754569974689999999999876750542378878204402589999998733678874468141 Q gi|254780142|r 450 QLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLF 529 (1398) Q Consensus 450 rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f 529 (1398) T Consensus 461 rLNlsvtsPynADFDGDemnlhvPQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd--------~F 532 (1605) T KOG0260 461 RLNLSVTSPYNADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRD--------VF 532 (1605) T ss_pred EECEEECCCCCCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEHHHHHHHHHHHHHH--------HH T ss_conf 9670204776578787513012673056789999986223643377689850343256678888876676--------55 Q ss_pred CCHHHHHHHH-----HCCCCC-CCCEEEEEECCCCCCCCCCCEE-----ECC--CC----CCCCC---CEEEECCCCCEE Q ss_conf 7999999999-----888986-7852365204645667614245-----217--97----75112---205545875101 Q gi|254780142|r 530 ADMGEVYHAL-----ENKIVT-LHSKIRGRYKSVDKDGNSISKI-----YDT--TP----GRMII---GEILPRHHEISF 589 (1398) Q Consensus 530 ~~~~~~~~~~-----~~~~~~-~~a~i~~~~~~~~~~~~~~~~~-----~~t--t~----Gr~~~---~~ilp~~~~~~~ 589 (1398) T Consensus 533 l~r~~vmnLlm~~p~~d~~~Pa~pai~Kp~PlWTGkQifsliiP~~in~~r~~s~h~d~~~~~~~p~dt~~lie~g~l~~ 612 (1605) T KOG0260 533 LNRAQVMNLLMYVPDWDGPPPAKPAILKPKPLWTGKQIFSLIIPGGINYIRDHSTHPDSEDELISPGDTRVLIEGGELLI 612 (1605) T ss_pred HCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHEEEECCCCCCEECCCCCCCCCCCCCCCCCCCEEEEECCCEEE T ss_conf 06999997875136657889987556788765213101146547974233134467677764316888469995783378 Q ss_pred EEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH----HHHHHHHHHHHHHHHH Q ss_conf 775110020136669999999808178999875588999999985398613212326836----9999999997899999 Q gi|254780142|r 590 DICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPES----KEKIIAEADKMVKEYE 665 (1398) Q Consensus 590 ~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~----k~~~i~~a~~~~~~~~ 665 (1398) T Consensus 613 g~l~Kkt~G~s~g~lvh~i~~e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi 692 (1605) T KOG0260 613 GVLCKKTVGSSAGGLVHVIFLEKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNTIKEAKRDVLAVI 692 (1605) T ss_pred EEEECCCCCCCCCCEEEEEEHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 77650114554574578753121779999887878999999998627401203212588899999999999899999999 Q ss_pred HHHHCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEE Q ss_conf 98864897-------667888788642346589999999999876115654322224688376422555578---42411 Q gi|254780142|r 666 NQYNDGLI-------TRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMR 735 (1398) Q Consensus 666 ~~~~~G~~-------t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ 735 (1398) T Consensus 693 ~~a~~~~L~~~pg~tlretfe~~v~~vlndArd~~gssA~~------------sl~esNn~k~Mv~aGSKGs~inisQ~s 760 (1605) T KOG0260 693 REAQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQK------------SLSESNNFKTMVVAGSKGSFINISQVS 760 (1605) T ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHCCCHHHHHHHCCCCCCEEHHHHH T ss_conf 88765004678213578999999999999998865407876------------431020087787513777620054433 Q ss_pred EEEEECCCCCC--CCCCCC----------CCC-----CCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHH Q ss_conf 20010000246--443444----------566-----6301110888989764057610322101210156740110154 Q gi|254780142|r 736 QLGGMRGLIAK--PSGEII----------ESP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLV 798 (1398) Q Consensus 736 ql~Gqq~l~gk--p~G~~~----------~~P-----V~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLv 798 (1398) T Consensus 761 aCVGqQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~ 840 (1605) T KOG0260 761 ACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLM 840 (1605) T ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHH T ss_conf 44301000120124577754566656699982104423212025798899999874253011010011466425999999 Q ss_pred HHHCCCEEEEECCCCCCCC--EEEEEE--ECC-------EEEEEEC--CCCCCCCC------------HHHCCCCCC--- Q ss_conf 2301432775138876665--121110--088-------4886500--01012211------------442017789--- Q gi|254780142|r 799 DVAQNCVVNQVDCNTKKGL--TITHIV--DSG-------QVVYSLG--SRVLGRTA------------LDDIINPLT--- 850 (1398) Q Consensus 799 k~~eDl~V~~~D~~t~~g~--~~~~~~--~~~-------~~~~~l~--~~~~~r~~------------~~di~~~~~--- 850 (1398) T Consensus 841 kameDimv~-yDgTVRNs~gqviQf~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~ 919 (1605) T KOG0260 841 KAMEDIMVA-YDGTVRNSLGQVIQFKYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELL 919 (1605) T ss_pred HHHHHHHHH-CCCCEECCCCEEEEEEECCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 999988744-3754130456058987226766664010024553440588887543013331755421566766444457 Q ss_pred ----------CC---------EEEECCCC---CCHHHH----HHHHHCCCCEEE------------------------CC Q ss_conf ----------71---------88517865---789999----999975984020------------------------23 Q gi|254780142|r 851 ----------NE---------CIVKAGQL---ILESHV----NEIEKCGIRSVR------------------------IR 880 (1398) Q Consensus 851 ----------~~---------~i~~~~~~---i~~~~~----~~i~~~~i~~v~------------------------ir 880 (1398) T Consensus 920 ~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~l~iv~g~ 999 (1605) T KOG0260 920 KLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVIVRGE 999 (1605) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHEEEEEECC T ss_conf 78999988787633114423200245775611413699999977751034433543222456544045430236886074 Q ss_pred CCCCH-------HHHHCCC-----------HHHHHHHC------CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 31000-------3551865-----------78875420------178520001014602111100788987764202454 Q gi|254780142|r 881 SALTC-------ESSRGVC-----------VLCYGRDL------ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936 (1398) Q Consensus 881 s~lt~-------~~~~~v~-----------~~cy~~~l------~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAG 936 (1398) T Consensus 1000 ~~~sraqrl~~~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aG 1079 (1605) T KOG0260 1000 DYISRAQRLFNILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAG 1079 (1605) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHEEEEECCCCCHHHHHHHHHHCCCHHHCCCCHHCCCC T ss_conf 16788888888998766778988987035578888776434311123413762047688887717715434620001034 Q ss_pred CCCCCCCCEEEECCCCEEEEEE-EEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEE Q ss_conf 3222112202401487689721-134651788778974276046640677600000011000013567855322507862 Q gi|254780142|r 937 AVTVMDRSFIESPCDGIVKIKN-RNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE 1015 (1398) Q Consensus 937 VAS~~~~~~iknvTlGVPRlkE-i~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~ 1015 (1398) T Consensus 1080 Vss-------knVt~gvprlkei~Nv~k~~ktpsLtV~l------~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~yd 1146 (1605) T KOG0260 1080 VSS-------KNVTLGVPRLKEIINVAKNAKTPSLTVYL------TGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYD 1146 (1605) T ss_pred EEE-------EEEECCCCCHHHHHHHHCCCCCCEEEEEE------CCHHHCCHHHHHHHHHHCCCCCHHHHHCCCCCEEC T ss_conf 011-------01321586513441010157996079996------42110165778777651331338765305763026 Q ss_pred CCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEEC Q ss_conf 13543113202463689753127832001230236860267751011012212385347742778253224788420213 Q gi|254780142|r 1016 WDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFL 1095 (1398) Q Consensus 1016 ~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~ 1095 (1398) T Consensus 1147 pdp~~tvI~ed~e~v~a~~e~pd~D~~-----~ispwlLrlelDr~~-----m-------~dk~ltm~~ia~~i~~~f~~ 1209 (1605) T KOG0260 1147 PDPQSTVIDEDREFVVAYYEMPDEDVG-----RISPWLLRLELDRAS-----M-------TDKKLTMEQIAEKINRGFGS 1209 (1605) T ss_pred CCCCCEEECCCHHHHHHHHCCCCCCHH-----HCCHHHHHHHHHHHH-----C-------CCCCCCHHHHHHHHHHHCCC T ss_conf 887520334665557744407643142-----307688875330655-----0-------36533399999998742068 Q ss_pred CCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECC--CCCEEEEEEECCCCEEEEEEE Q ss_conf 778445413676135484222101320245543367732889887525111101113--478678633127944999983 Q gi|254780142|r 1096 PVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAE--ISGTIRIKRNYKNKSRVVIEP 1173 (1398) Q Consensus 1096 ~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiise--i~Giv~i~~~~~~k~~~vi~~ 1173 (1398) T Consensus 1210 d~~~i~~ddna~klv~r~ri~~~~---------------e~D~~l-~~Ie~-~ml~~~~l~G~~~-------i~kV~m~~ 1265 (1605) T KOG0260 1210 DLACIFSDDNAEKLVLRLRIAKEE---------------EDDVFL-KCIEA-NMLGDMTLRGIPD-------IFKVYMSP 1265 (1605) T ss_pred CCCEEECCCCCCCEEEEEEECCCC---------------CHHHHH-HHHHH-HHHHHCCCCCCCC-------CCEEEEEE T ss_conf 875054166776227999834764---------------066888-87887-6654143578566-------10699863 Q ss_pred CCCCCCEE-EEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHH Q ss_conf 68984026-89813896589841987740864643899999998752799999999999999999809700612560124 Q gi|254780142|r 1174 FEDGVEPA-EYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVV 1252 (1398) Q Consensus 1174 ~~~g~~~~-e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIa 1252 (1398) T Consensus 1266 ~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~ 1345 (1605) T KOG0260 1266 TEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLC 1345 (1605) T ss_pred CCCCCEEECCEEEEECCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHEEEECCCCHHHHHHHHHH T ss_conf 37786111222688328612776646678885201455333565551479887653564441676245303388899999 Q ss_pred HHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHH Q ss_conf 76286148941886454566410699999999999972898752012100001453023107765040258999999745 Q gi|254780142|r 1253 RHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAI 1332 (1398) Q Consensus 1253 D~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi 1332 (1398) T Consensus 1346 dvmT~~g~lm------~itRhg~nr~~tgaLmr--------------------------------cSfEetv~il~~aa~ 1387 (1605) T KOG0260 1346 DVMTARGHLM------AITRHGINRQDTGALMR--------------------------------CSFEETVDILMDAAA 1387 (1605) T ss_pred HHHHCCCCEE------EEECCCCCHHHCCCCCC--------------------------------CCHHHHHHHHHHHHH T ss_conf 9985102024------55213520430201145--------------------------------438777788987776 Q ss_pred CCCEECCCCCCEEEECCCCCCCCCCHH Q ss_conf 285523665322155073056553546 Q gi|254780142|r 1333 AGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398) Q Consensus 1333 ~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398) T Consensus 1388 ~~ekd~~rgvsEnImlgqlap~gTg~~ 1414 (1605) T KOG0260 1388 HAEKDPCRGVSENIMLGQLAPMGTGCF 1414 (1605) T ss_pred HHCCCCCCCCEEEEEECCCCCCCCCCE T ss_conf 513377766111356536456777633 |
|
| >KOG0261 consensus | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1998.59 Aligned_cols=1176 Identities=25% Similarity=0.334 Sum_probs=844.8 Q ss_pred HHHCCCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 751356786405368984588678850144897175542545687-5688733621368566772156641563448835 Q gi|254780142|r 7 RFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFK-PERDGLFCARIFGPIKDYECICGKYKRMKYKGII 85 (1398) Q Consensus 7 ~~~~~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~k-P~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~ 85 (1398) T Consensus 2 k~~~e~~~~kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~---------------~~ 66 (1386) T KOG0261 2 KQFREDEIPKKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKK---------------DK 66 (1386) T ss_pred CCCCCCCCCCEEEEEEECCCCHHHHHHCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCCCCCC---------------CC T ss_conf 741102244222257623699899974016776415155542144877689867345888777---------------73 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHH---HHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCC Q ss_conf 6757885304775787677200277622013012257---8999980999656301332111232178865104322369 Q gi|254780142|r 86 CEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLP---SRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILT 162 (1398) Q Consensus 86 C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~---~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~ 162 (1398) T Consensus 67 C~TCg~~la~C~---GHfGy~~L~LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl-~~lr~p~~~~l~k~~l~k 142 (1386) T KOG0261 67 CATCGEGLADCI---GHFGYLKLALPVFHIGYFKATIQILQCICKNCSSILLSEEDKRQFL-KKLRNPGLDNLRKKALLK 142 (1386) T ss_pred CCHHCCCHHHCC---CCCCEEEECCEEEEEHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHCCCCCHHHHHHHHH T ss_conf 201105644355---4344276424045406599999999999886466556998999999-986278987477889999 Q ss_pred H----HHHHHHHHHCCCCCEEECCCHHHHHHHH------HHCC--HHHHHHHHHHHHHCCC----CCHHHHHHHHHHHHH Q ss_conf 9----9998867635855506115526778887------7267--4889999998731032----203478864477888 Q gi|254780142|r 163 E----EEYVEAVSQFGQDQFIAMMGADAIYELL------IALD--LQNLALTLRDQLSKSS----SIFRRKKIIKRLKIV 226 (1398) Q Consensus 163 ~----~~~~~~~~~~~~~~~~~~~g~~~i~~~l------~~~~--~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~ 226 (1398) T Consensus 143 ri~~~CkK~~~C~hCg~~NG~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~~~~~n~e~~~~~~~~~~~LnPl~vL 222 (1386) T KOG0261 143 RIVAKCKKVNTCSHCGALNGTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKTAISHNKELEGHLSSCCEELNPLVVL 222 (1386) T ss_pred HHHHHHHCCCCCCCCCCCCCEEECCCCCEEEEEEHHHCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHH T ss_conf 99998652652565677676121135410476332220455661123467888887652720576777787642859999 Q ss_pred HHHHH-------------CCCCCCEEEEEECCCCCCCCCCEEEECC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHH Q ss_conf 66663-------------4898511286304507622351388469-731310037899999998699999987398356 Q gi|254780142|r 227 DSFIT-------------SGNNPGWMIIRKLPVLPPDLRPLVALDF-GRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEI 292 (1398) Q Consensus 227 ~~f~~-------------~~~~Pewmil~~lpV~P~~~RP~v~~~~-g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~ 292 (1398) T Consensus 223 nLFk~i~~~D~eLLg~~~~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~KltEIi~tn~vik~~~~~g~~~~ 302 (1386) T KOG0261 223 NLFKQIKEDDCELLGMDSEEGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTMKLTEIILTNDVIKKHLSKGTPIN 302 (1386) T ss_pred HHHHHCCCCCCCEEEECCCCCCCHHEEEEECCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCH T ss_conf 99862882351403134676981134788335895114540131577777843132423555357789999861599710 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHH Q ss_conf 77769999999888874277678772478765067899861023782000346510045774034125543546200348 Q gi|254780142|r 293 IIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPK 372 (1398) Q Consensus 293 i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~ 372 (1398) T Consensus 303 ~imE~Wd~lQl~~AlyINSEl~g~~~~~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~ 382 (1386) T KOG0261 303 LIMEDWDFLQLQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPI 382 (1386) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCEECCCCCCEEECCCCEEECCCCCCCEEECCCHH T ss_conf 24555677777887764033779999989887418999973266771202346744402485353799985210125118 Q ss_pred HHHHHHHHHHH--------HHHHHHCCCCCCCCCCCCEEE---------------------CCCCCEEHHHHHHHCCCEE Q ss_conf 98776128999--------999998798666300010012---------------------2488250132666569789 Q gi|254780142|r 373 LMALELFKPFL--------YAQLEKKGYVSTVKQAKKFVE---------------------KERPEVWDVLAEVVHQHVV 423 (1398) Q Consensus 373 ~~A~~L~~P~~--------~~~L~~~g~~~~i~~~k~~i~---------------------~~~~~v~~v~rhl~~gd~V 423 (1398) T Consensus 383 rvAkiLTfpE~Vt~~Ni~klr~lV~NG--P~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~Gdv--VERHL~DgDvV 458 (1386) T KOG0261 383 RVAKILTFPERVTRANIRKLRQLVRNG--PNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDV--VERHLMDGDVV 458 (1386) T ss_pred HHHHHHCCHHHCCHHHHHHHHHHHHCC--CCCCCCCCHHHHCCCCHHHHHHCCCHHHHHHHHCCCHH--HHHHCCCCCEE T ss_conf 788770536443687799999998429--98898730032256334567634768888876124247--87641468889 Q ss_pred EECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEE Q ss_conf 97576310111401235899449547973122545467877545699746899999999998767505423788782044 Q gi|254780142|r 424 LLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTV 503 (1398) Q Consensus 424 l~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~ 503 (1398) T Consensus 459 LFNRQPSLHkmSIM~H~akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiA 538 (1386) T KOG0261 459 LFNRQPSLHKMSIMSHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIA 538 (1386) T ss_pred EECCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEE T ss_conf 98478517788888777523667434312210477678888641004688417788999998555456446888981110 Q ss_pred EHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHH--H-HHCC----CCCCCCEEEEEECCCCCCCCCCC-EE-------E Q ss_conf 0258999999873367887446814179999999--9-9888----98678523652046456676142-45-------2 Q gi|254780142|r 504 PSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYH--A-LENK----IVTLHSKIRGRYKSVDKDGNSIS-KI-------Y 568 (1398) Q Consensus 504 ~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~--~-~~~~----~~~~~a~i~~~~~~~~~~~~~~~-~~-------~ 568 (1398) T Consensus 539 AtQDFiTg~YLlt~KD--------tF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~~LwTGKQ~fsvlirpn~~s~v~~ 610 (1386) T KOG0261 539 ATQDFITGGYLLTHKD--------TFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPVELWTGKQLFSVLIRPNDDSPVRV 610 (1386) T ss_pred HHHHHHHCCEEEECCC--------CCCCHHHHHHHHHHHHCCCCCCCCCCHHHCCCEEEECCCEEEEEEECCCCCCCEEE T ss_conf 3444321200100452--------11469999999999854443427997332374345326777899943689985388 Q ss_pred CCCC---------CCC-----CCCEEEECCCCCEEEEECCHHCCHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 1797---------751-----12205545875101775110020136-66999999980817899987558899999998 Q gi|254780142|r 569 DTTP---------GRM-----IIGEILPRHHEISFDICNQEMIKKNI-SAMVDTIYRHCGQKSTVAFCDDLMRLGFRYAC 633 (1398) Q Consensus 569 ~tt~---------Gr~-----~~~~ilp~~~~~~~~~~~~~~~k~~~-~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~ 633 (1398) T Consensus 611 Nl~~k~k~~~~~~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lg 690 (1386) T KOG0261 611 NLDAKNKNFSLVKGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLG 690 (1386) T ss_pred EECCCCCEEECCCCCCCCCCCCCCEEEEECCHHHHCCCCCCCCCCCCCCCEEEEEHHHCCHHHHHHHHHHHHHHHHHHCC T ss_conf 40456614531468874327887769982452310333400016887463576520220617899999999985132406 Q ss_pred HCCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHHHCCCCC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 53986132123268----369999999997899999988648976-------6788878864234658999999999987 Q gi|254780142|r 634 SSGISFGKDDIIVP----ESKEKIIAEADKMVKEYENQYNDGLIT-------RGEKYNKVVDLWGKTTDKVTEEMMARIK 702 (1398) Q Consensus 634 ~~GfSigi~D~~~~----~~k~~~i~~a~~~~~~~~~~~~~G~~t-------~~e~~~~i~~~~~~~~~~~~~~~~~~~~ 702 (1398) T Consensus 691 nrGFSIGi~DVqPg~~L~~~k~~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~--- 767 (1386) T KOG0261 691 NRGFSIGIDDVQPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIR--- 767 (1386) T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH--- T ss_conf 66620144777854778887999998678888999998741540248999878879999998999999998889997--- Q ss_pred HHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEEECCCCCC--CCCCCCCC----------C-----CCCHHHC Q ss_conf 6115654322224688376422555578---4241120010000246--44344456----------6-----6301110 Q gi|254780142|r 703 RVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAK--PSGEIIES----------P-----IRSHFKG 762 (1398) Q Consensus 703 ~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gk--p~G~~~~~----------P-----V~~sF~~ 762 (1398) T Consensus 768 ---------eL~~~NsPliMa~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFyS 838 (1386) T KOG0261 768 ---------ELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYS 838 (1386) T ss_pred ---------HCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC T ss_conf ---------45865673799984589886669999998635430587699862013676643458993010211220135 Q ss_pred CCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCC-CEEEEEEECCEEEEEEC-------- Q ss_conf 888989764057610322101210156740110154230143277513887666-51211100884886500-------- Q gi|254780142|r 763 GLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKG-LTITHIVDSGQVVYSLG-------- 833 (1398) Q Consensus 763 GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g-~~~~~~~~~~~~~~~l~-------- 833 (1398) T Consensus 839 GLTptEFfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LEDL~~~-YDgTVR~s~~~vvqF~YG~DglDPa~mEg~~~pv 917 (1386) T KOG0261 839 GLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLSVQ-YDGTVRNSNGDVVQFTYGGDGLDPAMMEGKDQPV 917 (1386) T ss_pred CCCCHHHHEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCEECCCCCEEEEEECCCCCCHHHHCCCCCCH T ss_conf 788545520002564311566554321116899999999998876-0673322778678985258888856634777860 Q ss_pred --CCCCCCCCHHHCCCCCCCCEEEECCC-------CCCH-------HHHHH--------------HHHC-CC-------- Q ss_conf --01012211442017789718851786-------5789-------99999--------------9975-98-------- Q gi|254780142|r 834 --SRVLGRTALDDIINPLTNECIVKAGQ-------LILE-------SHVNE--------------IEKC-GI-------- 874 (1398) Q Consensus 834 --~~~~~r~~~~di~~~~~~~~i~~~~~-------~i~~-------~~~~~--------------i~~~-~i-------- 874 (1398) T Consensus 918 ~f~r~~~~~--~~~-~~~~~~~~l~~~el~e~~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~ 994 (1386) T KOG0261 918 NFNRVFDHA--KAI-FPHRHDPPLSSEELDETLEEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCP 994 (1386) T ss_pred HHHHHHHHH--HHC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 289999877--741-78978888898999999999988775540158999999999999998888765135445775674 Q ss_pred CEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEE Q ss_conf 40202331000355186578875420178520001014602111100788987764202454322211220240148768 Q gi|254780142|r 875 RSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIV 954 (1398) Q Consensus 875 ~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVP 954 (1398) T Consensus 995 ~~~~~~~~~t~kql~~f~~~~--~~ky~~a~~EpGTavGAi~aQSIGEPGTQMTLKTFHFAGVASM-------NiTlGVP 1065 (1386) T KOG0261 995 DLLYQISRLTEKQLEKFVERC--LDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASM-------NITLGVP 1065 (1386) T ss_pred CCEEEEEECCHHHHHHHHHHH--HHHHHHHHCCCCCHHHHHHCCCCCCCCCEEEEEEEEECCEEEE-------EECCCCC T ss_conf 303000013699999999999--9998765158851343443256899875124330455120211-------1025761 Q ss_pred EEEE-EEEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEE Q ss_conf 9721-134651788778974276046640677600000011000013567855322507862135431132024636897 Q gi|254780142|r 955 KIKN-RNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGF 1033 (1398) Q Consensus 955 RlkE-i~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~ 1033 (1398) T Consensus 1066 RIkEIINAsk~ISTPIItA~L--------~n~~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl~i~vd~~~I--- 1134 (1386) T KOG0261 1066 RIKEIINASKTISTPIITAEL--------ENPHDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFLLIRVDLKRI--- 1134 (1386) T ss_pred HHHHHHHHHCCCCCCCEEEEE--------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHH--- T ss_conf 499997444006754013231--------583257888887643434109889999998727763589999547677--- Q ss_pred EEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCC Q ss_conf 53127832001230236860267751011012212385347742778253224788420213778445413676135484 Q gi|254780142|r 1034 EDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGD 1113 (1398) Q Consensus 1034 ~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d 1113 (1398) T Consensus 1135 ---------~~l~L~i~~~---------~I~~sI~~s~~~k~~~~~v~v~~~---------------------------~ 1169 (1386) T KOG0261 1135 ---------SLLQLEITIE---------SIAYSILKSPKRKVKPNDVRVVGE---------------------------T 1169 (1386) T ss_pred ---------HHHHCCCCHH---------HHHHHHHCCCCCCCCCCCEEEECC---------------------------E T ss_conf ---------6662114199---------999998438730258762588433---------------------------4 Q ss_pred EEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECC-----CC-EEEEEEECCCCCCEEEEEECC Q ss_conf 222101320245543367732889887525111101113478678633127-----94-499998368984026898138 Q gi|254780142|r 1114 VLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYK-----NK-SRVVIEPFEDGVEPAEYFIPK 1187 (1398) Q Consensus 1114 ~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~-----~k-~~~vi~~~~~g~~~~e~~ip~ 1187 (1398) T Consensus 1170 ~~~v~~~~~~~~----------S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de~~~~y~L~vE----G~gLr~Vm~t- 1234 (1386) T KOG0261 1170 TLRVTPVSDTKS----------SVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDEKRGLYKLLVE----GTGLRAVMNT- 1234 (1386) T ss_pred EEEEEECCCCCC----------HHHHHHHHHHHHCCCEEEECCCCHHHHHEEECCCCCCEEEEEE----CCCHHHHHCC- T ss_conf 689862345652----------0565699997447761896475431455321046874599983----4456877555- Q ss_pred CCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCC Q ss_conf 96589841987740864643899999998752799999999999999999809700612560124762861489418864 Q gi|254780142|r 1188 NKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADT 1267 (1398) Q Consensus 1188 ~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt 1267 (1398) T Consensus 1235 ---------~GV---~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEV------ 1296 (1386) T KOG0261 1235 ---------DGV---KGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEV------ 1296 (1386) T ss_pred ---------CCC---CCCCCCCCCEEEEEHHHCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCEE------ T ss_conf ---------784---55012557358740221458889999999988887258644789999988776304426------ Q ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHC--CCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEE Q ss_conf 5456641069999999999997289875201210000145302--31077650402589999997452855236653221 Q gi|254780142|r 1268 EYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQ--TKSFISAASFQETTKVLTEAAIAGKVDTLDGFKEN 1345 (1398) Q Consensus 1268 ~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~--t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSEN 1345 (1398) T Consensus 1297 ----------------------------------lGITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEc 1342 (1386) T KOG0261 1297 ----------------------------------LGITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSEC 1342 (1386) T ss_pred ----------------------------------EEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH T ss_conf ----------------------------------6564120677778899887666556788888873276423560011 Q ss_pred EECCCCCCCCCCHHHH Q ss_conf 5507305655354665 Q gi|254780142|r 1346 VIVGRSIPAGTGAILH 1361 (1398) Q Consensus 1346 IIlGqliP~GTG~f~~ 1361 (1398) T Consensus 1343 IIlG~pm~iGTG~fkl 1358 (1386) T KOG0261 1343 IILGIPMCIGTGIFKL 1358 (1386) T ss_pred EECCCCEECCCCHHHH T ss_conf 1206520204217899 |
|
| >KOG0262 consensus | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1674.37 Aligned_cols=1234 Identities=22% Similarity=0.298 Sum_probs=761.8 Q ss_pred EEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 53689845886788501448971755425456875688733621368566772156641563448835675788530477 Q gi|254780142|r 18 FDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSS 97 (1398) Q Consensus 18 i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~~~~ 97 (1398) T Consensus 13 ~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~-lGhPi~GGLYDl~LG-p~~~~--------------~~C~TC~~~~~~CP 76 (1640) T KOG0262 13 QPSVSFGSYTDQEIRKLSVKKITNPITFDN-LGHPIPGGLYDLALG-PLDNS--------------DVCSTCNQDELNCP 76 (1640) T ss_pred CCCEEEECCCHHHHHHCCEEEECCCEEECC-CCCCCCCCCCCCCCC-CCCCH--------------HHHHHHCCHHHCCC T ss_conf 652135026899986415467317601202-589888764231338-75432--------------34403221433199 Q ss_pred CCCCCCCCCCCCCCCEEECHHHHHHHH---HHHHHC-CCHHHHHHHHHHCCEEEECCC--------------------CC Q ss_conf 578767720027762201301225789---999809-996563013321112321788--------------------65 Q gi|254780142|r 98 VRRDRMAHIDLASPVAHPWFLKSLPSR---ISTLLG-MSLRDVERVLYFESYVVVDPG--------------------LS 153 (1398) Q Consensus 98 ~r~ghfGhIeLa~PV~Hi~f~k~~~~~---i~~~l~-~~~~~~~~v~y~~~~~~~~~~--------------------~~ 153 (1398) T Consensus 77 ---GH~GHIeL~~pvynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~ 153 (1640) T KOG0262 77 ---GHMGHIELPVPVYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDE 153 (1640) T ss_pred ---CCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCH T ss_conf ---75670563431227789999999999887762210057077899999989987031888999987645541367526 Q ss_pred CH-----HHHCCCC-------------------HHH------H------HHHHHHCCCC-------CE----E----ECC Q ss_conf 10-----4322369-------------------999------9------8867635855-------50----6----115 Q gi|254780142|r 154 SL-----EKYQILT-------------------EEE------Y------VEAVSQFGQD-------QF----I----AMM 182 (1398) Q Consensus 154 ~~-----~~~~~~~-------------------~~~------~------~~~~~~~~~~-------~~----~----~~~ 182 (1398) T Consensus 154 ~~~~~k~~~~~~v~~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~ 233 (1640) T KOG0262 154 SLNEIKSCRAQYVTEAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKV 233 (1640) T ss_pred HHHHHHHHHHHHCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCEEEEEHHCCCC T ss_conf 67888765665412899988642788520006788899999999986445668754578803311343135651100233 Q ss_pred CHHHHHHH------HH------HCCHHHHHH-HHHH------HHH---C----CCCCHHHHHHHHHH-----HHHHH-HH Q ss_conf 52677888------77------267488999-9998------731---0----32203478864477-----88866-66 Q gi|254780142|r 183 GADAIYEL------LI------ALDLQNLAL-TLRD------QLS---K----SSSIFRRKKIIKRL-----KIVDS-FI 230 (1398) Q Consensus 183 g~~~i~~~------l~------~~~~~~~~~-~~~~------~~~---~----~~~~~~~~~~~~~~-----~~~~~-f~ 230 (1398) T Consensus 234 ~~~~~~~~~i~~~~~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~ 313 (1640) T KOG0262 234 GANVIRGAKIKKDVGSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFP 313 (1640) T ss_pred CCCCHHHEEEEHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 32002200221101344433235677542134551000036552113345641206799999999998514789988621 Q ss_pred -----HCCCCCC-EEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHC---CCCH---H------ Q ss_conf -----3489851-12863045076223513884697313100378999999986999999873---9835---6------ Q gi|254780142|r 231 -----TSGNNPG-WMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSL---HAPE---I------ 292 (1398) Q Consensus 231 -----~~~~~Pe-wmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~---~ap~---~------ 292 (1398) T Consensus 314 l~~~~~~k~~p~d~FFld~l~VpPtrfRP~s~~g-d~~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~ 392 (1640) T KOG0262 314 LWDSGSGKIDPSDMFFLDNLLVPPTRFRPPSMLG-DEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLR 392 (1640) T ss_pred CCCCCCCCCCCCCEEEEECCCCCCCCCCCCHHCC-HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 2345556638421122112356874568720126-244328077889999999999999988765313788888887644 Q ss_pred ----HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCE Q ss_conf ----7776999999988887427767877247876506789986102378200034651004577403412554354620 Q gi|254780142|r 293 ----IIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQC 368 (1398) Q Consensus 293 ----i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~ev 368 (1398) T Consensus 393 g~~~kl~~aw~~LQ~~vn~lfDs~~~~k---~~r~~~-pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEI 468 (1640) T KOG0262 393 GIFSKLINAWLQLQASVNVLFDSKMASK---WSRDSP-PGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEI 468 (1640) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCC---CCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCC T ss_conf 5889999999999987788726432444---356778-129999887540688875102002433043479998663556 Q ss_pred ECHHHHHHHHHHH-----HHHHHH---HHCCCCCCCCCCCCEEECCCC-------------------------------C Q ss_conf 0348987761289-----999999---987986663000100122488-------------------------------2 Q gi|254780142|r 369 GLPKLMALELFKP-----FLYAQL---EKKGYVSTVKQAKKFVEKERP-------------------------------E 409 (1398) Q Consensus 369 gvP~~~A~~L~~P-----~~~~~L---~~~g~~~~i~~~k~~i~~~~~-------------------------------~ 409 (1398) T Consensus 469 GIP~vFA~KLTyPepVt~~NV~elr~aViNG--P~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~ 546 (1640) T KOG0262 469 GIPPVFAKKLTYPEPVTPWNVNELRKAVING--PDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFG 546 (1640) T ss_pred CCCHHHHHHCCCCCCCCCCCHHHHHHHHHCC--CCCCCCCCEEECCCCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 7864777523688867742699999987149--98899831356698756516878879999999986064447876567 Q ss_pred EEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECC-CEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHH Q ss_conf 5013266656978997576310111401235899449-547973122545467877545699746899999999998767 Q gi|254780142|r 410 VWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISG-KAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLS 488 (1398) Q Consensus 410 v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~-~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~ 488 (1398) T Consensus 547 ~K~V~RHvknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~ 626 (1640) T KOG0262 547 TKKVHRHVKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANT 626 (1640) T ss_pred CCEEEEECCCCCEEEECCCCCCCCCHHHHHHHEECCCCCEEEEEECCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHHCC T ss_conf 72366540478489975787656524554443015776146631136543468888631015677135678888987505 Q ss_pred HHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCC--------CCCCCCEEEEEECCCCCC Q ss_conf 505423788782044025899999987336788744681417999999999888--------986785236520464566 Q gi|254780142|r 489 TNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENK--------IVTLHSKIRGRYKSVDKD 560 (1398) Q Consensus 489 ~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~--------~~~~~a~i~~~~~~~~~~ 560 (1398) T Consensus 627 dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd--------~Fftre~y~qLv~~~l~~~~~rI~~lpPtIlkP~~LWTGKQ 698 (1640) T KOG0262 627 DSQYLVPTDGTPLRGLIQDHIVSGVLLTMRD--------SFFTREDYQQLVFAGLSDTFKRIKLLPPTILKPAPLWTGKQ 698 (1640) T ss_pred CCCEECCCCCCCHHHHHHHHEEEEEEEEECC--------CCCCHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCH T ss_conf 7744216999711556664531047887324--------33579999999987402211402126842146524546531 Q ss_pred CCCC----------------CE---EECCCCC-----CCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHH Q ss_conf 7614----------------24---5217977-----5112205545875101775110020136669999999808178 Q gi|254780142|r 561 GNSI----------------SK---IYDTTPG-----RMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKS 616 (1398) Q Consensus 561 ~~~~----------------~~---~~~tt~G-----r~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~ 616 (1398) T Consensus 699 VIsTil~Ni~P~~~p~iNl~~kaKip~~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH~~~ElYG~~~ 778 (1640) T KOG0262 699 VISTILKNIIPEGHPPINLESKAKIPGKAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGATAYGLVHCCHELYGGET 778 (1640) T ss_pred HHHHHHHHCCCCCCCCCCCHHCCCCCHHHCCCCCCCCCCCCCEEEEECCCEEEEEECHHHCCCHHHHHHHHHHHHHCCCC T ss_conf 89999985288888751110004686131377887656775438984583689761154347103435664454407610 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCH----HHHHHHHHHHHHHHHHHHHHHCCCC---CHHHHHHHHHHHHH-- Q ss_conf 99987558899999998539861321232683----6999999999789999998864897---66788878864234-- Q gi|254780142|r 617 TVAFCDDLMRLGFRYACSSGISFGKDDIIVPE----SKEKIIAEADKMVKEYENQYNDGLI---TRGEKYNKVVDLWG-- 687 (1398) Q Consensus 617 ~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~----~k~~~i~~a~~~~~~~~~~~~~G~~---t~~e~~~~i~~~~~-- 687 (1398) T Consensus 779 s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~-~l~~da~~del~~~le~~y~~d 857 (1640) T KOG0262 779 SGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAF-GLDVDAPPDELRSRLEAIYLKD 857 (1640) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHHHCC T ss_conf 216999999999999988463214320565300037899999862000289999982-9987899799999999998635 Q ss_pred ----HHHHHHH----HHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEEECCCCCCC-----CCCC Q ss_conf ----6589999----999999876115654322224688376422555578---42411200100002464-----4344 Q gi|254780142|r 688 ----KTTDKVT----EEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAKP-----SGEI 751 (1398) Q Consensus 688 ----~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gkp-----~G~~ 751 (1398) T Consensus 858 ~~~~~~LD~~~k~~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKt 937 (1640) T KOG0262 858 ADKLAMLDRVMKSELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKT 937 (1640) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCEEECCCC T ss_conf 03777777999988866438888643562444308712689988725775642499987761237645775643542775 Q ss_pred CCC-------C-----CCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCC--CCC Q ss_conf 456-------6-----63011108889897640576103221012101567401101542301432775138876--665 Q gi|254780142|r 752 IES-------P-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTK--KGL 817 (1398) Q Consensus 752 ~~~-------P-----V~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~--~g~ 817 (1398) T Consensus 938 LPsF~p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~-YD~TVRDsDgs 1016 (1640) T KOG0262 938 LPSFAPYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVH-YDLTVRDSDGS 1016 (1640) T ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCEEE-CCCEEECCCCC T ss_conf 67757788897778722131024888267753332464301466775041068999999864001773-23167738996 Q ss_pred EEEEEEECCEEEEEECCCCCCCC-----CHHHCCCCCCCCEEEEC-------------------------------CC-- Q ss_conf 12111008848865000101221-----14420177897188517-------------------------------86-- Q gi|254780142|r 818 TITHIVDSGQVVYSLGSRVLGRT-----ALDDIINPLTNECIVKA-------------------------------GQ-- 859 (1398) Q Consensus 818 ~~~~~~~~~~~~~~l~~~~~~r~-----~~~di~~~~~~~~i~~~-------------------------------~~-- 859 (1398) T Consensus 1017 vVQF~Y-GEDglDitKssfl~~~~f~~~Ny~avl~~~~~~~v~s~~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv 1095 (1640) T KOG0262 1017 VVQFMY-GEDGLDITKSSFLNKKEFPTDNYEAVLLKYKSESVLSAFDIKKASKYIKKILKWKKKHMWFELDKKIACPDPV 1095 (1640) T ss_pred EEEEEE-CCCCCCCCHHHHCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCHH T ss_conf 899863-5865554377652444411223999986407487763213687899999998877651222121155788816 Q ss_pred -----------CCCHHHHHHHHHCCCCEE-ECCCC-CCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHH Q ss_conf -----------578999999997598402-02331-00035518657887542017852000101460211110078898 Q gi|254780142|r 860 -----------LILESHVNEIEKCGIRSV-RIRSA-LTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQ 926 (1398) Q Consensus 860 -----------~i~~~~~~~i~~~~i~~v-~irs~-lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQ 926 (1398) T Consensus 1096 ~~k~~p~~y~gsvsekf~~~i~~f~~~~~k~~~s~~~~~~~lr~ll~~K-----~~~SLa~PGE~VGvlAAQSIGEPSTQ 1170 (1640) T KOG0262 1096 LAKYNPDKYLGSVSEKFRKKIDDFDDENAKKEKSEEPSEEKLRRLLQLK-----YIRSLADPGEPVGVLAAQSIGEPSTQ 1170 (1640) T ss_pred HHHCCHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH-----HHHHHCCCCCCCEEEEECCCCCCCCE T ss_conf 5303624542104488999999998876654123211489999999999-----88876189874124422136887531 Q ss_pred HHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCC Q ss_conf 776420245432221122024014876897211--346517887789742760466406776000000110000135678 Q gi|254780142|r 927 LTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDG 1004 (1398) Q Consensus 927 mTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~ 1004 (1398) T Consensus 1171 MTLNTFHfAGrGem-------NVTLGIPRLREIlMtASanIkTP~mt~pi~~g~s--------~~ra~~i~~~l~rV~L~ 1235 (1640) T KOG0262 1171 MTLNTFHFAGRGEM-------NVTLGIPRLREILMTASANIKTPSMTVPIKNGVS--------DERADDITKELRRVTLK 1235 (1640) T ss_pred EEHHHEEECCCCCE-------EEEECCHHHHHHHHHHHHCCCCCCEEEECCCCCC--------HHHHHHHHHHHHHHHHH T ss_conf 13214010466640-------1220656899999987640489733562368864--------77899999999898999 Q ss_pred CEEECCEEEEECCCCCCEEEECCCCEEEEEEEC---CC-CEEHHHHHCCC-----------------------CCEEE-- Q ss_conf 553225078621354311320246368975312---78-32001230236-----------------------86026-- Q gi|254780142|r 1005 GVIECGQRISEWDPHTFPIITEVSGTVGFEDLV---DG-ISVIESIGEST-----------------------GIAKR-- 1055 (1398) Q Consensus 1005 ~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~---~~-~~~~~~~~~~t-----------------------~~~~~-- 1055 (1398) T Consensus 1236 evlk~v~vte~~t~~~~~~~~~y~lr~~~~~~~~y~~e~~v~~e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~ 1315 (1640) T KOG0262 1236 EVLKKVGVTEKITMVENQSCKKYKLRFDLLPREEYQEEYDVRPEDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDA 1315 (1640) T ss_pred HHHHHEEEEEEEEEECCCCCEEEEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 99866412589985046430689999860687774233077999999999999999999999999877677524665667 Q ss_pred -EEEE----HHH-------CCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEE---CCCCCCCCCCEEEECHH Q ss_conf -7751----011-------01221238534774277825322478842021377844541---36761354842221013 Q gi|254780142|r 1056 -KVID----WRF-------ASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSV---SPGQKVSTGDVLARLPI 1120 (1398) Q Consensus 1056 -~~i~----~~~-------~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v---~~~~~v~~~d~l~~~~~ 1120 (1398) T Consensus 1316 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~~k~~~k~~~~~dYe~~de~e~~~~~~~e~~~~~e~~---e~d~ 1392 (1640) T KOG0262 1316 DPDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEESD---EDDE 1392 (1640) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCC---CCHH T ss_conf 8532346786533467765666421255676520367787652011267678753543202202566553222---2102 Q ss_pred HHC-------CCCCCCCCCC---HHHHH---------HH--------------------HHCCCC--CCEECCCCCEEEE Q ss_conf 202-------4554336773---28898---------87--------------------525111--1011134786786 Q gi|254780142|r 1121 SSA-------KTKDITSGLP---RVAEL---------FE--------------------ARRPKN--HAILAEISGTIRI 1159 (1398) Q Consensus 1121 ~~~-------k~~DIt~GLP---rV~eL---------FE--------------------ar~pk~--~aiisei~Giv~i 1159 (1398) T Consensus 1393 e~g~dg~~~~~~~~~e-~~~~~~~~er~~qs~~~~~~fi~~y~fd~~~~~wcev~~~lp~~~~k~~mssiVe~~~~-~~v 1470 (1640) T KOG0262 1393 EVGLDGTPEPEEEDQE-GQPEVNAVERREQSVKKRHDFISRYTFDKESGKWCEVELKLPLDKEKLDMSSIVESIAP-KSV 1470 (1640) T ss_pred HCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHC-CEE T ss_conf 3066788873324466-77213578889988888887765411012568379999981488752179999999725-014 Q ss_pred EEECCCCEEEEEEECCCCCCEEEEEECCCC-------EEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHH Q ss_conf 331279449999836898402689813896-------5898419877408646438999999987527999999999999 Q gi|254780142|r 1160 KRNYKNKSRVVIEPFEDGVEPAEYFIPKNK-------HFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEV 1232 (1398) Q Consensus 1160 ~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~-------~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EI 1232 (1398) T Consensus 1471 I~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~ly--------SNDI~ail~tyGVEAar~~Iv~Ev 1542 (1640) T KOG0262 1471 IHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLY--------SNDIHAILNTYGVEAARNAIVNEV 1542 (1640) T ss_pred EECCCCCEEEECCCCCCCCCCCCEEHHCCCCHHHHHHHHHHHHHHHHC--------CCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 640688226640687655433401010576589999777663331101--------305999999862899999999999 Q ss_pred HHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCC Q ss_conf 99999809700612560124762861489418864545664106999999999999728987520121000014530231 Q gi|254780142|r 1233 QEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTK 1312 (1398) Q Consensus 1233 q~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~ 1312 (1398) T Consensus 1543 ~~VF~vYGIsVd~RHLsLiADYMTf~G~-------------------y~pfnR~Gm~~--------------------ss 1583 (1640) T KOG0262 1543 NNVFKVYGISVDIRHLSLIADYMTFEGG-------------------YQPFNRMGMES--------------------SS 1583 (1640) T ss_pred HHHHHHEEEEECHHHHHHHHHHHHHCCC-------------------CCCCCCCCCCC--------------------CC T ss_conf 8766530156338898999888750565-------------------36200145555--------------------89 Q ss_pred CHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHH Q ss_conf 077650402589999997452855236653221550730565535466 Q gi|254780142|r 1313 SFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1313 S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~ 1360 (1398) T Consensus 1584 SP~qkMsFETt~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fd 1631 (1640) T KOG0262 1584 SPLQKMSFETTCQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGSFD 1631 (1640) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCEEE T ss_conf 756764199999999998734750025797502583366578765111 |
|
| >TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1927.40 Aligned_cols=753 Identities=29% Similarity=0.444 Sum_probs=610.6 Q ss_pred CCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 64053689845886788501448971755425456875688733621368566772156641563448835675788530 Q gi|254780142|r 15 DRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVT 94 (1398) Q Consensus 15 ~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~ 94 (1398) T Consensus 1 ~K~i~~I~FGlLSPe~IRK~Sv~~v~t~d~YD~DG~-PI~~GlmD~rlGVId---------------PGlRC~TCG~~~g 64 (901) T TIGR02390 1 PKKIKSIKFGLLSPEEIRKLSVVEVVTADTYDEDGY-PIEGGLMDPRLGVID---------------PGLRCKTCGGKVG 64 (901) T ss_pred CCCCCCCCCCCCCHHHHHHHCCCEEECCCCCCCCCC-CCCCCCCCCCCCEEC---------------CCCCCCCCCCCCC T ss_conf 973456344668847875314414761743578588-535775777572225---------------7661776778888 Q ss_pred CCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHH--------CCEEEE-----CCCCCCHHHHCCC Q ss_conf 477578767720027762201301225789999809996563013321--------112321-----7886510432236 Q gi|254780142|r 95 LSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYF--------ESYVVV-----DPGLSSLEKYQIL 161 (1398) Q Consensus 95 ~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~--------~~~~~~-----~~~~~~~~~~~~~ 161 (1398) T Consensus 65 eCP---GHFGhIELarPV~HVgF~~~----I~~iL~ATCr~CGR~~l~e~~~~~Y~~~~~~~~~~~~~~a~~nfiq~~l~ 137 (901) T TIGR02390 65 ECP---GHFGHIELARPVVHVGFAKE----IYKILRATCRKCGRILLTEEEIEQYLEKINKLKEEGGSLALSNFIQETLI 137 (901) T ss_pred CCC---CCCCEECCCCCEEEECHHHH----HHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 687---85661215587043261478----88887610875771144778999999999999734587467888888889 Q ss_pred ----CHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHH---HHHHCCCCCHHHHHHHHHHHHHHHHHHCCC Q ss_conf ----9999988676358555061155267788877267488999999---873103220347886447788866663489 Q gi|254780142|r 162 ----TEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLR---DQLSKSSSIFRRKKIIKRLKIVDSFITSGN 234 (1398) Q Consensus 162 ----~~~~~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~ 234 (1398) T Consensus 138 ~~i~k~A~k~~~CPhCg~~q~~ik~e-----KP~~f~---e~~~~G~eeW~KLTP~eiRErLEkiPdeD~~llG~~Pk~a 209 (901) T TIGR02390 138 EKIVKEAAKRMKCPHCGEEQKKIKFE-----KPTYFY---EEDKEGKEEWVKLTPSEIRERLEKIPDEDLELLGINPKVA 209 (901) T ss_pred HHHHHHHHHCCCCCCCCCCCCCEEEE-----CCEEEE---ECCCCCCCCCEECCCHHHHHHHHCCCHHHHHHCCCCCCCC T ss_conf 99999986178798887412432452-----771577---5575555121442817999975168742444106678878 Q ss_pred CCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 85112863045076223513884697313100378999999986999999873983567776999999988887427767 Q gi|254780142|r 235 NPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRH 314 (1398) Q Consensus 235 ~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~ 314 (1398) T Consensus 210 RPEWmvLTVLpVPPvtVRPSItLEtG~RSEDDLTHKLVDIiRiN~RL~e~~~~GAP~lIiEdLWeLLQYHV~TYFDNe~P 289 (901) T TIGR02390 210 RPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELP 289 (901) T ss_pred CCHHEEEECCCCCCCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCC T ss_conf 73010001047811854764100366752124677899998650799999753787304665578889987674314786 Q ss_pred CCCC-CCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHH-----HH---HH Q ss_conf 8772-478765067899861023782000346510045774034125543546200348987761289-----99---99 Q gi|254780142|r 315 KRVV-TGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP-----FL---YA 385 (1398) Q Consensus 315 ~~~~-~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P-----~~---~~ 385 (1398) T Consensus 290 GiPpArHRSGRPLKTLaQRLKGKEGRfR~NLSGKRVNFSARTVISPDP~iSINEVGVP~~IAk~LTvP~~VT~~Nid~~R 369 (901) T TIGR02390 290 GIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEEIAKELTVPERVTPWNIDELR 369 (901) T ss_pred CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCEECCCCEECCHHHHHHH T ss_conf 46866668884034576332043554145546650042116100688854546566884770562326236804489999 Q ss_pred HHHHCCCCCCCCC-------CCCEEECC----C-----------------------CCEEHHHHHHHCCCEEEECCCCCC Q ss_conf 9998798666300-------01001224----8-----------------------825013266656978997576310 Q gi|254780142|r 386 QLEKKGYVSTVKQ-------AKKFVEKE----R-----------------------PEVWDVLAEVVHQHVVLLNRAPSL 431 (1398) Q Consensus 386 ~L~~~g~~~~i~~-------~k~~i~~~----~-----------------------~~v~~v~rhl~~gd~Vl~NRqPsL 431 (1398) T Consensus 370 ~yv~NG--pd~~PqfGryvtGANYVi~p~rt~dGReeeyriki~~~~Dk~~laE~L~pGw~VERHL~dGDiVLFNRQPSL 447 (901) T TIGR02390 370 EYVLNG--PDSWPQFGRYVTGANYVIRPSRTPDGREEEYRIKIRDVNDKEELAERLEPGWVVERHLIDGDIVLFNRQPSL 447 (901) T ss_pred HHHHCC--CCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEECCCCCHHHHHHCCCCCCEEEEEECCCCEEEECCCCCH T ss_conf 996377--888764466641033366046688886544305522445378997407999789987126888766588642 Q ss_pred EECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHH Q ss_conf 11140123589944954797312254546787754569974689999999999876750542378878204402589999 Q gi|254780142|r 432 HRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLG 511 (1398) Q Consensus 432 Hr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G 511 (1398) T Consensus 448 HRmSmMgH~VkVLPgkTFRLNLaVCPPYNADFDGDEMNlHV~Q~EEarAEA~~lM~V~~hI~tPRyGGPIIGg~~D~IsG 527 (901) T TIGR02390 448 HRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISG 527 (901) T ss_pred HHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH T ss_conf 02101144546788885213667772888788876037640257335899999854111014688764011025678888 Q ss_pred HHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEEC----CCCCCCCCCEEEE----- Q ss_conf 9987336788744681417999999999888986785236520464566761424521----7977511220554----- Q gi|254780142|r 512 LCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKIYD----TTPGRMIIGEILP----- 582 (1398) Q Consensus 512 ~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~~~----tt~Gr~~~~~ilp----- 582 (1398) T Consensus 528 aYLLT~k~--------~~~t~~ev~~iL~~~~~~~~~----------~~~~~ie~~~~eGrdywTGK~ifS~~LP~dLn~ 589 (901) T TIGR02390 528 AYLLTVKS--------TLFTKEEVVTILKKAGLKGEP----------EEPKAIEKPKEEGRDYWTGKQIFSAFLPEDLNF 589 (901) T ss_pred HHHHHHCC--------CCCCHHHHHHHHHHCCCCCCC----------CCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCE T ss_conf 88865047--------776889999999860767787----------666633177866753221035554207887772 Q ss_pred ---------------------------CCCCCEEEEECCHHCCHHHH-HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------------------------58751017751100201366-69999999808178999875588999999985 Q gi|254780142|r 583 ---------------------------RHHEISFDICNQEMIKKNIS-AMVDTIYRHCGQKSTVAFCDDLMRLGFRYACS 634 (1398) Q Consensus 583 ---------------------------~~~~~~~~~~~~~~~k~~~~-~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~ 634 (1398) T Consensus 590 ~~~a~~~~G~c~~C~~e~Cp~D~YvVI~NG~Ll~GViDk~a~G~e~g~~il~~i~~~yG~e~ar~~lD~~trL~i~~i~~ 669 (901) T TIGR02390 590 EFRAKVCSGKCEACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGDKILDRIVREYGPEAARRFLDSVTRLAIRFIEL 669 (901) T ss_pred EEECCCCCCCCCCCCCCCCCCCCEEEEECCEEEEEECCHHHCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH T ss_conf 14013678850010036799865789866804320302011274663789999987607468999999999999998755 Q ss_pred CCCCCCCCCCCCCHH----HHHHHHHHHHHHHHHHHHHHCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 398613212326836----999999999789999998864897-------667888788642346589999999999876 Q gi|254780142|r 635 SGISFGKDDIIVPES----KEKIIAEADKMVKEYENQYNDGLI-------TRGEKYNKVVDLWGKTTDKVTEEMMARIKR 703 (1398) Q Consensus 635 ~GfSigi~D~~~~~~----k~~~i~~a~~~~~~~~~~~~~G~~-------t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~ 703 (1398) T Consensus 670 ~GfT~g~~D~dIP~eA~~~I~~~i~~A~~~V~~LIe~Y~~GeLeplPGRt~EEtlE~~I~~~L~~~Rd~~G~va------ 743 (901) T TIGR02390 670 RGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDKLIEEYRNGELEPLPGRTVEETLEMKILEVLGKARDEAGEVA------ 743 (901) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHH------ T ss_conf 16601336010467899999999999999999999985278230187786446558899999877766651120------ Q ss_pred HCCCCCCCCCCC-CCCEEEEECCCCCCC---HHHEEEEEEECCCCCCCC--C---CCCC-------CC-----CCCHHHC Q ss_conf 115654322224-688376422555578---424112001000024644--3---4445-------66-----6301110 Q gi|254780142|r 704 VEFDPETGRQKK-MNSIFMMSHSGARGS---IHQMRQLGGMRGLIAKPS--G---EIIE-------SP-----IRSHFKG 762 (1398) Q Consensus 704 ~~~~~~~~~~~~-~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gkp~--G---~~~~-------~P-----V~~sF~~ 762 (1398) T Consensus 744 ------~kyld~d~n~~~iMArtGARGs~LNi~qmaA~vGQQsVRG~Ri~RGY~~RtLPHFk~GDi~a~arGFVr~sf~~ 817 (901) T TIGR02390 744 ------EKYLDPDENHAVIMARTGARGSLLNITQMAAMVGQQSVRGERIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKK 817 (901) T ss_pred ------HCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHCCCEEEECCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHCC T ss_conf ------10268564662799602666136558888610040155450343035678788888888887666513431137 Q ss_pred CCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCC--CEEEEEEECCEEEEEE Q ss_conf 888989764057610322101210156740110154230143277513887666--5121110088488650 Q gi|254780142|r 763 GLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKG--LTITHIVDSGQVVYSL 832 (1398) Q Consensus 763 GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g--~~~~~~~~~~~~~~~l 832 (1398) T Consensus 818 GL~P~EyFFHA~gGREGLVDTAVRTsqSGYmQRRLvNALqDl~V-~yDgtVRD~~G~liQ~~-YGEDGvdP~ 887 (901) T TIGR02390 818 GLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLVNALQDLRV-EYDGTVRDTRGNLIQFK-YGEDGVDPA 887 (901) T ss_pred CCCCCEEEECCCCCCCCHHHHHHCCCCCCCHHHHHHHHHCCEEE-EECCEEEECCEEEEEEE-ECCCCCCCC T ss_conf 81830011204545531021111026653047788646616057-41775884223789874-036633653 |
7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription. |
| >PRK08566 DNA-directed RNA polymerase subunit alpha; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1674.31 Aligned_cols=780 Identities=27% Similarity=0.395 Sum_probs=607.4 Q ss_pred CCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 56786405368984588678850144897175542545687568873362136856677215664156344883567578 Q gi|254780142|r 11 PWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCG 90 (1398) Q Consensus 11 ~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg 90 (1398) T Consensus 2 ~~~~p~~I~~I~f~~~S~~eI~~~S~~eI~~~~~~~~~-~~p~~gGl~D~rmG~~~---------------~~~~C~TCg 65 (881) T PRK08566 2 MMDVPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDD-GYPIEGGLMDPRLGVID---------------PGLRCKTCG 65 (881) T ss_pred CCCCCEEECEEEEEECCHHHHHHHCEEEEECCCCCCCC-CCCCCCCCCCCCCCCCC---------------CCCCCCCCC T ss_conf 88887301459998158999986257899561238889-98588997761118999---------------729789999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCC----EE--EECCCCCCHHHHCCC--- Q ss_conf 853047757876772002776220130122578999980999656301332111----23--217886510432236--- Q gi|254780142|r 91 VEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFES----YV--VVDPGLSSLEKYQIL--- 161 (1398) Q Consensus 91 ~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~----~~--~~~~~~~~~~~~~~~--- 161 (1398) T Consensus 66 ~~~~~Cp---GHfGHIeLa~PV~hp~f~~~i~----~iL~~~C~~C~rl~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 138 (881) T PRK08566 66 GRAGECP---GHFGHIELARPVIHVGFAKLIY----KLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGGLAKDLIKEI 138 (881) T ss_pred CCCCCCC---CCCEEEEECCCCCCHHHHHHHH----HHHHCCCCHHCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9789589---9684874067510287899999----99956011230185779999999999987643115699999999 Q ss_pred -CHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEE Q ss_conf -9999988676358555061155267788877267488999999873103220347886447788866663489851128 Q gi|254780142|r 162 -TEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240 (1398) Q Consensus 162 -~~~~~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmi 240 (1398) T Consensus 139 ~k~~~k~~~C~~Cg~~~~~i~~~--------~~~~f~~~~~~~~~~L~p~~v~~il~~I~~ed~~~Lg~~~~~~rPe~~i 210 (881) T PRK08566 139 KKEAAKRMVCPHCGEEQYKIKFE--------KPTTFYEERKEGAVKLTPSEIRERLEKIPDEDLELLGINPEVARPEWMV 210 (881) T ss_pred HHHHHHCCCCCCCCCCCCEEEEE--------CCHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHH T ss_conf 99875245685558857203631--------5436766203230357999999999718987899848996668807834 Q ss_pred EEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-C Q ss_conf 630450762235138846973131003789999999869999998739835677769999999888874277678772-4 Q gi|254780142|r 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVV-T 319 (1398) Q Consensus 241 l~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~-~ 319 (1398) T Consensus 211 l~~lpVpP~~~RP~i~~~~g~~~~ddlt~~l~~Ii~~n~~l~~~~~~~a~~~~i~~~~~~LQ~~V~~~~Dn~~~~~~~~~ 290 (881) T PRK08566 211 LTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNELPGIPPAR 290 (881) T ss_pred HHCCCCCCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 22255799767874023787345773889999999999999999876995767899999999999999725778987434 Q ss_pred CCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHH-----HH---HHHHHCC Q ss_conf 787650678998610237820003465100457740341255435462003489877612899-----99---9999879 Q gi|254780142|r 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPF-----LY---AQLEKKG 391 (1398) Q Consensus 320 ~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~-----~~---~~L~~~g 391 (1398) T Consensus 291 ~~~~r~~k~i~q~L~gK~GrfR~nlmGKRVd~saRSVIspDP~L~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~~v~nG 370 (881) T PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTPWNIEELREYVLNG 370 (881) T ss_pred CCCCCCCCCHHHHHCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHCCCCEEEEHHHHHHHHHHHHCC T ss_conf 56898564188885466630100224453355430343268876367025879999757868076087899999999739 Q ss_pred CCCCCCCCCCEEE------------------CCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEEC Q ss_conf 8666300010012------------------2488250132666569789975763101114012358994495479731 Q gi|254780142|r 392 YVSTVKQAKKFVE------------------KERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHP 453 (1398) Q Consensus 392 ~~~~i~~~k~~i~------------------~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~ 453 (1398) T Consensus 371 ~~--~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~iV~Rhl~dgD~Vl~NRqPTLHr~sima~~v~v~~gktirln~ 448 (881) T PRK08566 371 PD--KHPGANYVIRPDGRRIKLTDKNKEELAERLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 448 (881) T ss_pred CC--CCCCCEEEECCCCCEEEHHHHHHHHHHHHCCCCCEEEEEEECCCEEEECCCCHHHHHCCCCEEEEEEECCEEEECC T ss_conf 85--5677437882578366425756999998526786896564359667752773354420001037997434577566 Q ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHH Q ss_conf 22545467877545699746899999999998767505423788782044025899999987336788744681417999 Q gi|254780142|r 454 LVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMG 533 (1398) Q Consensus 454 ~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~ 533 (1398) T Consensus 449 ~vc~~yNADFDGDeMn~HvPqs~~A~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~LT~~~--------~f~~k~ 520 (881) T PRK08566 449 AVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIHDHISGAYLLTRKS--------TLFTKE 520 (881) T ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCC--------CCCCHH T ss_conf 567870677644102331257898999999986263026337899824651188887789986487--------668999 Q ss_pred HHHHHHHC----CCCCCCCEEEEEECCCCCCCCCCCEE--------ECCC----CCC----CCCCEEEECCCCCEEEEEC Q ss_conf 99999988----89867852365204645667614245--------2179----775----1122055458751017751 Q gi|254780142|r 534 EVYHALEN----KIVTLHSKIRGRYKSVDKDGNSISKI--------YDTT----PGR----MIIGEILPRHHEISFDICN 593 (1398) Q Consensus 534 ~~~~~~~~----~~~~~~a~i~~~~~~~~~~~~~~~~~--------~~tt----~Gr----~~~~~ilp~~~~~~~~~~~ 593 (1398) T Consensus 521 ~~~~ll~~~~~~~~~~~pai~kp~~~wTGkqi~s~iLP~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~G~ll~G~ld 600 (881) T PRK08566 521 EALDLLGAVGIDELPPEPAIENGKEYWTGKQIFSLFLPKDLNLVFKAKICSKCDECKKEDCEHDAYVVIKNGKLLKGVID 600 (881) T ss_pred HHHHHHHHCCCCCCCCCCHHCCCCCCCCHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEECCEEEEEECC T ss_conf 99999983585656775200278412538999998746887525431024675544334577876699876977762046 Q ss_pred CHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH----HHHHHHHHHHHHHHHHHHHH Q ss_conf 10020136669999999808178999875588999999985398613212326836----99999999978999999886 Q gi|254780142|r 594 QEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPES----KEKIIAEADKMVKEYENQYN 669 (1398) Q Consensus 594 ~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~----k~~~i~~a~~~~~~~~~~~~ 669 (1398) T Consensus 601 K~~lG~~~~~LI~~i~~~yG~~~a~~fLd~lq~L~~~~l~~~GFSvGi~Dl~i~~~~~~~i~e~i~~~~~~v~~l~~~~~ 680 (881) T PRK08566 601 KKAIGAEQGSILDRIVKEYGPERARRFLDSVTKLAIRFIMLRGFTTGIDDEDIPEEAYEEIDEIIEEAEKRVEELIEAYE 680 (881) T ss_pred HHHHCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 77734343439999999859799999999999999999997784766644275889999999999999999999999998 Q ss_pred CCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEE Q ss_conf 4897-------667888788642346589999999999876115654322224688376422555578---424112001 Q gi|254780142|r 670 DGLI-------TRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGG 739 (1398) Q Consensus 670 ~G~~-------t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~G 739 (1398) T Consensus 681 ~g~l~~~~~~t~~e~~E~~i~~~l~~~r~~~~~i~~~~l------------~~~N~~~~Mv~SGAKGS~~Ni~Qi~g~lG 748 (881) T PRK08566 681 NGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYL------------GLDNPAVIMARTGARGSMLNITQMAACVG 748 (881) T ss_pred HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC------------CCCCCHHHHHHCCCCCCHHHHHHHHHCCC T ss_conf 298665889867899999999999999999999998628------------99995775311367677999999995345 Q ss_pred ECCCCCCC--C---CCCCCC-------C-----CCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHC Q ss_conf 00002464--4---344456-------6-----63011108889897640576103221012101567401101542301 Q gi|254780142|r 740 MRGLIAKP--S---GEIIES-------P-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQ 802 (1398) Q Consensus 740 qq~l~gkp--~---G~~~~~-------P-----V~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~e 802 (1398) T Consensus 749 QQ~~~G~Ri~~~~~~RtLP~f~~~d~~~~a~GfI~~sF~~GL~p~Efffh~m~gReGLiDTAvKTa~sGYlqRrLvk~lE 828 (881) T PRK08566 749 QQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEYFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQ 828 (881) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCHHCCCHHHHCCCCCCCCHHHHHHHHHHHC T ss_conf 61048976746777888899988898867895161245379988999970521040186677314752099999999861 Q ss_pred CCEEEEECCCCCC--CCEEEEEEECCEEEEEEC---------CCCCCCCCHHHC Q ss_conf 4327751388766--651211100884886500---------010122114420 Q gi|254780142|r 803 NCVVNQVDCNTKK--GLTITHIVDSGQVVYSLG---------SRVLGRTALDDI 845 (1398) Q Consensus 803 Dl~V~~~D~~t~~--g~~~~~~~~~~~~~~~l~---------~~~~~r~~~~di 845 (1398) T Consensus 829 dl~v~-yD~tVR~~~~~ivq-f~YG~Dg~dp~~~~~~~~~~~~~~~~~~~~~~~ 880 (881) T PRK08566 829 DLKVE-YDGTVRDTRGNIVQ-FKYGEDGVDPMKSDHGKPVDVDRIIERVLGKEV 880 (881) T ss_pred CEEEE-CCCCEECCCCCEEE-EECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC T ss_conf 86992-79973869997899-765787768000258973349999999754007 |
|
| >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1601.13 Aligned_cols=780 Identities=50% Similarity=0.741 Sum_probs=704.4 Q ss_pred CCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 40536898458867885014489717554254568756887336213685667721566415634488356757885304 Q gi|254780142|r 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTL 95 (1398) Q Consensus 16 ~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~~ 95 (1398) T Consensus 3 ~~~~-i~~gl~sp~~ir~~s-~ev~~pet~~~~~-~P~~~Gl~d~ri~~~~~~~~C~Cg~~~~~---------------- 63 (808) T COG0086 3 RIFD-IKFGLASPEEIRSWS-GEVKKPETINYRT-KPERGGLFDERIFGPDKDYECTCGKYKRI---------------- 63 (808) T ss_pred CEEE-EEEECCCHHHHHHCC-EEECCCCCCCCCC-CCCCCCCCCHHHCCCCCCCEECCCCCCCC---------------- T ss_conf 3003-798058989997443-3876702027888-51688752043169899840228885675---------------- Q ss_pred CCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCCHHHHCCCCHHHHHHHHHHCCC Q ss_conf 77578767720027762201301225789999809996563013321112321788651043223699999886763585 Q gi|254780142|r 96 SSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQ 175 (1398) Q Consensus 96 ~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 175 (1398) T Consensus 64 ~~---~~~GhIeLa~Pv~hi~f~k~~~~----~L~~~~~~~~~v~~~~~~~~~--~-~~l~~~~~~~~~~~-------~~ 126 (808) T COG0086 64 CP---GGFGHIELAAPVAHIWFFKSIPS----LLDMTCRDCERVLYFEAYVVL--G-TDLEKIQLLNETEY-------VY 126 (808) T ss_pred CC---CCCEEEEEECCEEEECHHHCCHH----HHHHHHHHHHHHHHHHHHHHH--C-CCHHHHCCCCHHHH-------HH T ss_conf 88---97314776263588335445799----985137744562567666662--5-62244214403331-------12 Q ss_pred CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEE Q ss_conf 55061155267788877267488999999873103220347886447788866663489851128630450762235138 Q gi|254780142|r 176 DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLV 255 (1398) Q Consensus 176 ~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v 255 (1398) T Consensus 127 ~~~~~~~Ga~~~~~~~~~~~~~~~~----~~--~~~~~~~~~~~~~~l~~~d~~~~~~~~pewmil~vlpV~Pp~~RP~i 200 (808) T COG0086 127 DSFCAHCGAEAIKILLEKPDLETER----EE--ETLSPTKVKKLLKRLKVVDAFLLSGNRPEWMILTVLPVPPPDLRPSI 200 (808) T ss_pred CCCCCCCCCCCHHHHHHCCCHHHHH----HH--HCCCHHHHHHHHHHCCHHHHHHHCCCCCCEEEEEEECCCCCCCCCCE T ss_conf 0447898971399887367544312----13--03587889999751665677660478865368971035998888545 Q ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCC Q ss_conf 84697313100378999999986999999873983567776999999988887427767877247876506789986102 Q gi|254780142|r 256 ALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKG 335 (1398) Q Consensus 256 ~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkg 335 (1398) T Consensus 201 ~ld~g~~a~~dl~~~~~~ii~~n~rlk~~~~~~~~-~iv~~~~~~lQ~~v~~~~Dn-~~~~~~~~-~-rPlksl~~~Lkg 276 (808) T COG0086 201 QLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAP-IIVRNEKRMLQEAVDALFDN-RRPRAVTG-G-RPLKSLSQRLKG 276 (808) T ss_pred ECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHC-CCCCCCCC-C-CCCCCHHHHHCC T ss_conf 63898655668889999999998775776664545-77888999999999998616-89877658-9-764449998468 Q ss_pred CCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHHHH Q ss_conf 37820003465100457740341255435462003489877612899999999879866630001001224882501326 Q gi|254780142|r 336 KQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLA 415 (1398) Q Consensus 336 K~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v~r 415 (1398) T Consensus 277 K~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~~a~~~~~~~~~~~~~~w~Vl~ 356 (808) T COG0086 277 KQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRTGAKYAKRMVERRLPEVWDVLR 356 (808) T ss_pred CCCEEECCCCCCCCCCCCCEEECCCCCCCCCCCCCHHHHHHHHCCCEEEEEHHHHHHHCCCCEEEECCCCCCCCCCHHHH T ss_conf 77545134001511787862552799863400488799988744477987332223211771688012133565404678 Q ss_pred HHHCCCEEEECCCCCCEECCEEEEEEEEEC-CCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 665697899757631011140123589944-9547973122545467877545699746899999999998767505423 Q gi|254780142|r 416 EVVHQHVVLLNRAPSLHRLSMQAFEPKIIS-GKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494 (1398) Q Consensus 416 hl~~gd~Vl~NRqPsLHr~Simah~~~v~~-~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niis 494 (1398) T Consensus 357 evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AEa~~lm~tq~nils 436 (808) T COG0086 357 EVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILT 436 (808) T ss_pred HHHCCCCCCCCCCCHHHHHHHHHHCEEECCCCCEEECCHHHCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHHCCCCCCCC T ss_conf 77629800015577678999986510104555335310121552456537465536575059999998864055563256 Q ss_pred CCCCCCEEEEHHHHHHHHHHHHCCCCC----CCCCC---CEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEE Q ss_conf 788782044025899999987336788----74468---14179999999998889867852365204645667614245 Q gi|254780142|r 495 PASGAPVTVPSQDMVLGLCYLSTVHEG----DPGEG---MLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKI 567 (1398) Q Consensus 495 P~~g~Pi~~~~QD~i~G~y~lT~~~~~----~~~~~---~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~ 567 (1398) T Consensus 437 P~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~~~~~~e~~~ai~~~~~~~~~k~i~~~i~~~~---~~~~i 513 (808) T COG0086 437 PHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTISPDL---AELSI 513 (808) T ss_pred CCCCCCEEEECCEEEECCEEEEEECCCCCCCCCEEEEECCCCCCCHHHHHHHHCCCCEEEEEEEEEEEECCC---CCCEE T ss_conf 789995672020588134789983266888753489721233552255677754622126458999850378---75259 Q ss_pred ECCCCCCCCCCEEEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHH-HHHHHHHHHHHHHHHHCC-CCCCCCCC- Q ss_conf 217977511220554587510177511002013666999999980817899-987558899999998539-86132123- Q gi|254780142|r 568 YDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTV-AFCDDLMRLGFRYACSSG-ISFGKDDI- 644 (1398) Q Consensus 568 ~~tt~Gr~~~~~ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~-~~l~~~~~l~~~~l~~~G-fSigi~D~- 644 (1398) T Consensus 514 ~~t~~~~~~~~~~~~~~~d~~~~i~~~~l~~~~i~k~~~~~~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d 593 (808) T COG0086 514 IVTTDGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKD 593 (808) T ss_pred EEECCHHHHHHCCCCCCCCEEEEEECCCCCEEEEHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHEEEECCCEEEEECCC T ss_conf 99341365554068755540257731433123413458999998183055799999999998753133424207864354 Q ss_pred -CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE Q ss_conf -2683699999999978999999886489766788878864234658999999999987611565432222468837642 Q gi|254780142|r 645 -IVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMS 723 (1398) Q Consensus 645 -~~~~~k~~~i~~a~~~~~~~~~~~~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~ 723 (1398) T Consensus 594 ~~~~~~~~e~v~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~----~~~i~~m~ 669 (808) T COG0086 594 IEAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLD----FVDIRHMG 669 (808) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCC----HHHHHHHH T ss_conf 32057788999999999999998764587634577875687621779999999999876667752874----02399986 Q ss_pred CCCCCCCHHHEEEEEEECCCCCCCCCC-------------CCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCC Q ss_conf 255557842411200100002464434-------------4456663011108889897640576103221012101567 Q gi|254780142|r 724 HSGARGSIHQMRQLGGMRGLIAKPSGE-------------IIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASS 790 (1398) Q Consensus 724 ~SGAKGS~~qi~ql~Gqq~l~gkp~G~-------------~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~S 790 (1398) T Consensus 670 ~~Gs~~n~sq~~~~~G~~gv~g~r~~~~~~~~Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~s 749 (808) T COG0086 670 LSGARMNISQIVQLIGQQGVMGEKISVLARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADS 749 (808) T ss_pred HHHHCCCHHHHHHHHHHHEEECCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEEECCCCCCCHHHHHHHHCCC T ss_conf 43624489999998633203125788653222234665534554566455779972268750576653168876652346 Q ss_pred CEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCHHHCCCCC Q ss_conf 40110154230143277513887666512111008848865000101221144201778 Q gi|254780142|r 791 GYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPL 849 (1398) Q Consensus 791 GYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~~di~~~~ 849 (1398) T Consensus 750 GYl~RrLv~~~qdl~v~~d~~~~~-g~~~~~~~~~ged~~~~~~~~~~~~~~~~v~~~~ 807 (808) T COG0086 750 GYLTRRLVDVAQDLIVQEDDCVTD-GIGVVIQFEYGEDGEDLTERILGRVLEEDVLRPV 807 (808) T ss_pred CCCEEEEECHHCCEEEEECCEEEE-CCCEEEEEECCCCCCCHHHHHCCEEEHHHHCCCC T ss_conf 762577310222449995482872-6855888715764428888744847453402567 |
|
| >PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1478.32 Aligned_cols=571 Identities=56% Similarity=0.966 Sum_probs=537.7 Q ss_pred CCCCCEEEEEEECCCHHHHHHCC---------EEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 78640536898458867885014---------489717554254568756887336213685667721566415634488 Q gi|254780142|r 13 TDDRGFDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKG 83 (1398) Q Consensus 13 ~~~~~i~~i~f~l~spe~I~~~S---------~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g 83 (1398) T Consensus 4 ~~~~~f~~i~I~LASPe~Ir~WS~r~lpngeivGEVtkpeTINYrT~KPE~dGLFCErIFGP~Kd~eC~CGKyk~~k~kg 83 (627) T PRK02625 4 RTENHFDYVKIGLASPERIMQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRG 83 (627) T ss_pred CCCCCCCEEEEEECCHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCEEEHHHCCCCCCCEEECCCCCCCCCCC T ss_conf 31057672799836989999987530677865688889742125779988888830444087758377188721303287 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCCC-HHHHCCCC Q ss_conf 35675788530477578767720027762201301225789999809996563013321112321788651-04322369 Q gi|254780142|r 84 IICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSS-LEKYQILT 162 (1398) Q Consensus 84 ~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~~-~~~~~~~~ 162 (1398) T Consensus 84 ~vCe~CGVEvt~S~VRR~RMGHIeLA~PV~HIWYLK~~PS~Is~LLd~~~KeLE~ViYf~~yiV~dpg~~~~l~~k~ll~ 163 (627) T PRK02625 84 IVCERCGVEVTESRVRRHRMGYIKLAAPVSHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLT 163 (627) T ss_pred EECCCCCCCCCCCCCCCCCCCCEEECCCCEEEEEECCCCHHHHHHCCCCHHHHHHHHHCCEEEEECCCCCCCHHHHHHCC T ss_conf 16687685734352110135644465870443340688269999808868888875612306875677686346664315 Q ss_pred HHHHHHHHHHCCC-C-----CEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 9999886763585-5-----506115526778887726748899999987310322034788644778886666348985 Q gi|254780142|r 163 EEEYVEAVSQFGQ-D-----QFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNP 236 (1398) Q Consensus 163 ~~~~~~~~~~~~~-~-----~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~P 236 (1398) T Consensus 164 e~~~~e~~~~i~~~~~~~~~~~~~~~GaeAI~~lL~~lDL~~~~~~Lr~ei~~~k-~qkr~KliKRLkli~~Fi~S~~rP 242 (627) T PRK02625 164 EDQWLEIEDEIYAEDSELENEEVVGIGAEALKQLLEDLNLEEEAEQLREEIANSK-GQKRAKLIKRLRVIDNFIATGARP 242 (627) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 8999998988640221004764015449999999886798999999999976474-256899999999999998669883 Q ss_pred CEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 11286304507622351388469731310037899999998699999987398356777699999998888742776787 Q gi|254780142|r 237 GWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKR 316 (1398) Q Consensus 237 ewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~ 316 (1398) T Consensus 243 EWMIL~vLPVlPP~LRP~v~Ldggr~a~sDlN~lYrriI~rNnrLk~~~~~~ap~~ii~~ekrlLQeaVd~L~DN~~~g~ 322 (627) T PRK02625 243 EWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGR 322 (627) T ss_pred HHEEEECCCCCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 50787323558987774278668865666658999999999999999886599578888899999999888544655688 Q ss_pred CCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 72478765067899861023782000346510045774034125543546200348987761289999999987986663 Q gi|254780142|r 317 VVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTV 396 (1398) Q Consensus 317 ~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i 396 (1398) T Consensus 323 ~~~~~~~RplKSlsd~lkGK~GRfRqnLlGKRVDySgRsVIvvgP~L~l~qcGlP~~mA~elf~Pfvi~~l~~~~~~~~i 402 (627) T PRK02625 323 TVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQNIVNNI 402 (627) T ss_pred CCCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCCCCCCEEECCCCCCHHHCCCCHHHHHHHCCHHHHHHHHHHCCCCCH T ss_conf 64279997021357662687880212146551056787068249865214308848999984418999999970664545 Q ss_pred CCCCCEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCH Q ss_conf 00010012248825013266656978997576310111401235899449547973122545467877545699746899 Q gi|254780142|r 397 KQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISP 476 (1398) Q Consensus 397 ~~~k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~ 476 (1398) T Consensus 403 ~~ak~~i~~~~~~v~~~l~~v~~~~pVllNRaPTLHRlgiqaf~p~l~~g~ai~lhplvc~~fNADFDGDqMavhvPls~ 482 (627) T PRK02625 403 KAAKKLIQRADDEVWQVLQEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSL 482 (627) T ss_pred HHHHHHHHHCCCHHHHHHHHHHCCCEEEECCCCCCCCCEEECEEEEEECCEEEEECCCCCCCCCCCCCCCCEEECCCCCH T ss_conf 77999988668389999999973995787588521004111104688778048865545776689988721441378998 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCC-CCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEEC Q ss_conf 999999998767505423788782044025899999987336788-7446814179999999998889867852365204 Q gi|254780142|r 477 EAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEG-DPGEGMLFADMGEVYHALENKIVTLHSKIRGRYK 555 (1398) Q Consensus 477 eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~-~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~ 555 (1398) T Consensus 483 ea~~Ea~~lmls~~nilsPa~g~pi~~psQDmvlG~yylT~~~~~~~~~~~~~f~~~~~~~~a~~~~~i~lh~~i~~r~~ 562 (627) T PRK02625 483 EAQTEARMLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQKDAGRYFASLEDVIHAFEDGRIDLHAWVWVRFN 562 (627) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEEC T ss_conf 99999999853115777788899722355121103236503567764788865789999999997696024665899965 Q ss_pred CCC--------------------------------CCCCCCCEEECCCCCCCCCCEEEECC Q ss_conf 645--------------------------------66761424521797751122055458 Q gi|254780142|r 556 SVD--------------------------------KDGNSISKIYDTTPGRMIIGEILPRH 584 (1398) Q Consensus 556 ~~~--------------------------------~~~~~~~~~~~tt~Gr~~~~~ilp~~ 584 (1398) T Consensus 563 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~TT~Gri~fn~~i~~~ 623 (627) T PRK02625 563 GEVEDDDEDDEPLKTETLEDGTRIEQWNYRRDRFDEDGNLISQYILTTVGRVIMNKTIQDA 623 (627) T ss_pred CCCCCCCCCCCCCEEEECCCCCEEEEECCEEEEECCCCCEEEEEEEECCCEEEHHHHHHHH T ss_conf 7402465445650368627884377501204553367876568999477444446665887 |
|
| >CHL00018 rpoC1 RNA polymerase beta' subunit | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1460.35 Aligned_cols=571 Identities=43% Similarity=0.711 Sum_probs=513.6 Q ss_pred CCCEEEEEEECCCHHHHHHCCE---------EEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCC Q ss_conf 6405368984588678850144---------8971755425456875688733621368566772156641563---448 Q gi|254780142|r 15 DRGFDSVRISIASPAKIASLSY---------GEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRM---KYK 82 (1398) Q Consensus 15 ~~~i~~i~f~l~spe~I~~~S~---------~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~---~~~ 82 (1398) T Consensus 4 ~~~f~~i~I~lASPe~Ir~WS~r~lpng~~vGEV~kpeTINYrT~KPE~dGLFCErIFGP~kd~eC~CGKYK~i~~~k~~ 83 (668) T CHL00018 4 RYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEKED 83 (668) T ss_pred CCCCCEEEEEECCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCCCCCCEEEHHHHCCCCCCEEECCCCCCCCCCCCC T ss_conf 24666379982698999998763066776031688965400577898888881003208885866758775224655657 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCCC----CHHHH Q ss_conf 83567578853047757876772002776220130122578999980999656301332111232178865----10432 Q gi|254780142|r 83 GIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLS----SLEKY 158 (1398) Q Consensus 83 g~~C~~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~~----~~~~~ 158 (1398) T Consensus 84 g~vCerCGVEvt~S~VRR~RMGHIeLAaPV~HIWYlK~~PS~Ia~LLdls~KeLEkViYf~~~iv~~~~~~~~~~~lk~~ 163 (668) T CHL00018 84 PKFCEQCGVEFVDSRIRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRLRGL 163 (668) T ss_pred CCCCCCCCCCCCCCHHHHHCCCCEEECCCCCCHHHHCCCCHHHHHHHCCCHHHHHHEEEEEEEEEECCCCCCCHHHHHHH T ss_conf 62468778360401666750575545587130234268805999984898888754211037985246778413436777 Q ss_pred CCCCHHHHHHHHHHCCC-------CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCC-------------CCCHHHHH Q ss_conf 23699999886763585-------55061155267788877267488999999873103-------------22034788 Q gi|254780142|r 159 QILTEEEYVEAVSQFGQ-------DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKS-------------SSIFRRKK 218 (1398) Q Consensus 159 ~~~~~~~~~~~~~~~~~-------~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~ 218 (1398) T Consensus 164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~GaeAIkklL~~lDL~~~~~~l~~elk~l~~~~~~~~e~e~~ki~~kk~k 243 (668) T CHL00018 164 FEYEIQSWKYSIPLFFTTQGFDTFRNREISTGAGAIREQLADLDLRIIIENSLVEWKELGEEGPTGNEWEDRKIGRRKDF 243 (668) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH T ss_conf 89999999987776530110032220221656999999997269999999999999975552010123445567788999 Q ss_pred HHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH--CCCCHHHHHH Q ss_conf 64477888666634898511286304507622351388469731310037899999998699999987--3983567776 Q gi|254780142|r 219 IIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKS--LHAPEIIIRN 296 (1398) Q Consensus 219 ~~~~~~~~~~f~~~~~~Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~--~~ap~~i~~~ 296 (1398) T Consensus 244 liKRLkli~~F~~SgnkPEWMILtVLPVLPPdLRPmVqLDGGrFatSDlN~lYrriI~rNnrL~~l~~~~~~~p~iIi~n 323 (668) T CHL00018 244 LVRRIELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGELVMC 323 (668) T ss_pred HHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH T ss_conf 99999999999866999424886345548987742489579841578517899999999999988775024895899999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHH Q ss_conf 99999998888742776787724787650678998610237820003465100457740341255435462003489877 Q gi|254780142|r 297 EKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMAL 376 (1398) Q Consensus 297 ~~~lLQ~~v~~~~dn~~~~~~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~ 376 (1398) T Consensus 324 EkR~LQeaVd~lidN~~~g~~~~~~~~rplKslsd~lkGK~GrfRqnLlGKRVdySgRsVI~vgP~L~l~qcGlP~~mA~ 403 (668) T CHL00018 324 QKKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAI 403 (668) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCEEECCCCCHHHHH T ss_conf 99999999999872678788751889983411898854667610100366510455650332699732101288789999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCC Q ss_conf 61289999999987986663000100122488250132666569789975763101114012358994495479731225 Q gi|254780142|r 377 ELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVC 456 (1398) Q Consensus 377 ~L~~P~~~~~L~~~g~~~~i~~~k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc 456 (1398) T Consensus 404 eLf~pf~i~~l~~~~~~~~~~~ak~~i~~~~~~~~~~l~~v~~~~~vllNRaPTLHrl~iqaf~p~l~~g~ai~lhplvc 483 (668) T CHL00018 404 ELFQPFVIRGLIRQHLASNIRVAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVC 483 (668) T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCEEEEEEECCCCEEEECCCCC T ss_conf 86028999999862776770788899986585999999987439847981785212132200025632783477244567 Q ss_pred CCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCC-------------CCC Q ss_conf 4546787754569974689999999999876750542378878204402589999998733678-------------874 Q gi|254780142|r 457 AGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHE-------------GDP 523 (1398) Q Consensus 457 ~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~-------------~~~ 523 (1398) T Consensus 484 ~~fNADFDGDqMavhvpls~ea~~Ea~~lm~s~~NilsPa~G~Pi~~psqdmvlg~yylt~~~~~~~~~~~~~~~~~~~~ 563 (668) T CHL00018 484 KGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTSGNRRGICANRYNYQNDDNN 563 (668) T ss_pred CCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCC T ss_conf 87679988830465168998999999998644057777888997124442201143365035655432222211133546 Q ss_pred CCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCC--------------------------------CCCCCCCEEECCC Q ss_conf 46814179999999998889867852365204645--------------------------------6676142452179 Q gi|254780142|r 524 GEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVD--------------------------------KDGNSISKIYDTT 571 (1398) Q Consensus 524 ~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~--------------------------------~~~~~~~~~~~tt 571 (1398) T Consensus 564 ~~~~~f~~~~~~~~ay~~~~i~l~~~i~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~i~TT 643 (668) T CHL00018 564 TKEPYFSNSYDAIGAYRQKRINLDSPLWLRWRLDQRVIASREVPIEVQYESLGTYHEIYEHYLIVKSVKKEILSIYIRTT 643 (668) T ss_pred CCCCEECCHHHHHHHHHCCCEECCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEECCCCEEEECCCCCEEEEEEEEC T ss_conf 78864689999999997594112560699723654444554565157751578511311011134225787556899707 Q ss_pred CCCCCCCEEEECCC Q ss_conf 77511220554587 Q gi|254780142|r 572 PGRMIIGEILPRHH 585 (1398) Q Consensus 572 ~Gr~~~~~ilp~~~ 585 (1398) T Consensus 644 ~Gri~fn~~i~~~l 657 (668) T CHL00018 644 VGRILFNREIEEAI 657 (668) T ss_pred CCEEEHHHHHHHHH T ss_conf 76113555659988 |
|
| >PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1336.17 Aligned_cols=767 Identities=41% Similarity=0.647 Sum_probs=634.3
Q ss_pred EEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 77511002013666999999980817899987558899999998539861321232683699999999978999999886
Q gi|254780142|r 590 DICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYN 669 (1398)
Q Consensus 590 ~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~ 669 (1398)
T Consensus 7 ~f~N~~~~k~~l~~li~~~~~~~g~~~t~~~ld~lk~lGf~~at~ag~s~~i~D~~~p~~k~~~~~~a~~~~~~~~~~~~ 86 (1295)
T PRK02597 7 PFRNRVVDKKALKKLIAWAFKNYGTARTAAMADNLKDLGFRYATQAAVSISVDDLKVPPAKRDLLEQAEEEITATEERYR 86 (1295)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEEHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 85644156889999999999984989999999999876678762120498563255680399999999999999999865
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC
Q ss_conf 48976678887886423465899999999998761156543222246883764225555784241120010000246443
Q gi|254780142|r 670 DGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG 749 (1398)
Q Consensus 670 ~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G 749 (1398)
T Consensus 87 ~g~it~~er~~~~i~~W~~~~~~~~~~~~~~~~~~---------~~~n~v~mm~~SGARGn~~qv~Ql~gmRGlma~p~g 157 (1295)
T PRK02597 87 RGEITEVERFQKVIDTWNETNERLKDEVKKNFNQN---------DPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 157 (1295)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------CCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCC
T ss_conf 68877888777999999997999999998640012---------898765788667766788898777422103588699
Q ss_pred CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEE
Q ss_conf 44456663011108889897640576103221012101567401101542301432775138876665121110088488
Q gi|254780142|r 750 EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVV 829 (1398)
Q Consensus 750 ~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~ 829 (1398)
T Consensus 158 ~ii~~Pi~snfreGl~v~ey~is~~GaRKGl~DTAlrTadsGYlTRrLvdvaq~vii~~~dcgt~~gi~~~~~~~~~~~~ 237 (1295)
T PRK02597 158 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVL 237 (1295)
T ss_pred CEECCCHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHHHHHHCCCCEEECCCCCCCCCEEEEEEECCCEEE
T ss_conf 86573422203256348687553775541114536561254620005466327229966248999998998883797299
Q ss_pred EEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHH
Q ss_conf 65000101221144201778971885178657899999999759840202331000355186578875420178520001
Q gi|254780142|r 830 YSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVG 909 (1398)
Q Consensus 830 ~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pG 909 (1398)
T Consensus 238 ~~l~~r~~Gr~~~~~v~~~-~~~~i~~~~~~i~~~~~~~~~~~~~~~v~irs~ltc~~~~~vc~~cYG~~la~~~~v~~G 316 (1295)
T PRK02597 238 IKLGDRLVGRVTAEDVVDP-DGEVIAERNTEIDPDLAKKIEKAGVEEVMVRSPLTCEANRSVCRKCYGWSLAHNHLVDLG 316 (1295)
T ss_pred EEECCEEEEEEEHHHEECC-CCCEEEECCCCCCHHHHHHHHHCCCCEEEECCCCEECCCCCCCHHHCCCCCCCCCCCCCC
T ss_conf 9810355646387567889-996899798675999999999869978997898053799737442008564588856567
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEE---EEEEECCCCCEEEEEC-CCCEEEEECCC
Q ss_conf 0146021111007889877642024543222112202401487689721---1346517887789742-76046640677
Q gi|254780142|r 910 EAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKN---RNVCRNSTNDLISMGR-NTTLQILDMSG 985 (1398)
Q Consensus 910 e~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkE---i~~~~n~~~~~i~vs~-~~~~~i~d~~~ 985 (1398)
T Consensus 317 eaVGiiAaQSIGEPGTQLTmRTFHtGGvFTge~a~~vrap~~G~I~f~~~l~~~~~RTrhG~~A~~~~~~~~l~I~~~~~ 396 (1295)
T PRK02597 317 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARVVRSPFAGTVEFGSKARTRPYRTRHGVEAQQAEVDFDLVLKPSGK 396 (1295)
T ss_pred CEEEEEEECCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEECCCCCCCCEEECCCCCEEEEEECCCEEEEEECCC
T ss_conf 72107764037886234546432417644576310550564758966766643033568995779875062899997799
Q ss_pred CEEEEEECCCHHCCCCCCCCEEECCEEEEECCCC---------CCEEEECCCCEEEEEEECCCC----------------
Q ss_conf 6000000110000135678553225078621354---------311320246368975312783----------------
Q gi|254780142|r 986 QEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPH---------TFPIITEVSGTVGFEDLVDGI---------------- 1040 (1398)
Q Consensus 986 ~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~---------~~~i~~e~~~~v~~~~~~~~~---------------- 1040 (1398)
T Consensus 397 ~~~~~~~ip~~SlL~V~n~q~V~~~qvIAEi~a~~~~~~~Ek~~K~I~sd~~GEv~~~~~v~~~~~~~~gn~~~~~~~~g 476 (1295)
T PRK02597 397 GKPQKIEITQGSLLFVDDGQTVEADQTLAEIAAGAVKKSTEKATKDVICDLAGEVRFADLIPEEKTDRQGNTTLKAQRLG 476 (1295)
T ss_pred CCEEEEECCCCCEEEEECCCEEECCCEEEEEECCCCCCCEEEEEEEEEECCCCEEEECCCCCCCCCCCCCCEEEECCCCC
T ss_conf 82689713898689998996984273899995376311126663226725775599503443443223376675225575
Q ss_pred ---------------------------------------------------------EE---------------------
Q ss_conf ---------------------------------------------------------20---------------------
Q gi|254780142|r 1041 ---------------------------------------------------------SV--------------------- 1042 (1398)
Q Consensus 1041 ---------------------------------------------------------~~--------------------- 1042 (1398)
T Consensus 477 ~lWILsG~vy~lp~~~~~~~k~~d~v~~~~~la~~~~~s~~gg~vr~~~~~~~~~e~~ii~~s~~l~~~~~~~~~~~~~~ 556 (1295)
T PRK02597 477 LLWVLSGDVYNLPPGAEPVVKNGDRVEEGTVLAETSLVSEHGGVVRLRESIGDSREVEIVTASVTLDQAKVLEESTHGRE 556 (1295)
T ss_pred EEEEEECCEECCCCCCCCEEECCCEECCCCEEEEEEEECCCCCEEECCCCCCCCCEEEEECCCCEECHHHHHHHHCCCCC
T ss_conf 36998376014687645325147631136435775465166986753566888732443121001030112102014673
Q ss_pred ---HH-------------------------HHH----------------------------------------CCCC---
Q ss_conf ---01-------------------------230----------------------------------------2368---
Q gi|254780142|r 1043 ---IE-------------------------SIG----------------------------------------ESTG--- 1051 (1398)
Q Consensus 1043 ---~~-------------------------~~~----------------------------------------~~t~--- 1051 (1398)
T Consensus 557 ~~~l~~~~~~~~~l~~~p~~ki~n~~iiA~~~d~rYrT~t~GiiKY~~i~v~k~~~~k~~y~v~k~g~~~~IPEEth~i~ 636 (1295)
T PRK02597 557 QYNLETKDGQRFRLNATPGTKVGNGEVVAELIDDRYRTKTGGLVKYAGLEVKKAGSAKNGYEVSKGGTLLWIPEETHEVN 636 (1295)
T ss_pred EECCCCCCCCEEEECCCCCCCCCCCCEEEEECCCCEECCCCCCEEECCEEEEECCCCCCCCEEECCCEEEECCHHHCCCC
T ss_conf 01011366624673048887323696778860675132788715665544410356566716712762897020531046
Q ss_pred --CEEEEE--------------------------EEHHHCCCCCC----------------------C------------
Q ss_conf --602677--------------------------51011012212----------------------3------------
Q gi|254780142|r 1052 --IAKRKV--------------------------IDWRFASRSQN----------------------L------------ 1069 (1398)
Q Consensus 1052 --~~~~~~--------------------------i~~~~~~~~~~----------------------~------------ 1069 (1398)
T Consensus 637 k~~Sli~V~ng~~I~~gTeI~kni~s~~~GlV~v~~Kn~il~EI~IkpG~i~~~~~~~~i~~~~~~li~PGe~I~~~~~~ 716 (1295)
T PRK02597 637 KDISLLMVEDGQYVEAGTEVVKDIFCQTSGVVEVTQKNDILREIIVKPGELHLCDDPEALETGDGQLVNPGEEVLPGVVT 716 (1295)
T ss_pred CCCCEEEEECCCEECCCCEEECCEEECCCCEEEEEECCCCEEEEEECCCCEECCCCCCHHHCCCCCEECCCCCCCCCCCC
T ss_conf 65440687668354269565136040257369998716631489961572433676110010478477887543566322
Q ss_pred -------------------CC------------------------CEE------EECCCCC-------------------
Q ss_conf -------------------85------------------------347------7427782-------------------
Q gi|254780142|r 1070 -------------------KP------------------------AIV------VTDENGV------------------- 1081 (1398)
Q Consensus 1070 -------------------~~------------------------~~~------i~d~~~~------------------- 1081 (1398)
T Consensus 717 ~~l~y~e~I~~~~~~~lLiRPv~~Y~I~~~~~~~~~~~~~~~~~~~i~l~~v~~i~ykdge~Iksi~gIqLvrT~LvL~~ 796 (1295)
T PRK02597 717 DELVYVETVETPEGPGLLLRPVEEFTIPDEPQLPSQGSVKQEKGRSIGLRAVQRLPYKDGERVKSVEGVELLRTQLVLEI 796 (1295)
T ss_pred CCEEEEEEEECCCCCEEEECCCEEEECCCCCCCCCCCCHHHCCCCCEEEEEEEEEECCCCCEEEEECCEEEEEEEEEEEE
T ss_conf 52599999825877408863317986368866666552233247733688989997059966643157068988899983
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780142|r 1082 -------------------------------------------------------------------------------- 1081 (1398)
Q Consensus 1082 -------------------------------------------------------------------------------- 1081 (1398)
T Consensus 797 ~~~~~~~~~die~~~~~~~~~~~rl~lviles~l~r~d~~~d~~~~s~~t~llv~~~q~I~~~~via~t~il~~~~g~ir 876 (1295)
T PRK02597 797 FDTTPQLTADIELIPDKKDKTIQRLQLVILESLLVRRDTASDSSHGSTHTELLVKDGQSIKPGDVVARTQILCKEAGVVQ 876 (1295)
T ss_pred CCCCCEEEEEEEEECCCCCCCCCEEEEEEEEHHEEECCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEEEEECCEEEC
T ss_conf 58874367999980487544411002553000102157777867884102453157863188876524676554160451
Q ss_pred ------------------------------------------------------EEECCC-----CCCCEEECCCCCEEE
Q ss_conf ------------------------------------------------------532247-----884202137784454
Q gi|254780142|r 1082 ------------------------------------------------------VLKSAR-----GTDARWFLPVDALLS 1102 (1398)
Q Consensus 1082 ------------------------------------------------------~~~~~~-----~~~~~~~~~~~~~~~ 1102 (1398)
T Consensus 877 ~i~~~~~~~r~ili~~~~d~~~i~~~~~~~v~lGqlI~~g~~I~~~~~~~~SGQVi~I~~~~ivIRlakPYL~s~gA~ih 956 (1295)
T PRK02597 877 GIRVGDEPVRRLLVERDEDTITIPLSGKPVVKVGDLVVAGDELAPGVPAPESGEVEAVSGGSVTLRLGRPYMVSPGAVLH 956 (1295)
T ss_pred CHHCCCCCCEEEEECCCCCCEEECCCCCCEECCCCEEECCEEECCCCCCCCCCEEEEEECCEEEEEECCEEECCCCCEEE
T ss_conf 31025753006997477776565478874874888898781742898767861289984785899854617759996898
Q ss_pred ECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEE
Q ss_conf 13676135484222101320245543367732889887525111101113478678633127944999983689840268
Q gi|254780142|r 1103 VSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAE 1182 (1398)
Q Consensus 1103 v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e 1182 (1398)
T Consensus 957 v~~GdiV~~GDtLvtLiyEr~KSGDIiQGLPKVEeLLEARkpk~~~~l~~~~G~v~~~~~~~~-~si~i~v~e~d~~~~e 1035 (1295)
T PRK02597 957 VRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKESCILCKKPGTVQIKYGDDD-ESVDVKVIEDDGTITE 1035 (1295)
T ss_pred EECCCEEECCCEEEEEEEEHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCEEECCCCCC-CCEEEEEEECCCCCEE
T ss_conf 426879714976788752010147745687017877543155531000035760232135666-6426787622674200
Q ss_pred EEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHH----------------HCHHHHHHHHHHHHHHHHHHHCCEECHH
Q ss_conf 981389658984198774086464389999999875----------------2799999999999999999809700612
Q gi|254780142|r 1183 YFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRI----------------KGVEALASYLINEVQEVYRLEGVAINHK 1246 (1398)
Q Consensus 1183 ~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~v----------------lGIEAAR~~Ii~EIq~V~~~~Gi~IN~R 1246 (1398)
T Consensus 1036 y~~~~g~~~~v~~g~~V~~ge~lTdg~~npH~iL~i~f~~~~~~~g~~~aA~lSi~q~Q~~LVneIQkVYrSQGV~IsDK 1115 (1295)
T PRK02597 1036 YPILPGQNVMVSDGQQVDAGEPLTDGPINPHELLECFFEDLRDRKGLYEAAQEALAKLQRFLVNEVQNVYQSQGVDIDDK 1115 (1295)
T ss_pred CCCCCCCCEEECCCCEEECCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCEEECC
T ss_conf 13455632242257366136524578788788876566653021667889999999999999987651504489566041
Q ss_pred HHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHH
Q ss_conf 56012476286148941886454566410699999999999972898752012100001453023107765040258999
Q gi|254780142|r 1247 HIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKV 1326 (1398)
Q Consensus 1247 HIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~v 1326 (1398)
T Consensus 1116 HIEIIVRQMTSKV~IeDgg~T~FLPGELIeL~raer~Nral~~~gg~~a~Y~PILLGITKASLNT~SFISAASFQETTRV 1195 (1295)
T PRK02597 1116 HIEVIVRQMTSKVRIDDGGDTTLLPGELIELRQVEQVNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRV 1195 (1295)
T ss_pred EEEEEEEECCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCCCHHHHHCHHHHHHH
T ss_conf 79999996344189972878742872244199999998999962798774698987676021156531244321548899
Q ss_pred HHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHHHHHHH
Q ss_conf 99974528552366532215507305655354665331210
Q gi|254780142|r 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVA 1367 (1398)
Q Consensus 1327 L~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~~~~~~ 1367 (1398)
T Consensus 1196 LTkAAIeGRiDWLrGLKENVIiGrlIPAGTGf~~~~~~~~~ 1236 (1295)
T PRK02597 1196 LTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEETAVL 1236 (1295)
T ss_pred HHHHHHCCCHHHHCCCCHHEEECCCEECCCCCCCCCCCCCC
T ss_conf 99998727703326852215722747567681754221235
|
|
| >TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit; InterPro: IPR012756 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1272.29 Aligned_cols=759 Identities=41% Similarity=0.669 Sum_probs=609.4
Q ss_pred EECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 75110020136669999999808178999875588999999985398613212326836999999999789999998864
Q gi|254780142|r 591 ICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYND 670 (1398)
Q Consensus 591 ~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~ 670 (1398)
T Consensus 2 F~N~~vDK~~L~~Li~way~~~GtA~ta~~AD~lKdLGF~yAT~AgVSISVdDL~vP~~K~~lle~AE~~I~~te~rY~~ 81 (1252)
T TIGR02388 2 FKNRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPEKQDLLEAAEKEIRATEERYRR 81 (1252)
T ss_pred CCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 31005414678889999874058325788877765200011322401698705548878999999888876778876305
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCCC
Q ss_conf 89766788878864234658999999999987611565432222468837642255557842411200100002464434
Q gi|254780142|r 671 GLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGE 750 (1398)
Q Consensus 671 G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~ 750 (1398)
T Consensus 82 GEITEVERf~KVIDTW~~T~E~L~d~V~~~F~~~---------dpLNSVyMMAfSGARGN~SQVRQLVGMRGLMA~PQGE 152 (1252)
T TIGR02388 82 GEITEVERFQKVIDTWNGTNEELKDEVVNNFRQT---------DPLNSVYMMAFSGARGNLSQVRQLVGMRGLMADPQGE 152 (1252)
T ss_pred CCEEEEECCEEEEECCCCCCHHHHHHHHHHHHCC---------CCCCEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCC
T ss_conf 8613530200476455661168899999864205---------8732110002168756634565543131225689976
Q ss_pred CCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEE
Q ss_conf 44566630111088898976405761032210121015674011015423014327751388766651211100884886
Q gi|254780142|r 751 IIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVY 830 (1398)
Q Consensus 751 ~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~ 830 (1398)
T Consensus 153 IIDLPIkTNFREGLTVTEYvISSYGARKGLVDTALRTADSGYLTRRLVDVsQDVIvRE~DCgT~R~i~~~~mt~g~k~~~ 232 (1252)
T TIGR02388 153 IIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKVVI 232 (1252)
T ss_pred EEECCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHCCCCCHHHEEEEEECCEEEECCCCCCCCCEEEEEECCCCEEEE
T ss_conf 78468544653685356456632354422034554312553101101333231589614688524358876247872799
Q ss_pred EECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHH
Q ss_conf 50001012211442017789718851786578999999997598402023310003551865788754201785200010
Q gi|254780142|r 831 SLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGE 910 (1398)
Q Consensus 831 ~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe 910 (1398)
T Consensus 233 ~l~~RL~GR~~~~Dv~~p~tge~i~~~N~~I~~~Lak~i~~~~~~~V~vRSPLTCEA~rSVC~~CYGWsLAH~~~VDlGE 312 (1252)
T TIGR02388 233 KLADRLLGRLVAEDVLHPETGEVIVPKNTAIDEDLAKKIEKAGIEEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGE 312 (1252)
T ss_pred EECCCCEEEEEHHHCCCCCCCEEEECCCCCCCHHHHHHHHHHHHCEEEECCCCCCCCCCCCCCCCCCHHHHHCCCEECCC
T ss_conf 86254022332100247654606611676021899999975111576871687401252210045422555356010222
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE---EEEECCCCCE-EEEECCCCEEEEECCCC
Q ss_conf 1460211110078898776420245432221122024014876897211---3465178877-89742760466406776
Q gi|254780142|r 911 AVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR---NVCRNSTNDL-ISMGRNTTLQILDMSGQ 986 (1398)
Q Consensus 911 ~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi---~~~~n~~~~~-i~vs~~~~~~i~d~~~~ 986 (1398)
T Consensus 313 AVGIIAAQSIGEPGTQLTMRTFHTGGVfTgEva~~~r~~~~G~v~~g~kl~~R~~RTrHG~dA~~vE~~g~l~~~~~~~~ 392 (1252)
T TIGR02388 313 AVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVEFGKKLRIRKYRTRHGEDAKQVEVAGLLILKPEGKK 392 (1252)
T ss_pred CEEEEEEECCCCCCCCCCCEEEECCCEEECCCCEEEECCCCCEEECCCCCEECCCCCCCCCCCEEEEEEEEEEECCCCCC
T ss_conf 01200210368797533220342386431332202214545337558721234556887644002333106898357654
Q ss_pred ----EEEEEECCCHHCCCCCCCCEEECCEEEEECC-----------CCCCEEEECCCCEEEEEEEC--------------
Q ss_conf ----0000001100001356785532250786213-----------54311320246368975312--------------
Q gi|254780142|r 987 ----EQYSHRIMYGAKLFVDDGGVIECGQRISEWD-----------PHTFPIITEVSGTVGFEDLV-------------- 1037 (1398)
Q Consensus 987 ----~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~D-----------p~~~~i~~e~~~~v~~~~~~-------------- 1037 (1398)
T Consensus 393 ~~~~~~Q~~~~t~GS~~~v~DG~~v~~g~l~a~~~~~~r~~~~~~Eka~KDV~~DLAGeV~f~~~~~p~e~~DRQGn~T~ 472 (1252)
T TIGR02388 393 TETAAAQEIEVTQGSLLFVEDGQTVKAGQLLAEIALGARAVRKSTEKATKDVASDLAGEVKFDKVVQPEEKTDRQGNTTR 472 (1252)
T ss_pred CCCCCCCEEEECCCCEEEEECCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCHHH
T ss_conf 45656544772377389986376100061000134410244443222222123103473353221062203367763113
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398)
Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398)
T Consensus 473 ~A~rgGl~WvLsGeVYNLPPgA~pVV~~~~~vE~g~vlAEt~~~t~~GG~VRL~e~~~~k~~REv~IiTaSvlLd~~~v~ 552 (1252)
T TIGR02388 473 IAQRGGLIWVLSGEVYNLPPGAEPVVKNGDRVEAGTVLAETKLSTEHGGVVRLPESVDSKDSREVEIITASVLLDQAKVI 552 (1252)
T ss_pred HHHCCCEEEEEECCEECCCCCCEEEECCCCEECCCCEEEEEEEEECCCCEEEECCCCCCCCCCEEEEEEEEEEECCCEEE
T ss_conf 32026758998332103888871164068775124266423542047875872245788876458888722100111235
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398)
Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398)
T Consensus 553 ~es~~gre~y~i~t~~~~~f~L~a~PGtKv~~g~vvAeLiDdRyrT~TGG~~kyApg~~V~K~g~~K~GyEV~~GGTLLW 632 (1252)
T TIGR02388 553 EESSQGREQYLIETADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTTTGGLLKYAPGVEVAKKGKAKQGYEVVKGGTLLW 632 (1252)
T ss_pred EECCCCCEEEEEECCCCCEEEEECCCCCCCCCCCEEEEECCCCCCCCCCCEEEECCCCEEEECCCCCCCCEEECCCEEEE
T ss_conf 21127750478981787189986588861126646465215651014575478628732721676667707613873752
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398)
Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398)
T Consensus 633 IP~ETHE~NKDISLL~vED~~yvEAGTEVVKDIFcQ~SG~V~V~QKNDILREi~vk~G~~~~~~D~e~~~rf~~~g~L~~ 712 (1252)
T TIGR02388 633 IPEETHEINKDISLLLVEDGQYVEAGTEVVKDIFCQNSGIVEVVQKNDILREIIVKPGELHEVDDPEAVKRFLEEGTLLQ 712 (1252)
T ss_pred CCCCCCCCCCCEEEEEEECCCEEEECCEEEEEEEECCCCEEEEEECCCCEEEEEEECCCEEEECCHHHHHHHHHCCCCCC
T ss_conf 67532100243468775266345406347764551588669998527505788971782244358799999873684027
Q ss_pred ------------------------------------------------------------------------------CC
Q ss_conf ------------------------------------------------------------------------------78
Q gi|254780142|r 1038 ------------------------------------------------------------------------------DG 1039 (1398)
Q Consensus 1038 ------------------------------------------------------------------------------~~ 1039 (1398)
T Consensus 713 PGe~~~~G~~~~~l~~~~~~E~~p~G~~lLlRpV~Ey~vp~ep~~P~~~~~~~~~G~~i~lravQRL~YKd~e~vKSVeG 792 (1252)
T TIGR02388 713 PGEEVLPGVVVDELSQVQYLEDTPEGKGLLLRPVEEYKVPDEPEVPSQSSVSQEKGRSIELRAVQRLPYKDGERVKSVEG 792 (1252)
T ss_pred CHHHHHCCCCHHHHHHHHHHHCCCCCCEEEECCEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEECC
T ss_conf 81666288302454544654148898735533302331578756786344112578668887664134447861355448
Q ss_pred CEEH------H---HHHC---CCCCEE-----------------------------------------------------
Q ss_conf 3200------1---2302---368602-----------------------------------------------------
Q gi|254780142|r 1040 ISVI------E---SIGE---STGIAK----------------------------------------------------- 1054 (1398)
Q Consensus 1040 ~~~~------~---~~~~---~t~~~~----------------------------------------------------- 1054 (1398)
T Consensus 793 v~LL~T~LvlE~~~~~~~~~~~s~l~~DiE~~~D~~d~~~~RL~LVILESl~~RRD~~~D~~~Gst~T~L~v~dgd~i~p 872 (1252)
T TIGR02388 793 VELLRTQLVLEIEDEGPQEHNISHLAADIELIQDEEDKDIQRLQLVILESLVLRRDIASDSTQGSTKTSLLVKDGDLIKP 872 (1252)
T ss_pred CHHHCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCHHCCCCCCCEEEEEECCCCEECC
T ss_conf 11001024677424573000753036777764487543102555554345444302000356884125788416876167
Q ss_pred -----------------------------EEEEEHH-------------------HCCCCCCCCCCEEEECCCCCEEECC
Q ss_conf -----------------------------6775101-------------------1012212385347742778253224
Q gi|254780142|r 1055 -----------------------------RKVIDWR-------------------FASRSQNLKPAIVVTDENGVVLKSA 1086 (1398)
Q Consensus 1055 -----------------------------~~~i~~~-------------------~~~~~~~~~~~~~i~d~~~~~~~~~ 1086 (1398)
T Consensus 873 G~V~A~T~I~~Ke~G~v~g~~~~~~E~~RR~lv~r~~D~~~~~~~g~kp~VK~Gdl~v~G~~l~~G-v~~~~~g~~~~v~ 951 (1252)
T TIGR02388 873 GAVVARTQILCKEAGVVRGIKKGEGESIRRVLVERNSDRLKVNIKGAKPKVKTGDLVVAGDELAKG-VKAEESGEVLEVK 951 (1252)
T ss_pred CCEEEEEEECCCCCCEEEECCCCCCCCEEEEEEEECCCEEEEEECCCCCCCCCCCEEECCCHHCCC-CCCCCCCEEEEEC
T ss_conf 755873000015676685033467761358999725764898405788612467654176121277-3444662056731
Q ss_pred CCC---------CCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEE
Q ss_conf 788---------42021377844541367613548422210132024554336773288988752511110111347867
Q gi|254780142|r 1087 RGT---------DARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTI 1157 (1398)
Q Consensus 1087 ~~~---------~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv 1157 (1398)
T Consensus 952 ~~~~~~~v~lR~~RPY~VSPgaVL~i~dGDLV~RGDnL~LLVFER~KTGDIvQGLPRIEELLEAR~Pke~c~La~~~G~~ 1031 (1252)
T TIGR02388 952 NADDNYAVILRIARPYRVSPGAVLHIEDGDLVQRGDNLVLLVFERAKTGDIVQGLPRIEELLEARKPKEACVLAKRPGVV 1031 (1252)
T ss_pred CCCCCCEEEEECCCCCEECCCCEEEEECCCEEEECCCEEEEEEECCCCCCEECCCCCHHHHHHCCCCCCCEEEECCCCEE
T ss_conf 58885079996178843478654775458566517855899873046686211885068886227972113662279769
Q ss_pred EEEEECCCC--EEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHH----------------
Q ss_conf 863312794--49999836898402689813896589841987740864643899999998752----------------
Q gi|254780142|r 1158 RIKRNYKNK--SRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIK---------------- 1219 (1398)
Q Consensus 1158 ~i~~~~~~k--~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vl---------------- 1219 (1398)
T Consensus 1032 ~v~~~~~desv~i~ViE--~dg-~~~eY~ll~GQN~~v~DG~~v~~g~~LtDGp~nPH~iL~~~F~~~~~~~g~~~aA~~ 1108 (1252)
T TIGR02388 1032 QVKYGEDDESVEIKVIE--EDG-TVSEYPLLPGQNIMVSDGQKVDVGEPLTDGPINPHDILDVFFSYYKDKDGLLEAAQE 1108 (1252)
T ss_pred EEEECCCCCEEEEEEEE--CCC-CEEECCCCCCCCCEEECCCEECCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf 99886887568999980--588-361213568785222078551367423688987378999887523575247999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf 79999999999999999980970061256012476286148941886454566410699999999999972898752012
Q gi|254780142|r 1220 GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSP 1299 (1398)
Q Consensus 1220 GIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p 1299 (1398)
T Consensus 1109 ~l~k~Q~~lVNEVQ~VY~SQGv~I~DKHIEVIVRQMT~KVRIdD~GDT~lLpGEL~~LRQvE~~N~aM~iTGgApA~yTP 1188 (1252)
T TIGR02388 1109 SLQKVQKFLVNEVQSVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTP 1188 (1252)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEECCCEEEEECCCCEEECCCCEEEEECHHCCCCCCCCCCCCCCCCCC
T ss_conf 99999887635554232107814533448999962465236635887055373202200021035521013678652331
Q ss_pred EEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHH
Q ss_conf 100001453023107765040258999999745285523665322155073056553546653
Q gi|254780142|r 1300 ILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHE 1362 (1398)
Q Consensus 1300 ~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~ 1362 (1398)
T Consensus 1189 VLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGf~~~~ 1251 (1252)
T TIGR02388 1189 VLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYE 1251 (1252)
T ss_pred EEEECHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCEEEEEEEEECCCCCCCCCCC
T ss_conf 320001121021013443100014566655430576023146600178863126888777577
|
7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. |
| >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1183.26 Aligned_cols=436 Identities=36% Similarity=0.568 Sum_probs=398.2 Q ss_pred EEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 77511002013666999999980817899987558899999998539861321232683699999999978999999886 Q gi|254780142|r 590 DICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYN 669 (1398) Q Consensus 590 ~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~ 669 (1398) T Consensus 8 ~f~n~~~~k~~~~~~i~~~~~~~g~~~t~~~~d~~k~~gf~~at~~g~s~~i~dl~~~~~k~~~~~~a~~~~~~~~~~~~ 87 (1350) T CHL00117 8 VFHNKVIDKTALKRLISRLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLLQDAEQQSLILEKHYH 87 (1350) T ss_pred EEEECCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 38801056889999999999985979999999999876768751132587450164680499999999999999999975 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCC Q ss_conf 48976678887886423465899999999998761156543222246883764225555784241120010000246443 Q gi|254780142|r 670 DGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSG 749 (1398) Q Consensus 670 ~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G 749 (1398) T Consensus 88 ~g~~~~~e~~~~~i~~w~~~~~~~~~~~~~~~~~~---------~~~n~v~~m~~sgarg~~~qv~ql~gmrglm~~p~g 158 (1350) T CHL00117 88 YGNVTAVEKLQQSIETWYATSEYLKQEMNPNFRMT---------DPLNPVYMMAFSGARGNASQVHQLVGMRGLMSDPQG 158 (1350) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------CCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCC T ss_conf 67876788777999999987999999998766316---------898871467657667888998887423214568799 Q ss_pred CCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEE Q ss_conf 44456663011108889897640576103221012101567401101542301432775138876665121110088488 Q gi|254780142|r 750 EIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVV 829 (1398) Q Consensus 750 ~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~ 829 (1398) T Consensus 159 ~ii~~pi~~nfregl~~~ey~is~~garkg~~dtalrta~~gyltrrlvdv~q~~iv~~~dc~t~~gi~~~~-~~~~~~~ 237 (1350) T CHL00117 159 QIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTALRTADAGYLTRRLVDVVQHIVVRRTDCGTIRGISVSP-RNGMMPE 237 (1350) T ss_pred CEECCCHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHHCCEEEEECCCCCCCCCEEEEE-CCCCEEE T ss_conf 866743222121564776720137853311255565503646420043643363699554689988789992-6997575 Q ss_pred EEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHH Q ss_conf 65000101221144201778971885178657899999999759840202331000355186578875420178520001 Q gi|254780142|r 830 YSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVG 909 (1398) Q Consensus 830 ~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pG 909 (1398) T Consensus 238 ~~~~~~~~grv~~~~~~~~~~~~~i~~~~~~i~~~~~~~~~~~~~~~i~vrspltc~~~~~ic~~cyg~~l~~~~~v~~g 317 (1350) T CHL00117 238 RILIQTLIGRVLADDIYIPKGSRCIATRNQDIGIGLVNRFITFRIQPIYIRSPLTCRSTSWICQLCYGWSLTHGDLVELG 317 (1350) T ss_pred EEECCEEEEEEEHHHEECCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCEEECCCCCCCHHHCCCCCCCCCCCCCC T ss_conf 22001011157773578089985998399675999999999879988997898120688758653348552268876457 Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECCC-CEEEEECCCC Q ss_conf 01460211110078898776420245432221122024014876897211--34651788778974276-0466406776 Q gi|254780142|r 910 EAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRNT-TLQILDMSGQ 986 (1398) Q Consensus 910 e~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~~-~~~i~d~~~~ 986 (1398) T Consensus 318 eavgiia~qsigepgtqlt~rtfhtggvftge~ae~iraP~~G~I~f~~~~~~~~RTrhG~~A~l~~~~~~l~I~-~~~~ 396 (1350) T CHL00117 318 EAVGIIAGQSIGEPGTQLTMRTFHTGGVFTGGTAEQVRAPFNGKIKFNEDLVHPTRTRHGHPAFLCKIDLYVTIV-ESED 396 (1350) T ss_pred CEEEEEEEECCCCCCCCCEEEEEEECCEECCCHHHHCCCCCCCEEECCCCCCCCCCCCCCCEEEEEECCEEEEEE-CCCC T ss_conf 753588630158886420356543355003421432017767458536545543134688534887214069985-4788 Q ss_pred EEEEEECCCHHCCCCCCCCEEECCEEEEECCCC----------CCEEEECCCCEEEEEEE Q ss_conf 000000110000135678553225078621354----------31132024636897531 Q gi|254780142|r 987 EQYSHRIMYGAKLFVDDGGVIECGQRISEWDPH----------TFPIITEVSGTVGFEDL 1036 (1398) Q Consensus 987 ~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~----------~~~i~~e~~~~v~~~~~ 1036 (1398) T Consensus 397 ~~~~~~ip~~SlL~V~n~q~V~s~QvIAEi~~~~~~~~~~Ek~~K~i~S~~~GEv~~~~~ 456 (1350) T CHL00117 397 IIHNVNIPPKSLLLVQNDQYVESEQVIAEIRAGTSTLKFKEKVRKHIYSDSEGEMHWSTD 456 (1350) T ss_pred EEEEEEECCCCEEEEECCCEEECCCEEEEEECCCCCCCCCEEEEEEEECCCCCCEEECCC T ss_conf 179988679848999899587516189997057775545305887775488642681364 |
|
| >CHL00006 consensus | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1144.24 Aligned_cols=432 Identities=32% Similarity=0.525 Sum_probs=387.9 Q ss_pred EEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 17751100201366699999998081789998755889999999853986132123268369999999997899999988 Q gi|254780142|r 589 FDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQY 668 (1398) Q Consensus 589 ~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~ 668 (1398) T Consensus 7 ~~f~n~~~~k~~~~~~i~~~~~~~g~~~t~~~~d~~k~~gf~~at~~g~s~~~~dl~~~~~k~~~~~~a~~~~~~~~~~~ 86 (1372) T CHL00006 7 LVFHNKVIDGTAIKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHH 86 (1372) T ss_pred EEEEEEECCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHCCCCEEEEHHHCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 04882124689999999999998498999999999987677865104168755132568328999999999999999997 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCC Q ss_conf 64897667888788642346589999999999876115654322224688376422555578424112001000024644 Q gi|254780142|r 669 NDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPS 748 (1398) Q Consensus 669 ~~G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~ 748 (1398) T Consensus 87 ~~g~i~~~e~~~~~i~~w~~~~~~l~~~~~~~~~~~---------~~~n~v~~m~~sgarg~~~qv~ql~gmrglm~~p~ 157 (1372) T CHL00006 87 HYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMT---------DPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQ 157 (1372) T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---------CCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCC T ss_conf 668976788776999999987999999997665107---------99888267765767788899888742110256869 Q ss_pred CCCCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEE Q ss_conf 34445666301110888989764057610322101210156740110154230143277513887666512111008848 Q gi|254780142|r 749 GEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQV 828 (1398) Q Consensus 749 G~~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~ 828 (1398) T Consensus 158 g~ii~~pi~~nfregl~~~ey~is~~garkg~~dtal~ta~~gyltrrlvdv~q~~~v~~~dc~t~~gi~~~~~~-~~~~ 236 (1372) T CHL00006 158 GQMIDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSPRN-GMMP 236 (1372) T ss_pred CCEECCCHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCHHHHHCCEEEEECCCCCCCCCEEEEEEC-CCCE T ss_conf 986553222202256367562013785331125546550364642004365347259962368998877999605-8832 Q ss_pred EEEECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECH Q ss_conf 86500010122114420177897188517865789999999975984020233100035518657887542017852000 Q gi|254780142|r 829 VYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNV 908 (1398) Q Consensus 829 ~~~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~p 908 (1398) T Consensus 237 ~~~~~~~~~gr~~~~~i~--~~~~~i~~~~~~i~~~~~~~~~~~~~~~~~vrspltc~~~~~ic~~cyg~~l~~~~~v~~ 314 (1372) T CHL00006 237 ERIFIQTLIGRVLADDIY--IGSRCIATRNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVEL 314 (1372) T ss_pred EEEECCEEEEEEEEEEEE--ECCCEEEECCCCCCHHHHHHHHHCCCCEEEECCCEECCCCCCCCHHHCCCCCCCCCCCCC T ss_conf 431003322057814488--878389958955599999999987997799779810068873865333845226873555 Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECC-CCEEEEECCC Q ss_conf 101460211110078898776420245432221122024014876897211--3465178877897427-6046640677 Q gi|254780142|r 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRN-TTLQILDMSG 985 (1398) Q Consensus 909 Ge~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~-~~~~i~d~~~ 985 (1398) T Consensus 315 geavgiiaaqsigepgtqlt~rtfhtggvf~~~~~~~~~~~~~g~i~f~~~l~~ptRTrhG~~A~l~~~~~~v~i--~~~ 392 (1372) T CHL00006 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDLVHPTRTRHGHPAFLCYIDLYVTI--ESE 392 (1372) T ss_pred CCEEEEEEEECCCCCCCCCEEEEEECCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCCCCCEEEEEECCCEEEE--CCC T ss_conf 753347742015887643124421016521342011012776744752655676765779953599740307998--349 Q ss_pred CEEEEEECCCHHCCCCCCCCEEECCEEEEECCCC----------CCEEEECCCCEEEEE Q ss_conf 6000000110000135678553225078621354----------311320246368975 Q gi|254780142|r 986 QEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPH----------TFPIITEVSGTVGFE 1034 (1398) Q Consensus 986 ~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~----------~~~i~~e~~~~v~~~ 1034 (1398) T Consensus 393 ~~~~~~~ip~~SlL~V~n~q~V~s~QvIAEi~a~~~~~~~kEk~~K~i~s~~~GE~~~~ 451 (1372) T CHL00006 393 DIIHNVNIPPKSFLLVQNDQYVESEQVIAEIRAGTSTFNFKERVRKHIYSDSEGEMHWS 451 (1372) T ss_pred CEEEEEEECCCCEEEEECCCEEECCCEEEEEECCCCCCCCEEEEEEEEECCCCCCCCCC T ss_conf 86899887898389998995885052899982577666630258767752776412124 |
|
| >TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit; InterPro: IPR012755 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=1194.45 Aligned_cols=537 Identities=59% Similarity=1.000 Sum_probs=515.9 Q ss_pred CEEEEEEECCCHHHHHHCC---------EEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 0536898458867885014---------4897175542545687568873362136856677215664156344883567 Q gi|254780142|r 17 GFDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICE 87 (1398) Q Consensus 17 ~i~~i~f~l~spe~I~~~S---------~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~ 87 (1398) T Consensus 1 ~fdy~ki~~asPer~~~WG~rtlPnG~vvGevtkPetinyrtlkPemdGlfCe~ifGPskdWeC~CGkykrvrhrGivCe 80 (625) T TIGR02387 1 RFDYVKIAIASPERVMEWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECYCGKYKRVRHRGIVCE 80 (625) T ss_pred CCCEEEEEECCCHHHHHHCCCCCCCCCEEEEECCCCEECEEECCCCCCCEEEHHCCCCCCCCCCCCCCEEEEEECCEEEE T ss_conf 96259998528089986111238887378620377400001037321430001013788664110464015542212650 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCCEEEECCCC-CCHHHHCCCCHHHH Q ss_conf 57885304775787677200277622013012257899998099965630133211123217886-51043223699999 Q gi|254780142|r 88 KCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGL-SSLEKYQILTEEEY 166 (1398) Q Consensus 88 ~Cg~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~~~~~~~~~-~~~~~~~~~~~~~~ 166 (1398) T Consensus 81 rCGvevtes~vrrhrmG~iklaaPv~hvWylkGiPsy~~~lldm~lrdveq~vyfn~yvvl~PG~~~~l~ykqllted~~ 160 (625) T TIGR02387 81 RCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQW 160 (625) T ss_pred CCCEEEECCEEEEEECCEEEECCCCEEEEEECCHHHHHHHHHHHHHHHHHEEEEEEEEEEECCCCCCCCHHHHHHCCCCE T ss_conf 36502311200100011244315400110002516899998520023332023355578877887200013333034432 Q ss_pred HHHHHHCCC-------CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEE Q ss_conf 886763585-------5506115526778887726748899999987310322034788644778886666348985112 Q gi|254780142|r 167 VEAVSQFGQ-------DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWM 239 (1398) Q Consensus 167 ~~~~~~~~~-------~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewm 239 (1398) T Consensus 161 ~e~ed~iyae~s~~e~~~~~~~~Gaea~~~ll~~~~le~~ae~lr~~~~~s-kGqkr~klikrlrv~dnf~at~~~~eWm 239 (625) T TIGR02387 161 VEIEDQIYAEDSELENEEGVVGIGAEAVKELLAELELEEVAEKLREEINES-KGQKRAKLIKRLRVIDNFIATSSRPEWM 239 (625) T ss_pred EEECCHHCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHCCCCCCEE T ss_conf 543001000200002454301013799999998510578899999998621-4515788999988876655326776437 Q ss_pred EEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 86304507622351388469731310037899999998699999987398356777699999998888742776787724 Q gi|254780142|r 240 IIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVT 319 (1398) Q Consensus 240 il~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~~ 319 (1398) T Consensus 240 ~l~~iPviPPdlrPmvqldGGrfatsdlndlyrrvinrnnrlarlqeilaPeiivrnekrmlqeavdalidnGrrGrtvv 319 (625) T TIGR02387 240 VLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVV 319 (625) T ss_pred EEEEECCCCCCCCCEEEECCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHHHCCCCCCEEE T ss_conf 88872047887662034348611013477899998521015778887525400431025788999999982788654465 Q ss_pred CCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 78765067899861023782000346510045774034125543546200348987761289999999987986663000 Q gi|254780142|r 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQA 399 (1398) Q Consensus 320 ~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~~~~L~~~g~~~~i~~~ 399 (1398) T Consensus 320 Gannr~lkslsdiieGkqGrfrqnllGkrvdysGrsvivvGP~lk~~qCGlP~emaielfqPfvih~li~~~~vnnikaa 399 (625) T TIGR02387 320 GANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKLHQCGLPKEMAIELFQPFVIHRLIKRGIVNNIKAA 399 (625) T ss_pred CCCCCCHHHHHHHHCCCCCCHHHHHCCCEEECCCCEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 05763024567664166651135341340200574789987840476358855678876305899999986566677999 Q ss_pred CCEEECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHH Q ss_conf 10012248825013266656978997576310111401235899449547973122545467877545699746899999 Q gi|254780142|r 400 KKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQ 479 (1398) Q Consensus 400 k~~i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAr 479 (1398) T Consensus 400 kkli~~~d~~~~~vl~evi~GhP~~lnraPtlhrlGiqafeP~lv~GraiqlhPlvC~afnadfdGdqmavhvPl~~e~q 479 (625) T TIGR02387 400 KKLIQRADDEIWSVLEEVITGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQ 479 (625) T ss_pred HHHHHCCCHHHHHHHHHHHCCCCEEEECCCCHHHHCHHHCCCEEECCCEEEECCCCHHHHCCCCCCCEEEEEECCCCCHH T ss_conf 99874043689999998746872576267502330222227444236136640320000125667761578703100002 Q ss_pred HHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCC-----CCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEE Q ss_conf 999998767505423788782044025899999987336788-----744681417999999999888986785236520 Q gi|254780142|r 480 LEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEG-----DPGEGMLFADMGEVYHALENKIVTLHSKIRGRY 554 (1398) Q Consensus 480 aEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~-----~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~ 554 (1398) T Consensus 480 ~earllmla~~n~lsPatG~Pi~~P~qdmvlG~yylt~~~P~a~~~~~~~~~~~~~~~ed~~~a~~~~~~~lh~~~W~r~ 559 (625) T TIGR02387 480 AEARLLMLASNNVLSPATGKPIVTPSQDMVLGCYYLTAENPDAEKPEFGGAGRYFASLEDAVRAYEDGRIDLHDKIWVRH 559 (625) T ss_pred HHHHHHHHHHHHCCCCCCCCCEECCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 35788777753104766787301356110223213332388744321144432000157899864135200125444443 |
7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. |
| >smart00663 RPOLA_N RNA polymerase I subunit A N-terminus | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=763.31 Aligned_cols=276 Identities=54% Similarity=0.796 Sum_probs=248.6 Q ss_pred CEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 11286304507622351388469731310037899999998699999987398356777699999998888742776787 Q gi|254780142|r 237 GWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKR 316 (1398) Q Consensus 237 ewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~ 316 (1398) T Consensus 1 ew~il~~lpVpP~~~RP~~~~~~~~~~~ddlt~~y~~II~~N~~L~~~~~~~~~~~~~~~~~~~LQ~~V~~~~dn~~~~~ 80 (295) T smart00663 1 EWMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPEHIIRNEKRLLQEAVDTLFDNEGLPR 80 (295) T ss_pred CEEEEECCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 94699612439987186089699987348478999999999999999986599177899999999999999954889876 Q ss_pred CCCCCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHH-----HH---HHHH Q ss_conf 724787650678998610237820003465100457740341255435462003489877612899-----99---9999 Q gi|254780142|r 317 VVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPF-----LY---AQLE 388 (1398) Q Consensus 317 ~~~~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~-----~~---~~L~ 388 (1398) T Consensus 81 -~~~~~~~~~k~i~~rL~gK~Gr~R~nl~GKRvd~s~RsVItpdP~L~~~evGvP~~~A~~Lt~pe~V~~~n~~~l~~~v 159 (295) T smart00663 81 -ARQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV 159 (295) T ss_pred -CCCCCCCCCCCHHHHHCCCCCEECCCCCCCCCCCCCCCEEECCCCCCCCEECCCHHHHHHCCCCEEEEHHHHHHHHHHH T ss_conf -7677898575689884587731211336554476576436369876358764889999737834797277899999998 Q ss_pred HCCC--CCCCCCCCC-E--------EECCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCC Q ss_conf 8798--666300010-0--------1224882501326665697899757631011140123589944954797312254 Q gi|254780142|r 389 KKGY--VSTVKQAKK-F--------VEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCA 457 (1398) Q Consensus 389 ~~g~--~~~i~~~k~-~--------i~~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~ 457 (1398) T Consensus 160 ~~g~~ga~~~~~~~~~~~~~~~~~~~~~~l~~g~~v~r~l~~gd~vl~NRqPtLHr~si~a~~~~i~~~~tir~n~~~c~ 239 (295) T smart00663 160 RNGPNGAKYIIRGKKTNLKLAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCS 239 (295) T ss_pred HCCCCCCEEEECCCEEEHHHHHHHHHHHCCCCCCEEEEEEECCCEEEECCCCHHHHCCCEEEEEEEECCCEEEECCCCCC T ss_conf 52997744896186014055454566640576769865644597899737740211031036899976957898854578 Q ss_pred CCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHH Q ss_conf 54678775456997468999999999987675054237887820440258999999 Q gi|254780142|r 458 GYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLC 513 (1398) Q Consensus 458 pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y 513 (1398) T Consensus 240 ~~NADFDGDeMnih~pqs~~a~aEa~~L~~~~~~~~sp~~g~p~~~~~QD~~~g~y 295 (295) T smart00663 240 PYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295) T ss_pred CCCCCCCCCEEEEECCCCHHHHHHHHHHHHCHHCEEECCCCCEEEEEEHHHEEECC T ss_conf 70688776126764579989999999985032137507999805884215304349 |
|
| >pfam04998 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=690.53 Aligned_cols=434 Identities=28% Similarity=0.386 Sum_probs=269.1 Q ss_pred CCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCH Q ss_conf 88898976405761032210121015674011015423014327751388766651211100884886500010122114 Q gi|254780142|r 763 GLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTAL 842 (1398) Q Consensus 763 GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~ 842 (1398) T Consensus 1 GL~p~EfFfh~m~gReGLiDTAvKTa~SGYlqRrLvk~ledl~V~yD~tvr~~~g~ivqf~yG~Dg~d~~~~~~~~~~~~ 80 (447) T pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQFLYGEDGLDPLKIEGQGRFTI 80 (447) T ss_pred CCCHHHHHHCCCHHCCHHHHCCHHHHHHHHHHHHHHHHHCEEEEEECCCCCCCCEEEEEEEECCCCEECCEEEEECCEEE T ss_conf 96878998768401233876731565554689998887174799945982389906999898885665126896264356 Q ss_pred HHCCCCC--------CCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCC Q ss_conf 4201778--------97188517865789999999975984020233100035518657887542017852000101460 Q gi|254780142|r 843 DDIINPL--------TNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGV 914 (1398) Q Consensus 843 ~di~~~~--------~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~ 914 (1398) T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~slv~pGEaVGi 160 (447) T pfam04998 81 EDSDLKLEKKFKIDLNDVLLLLSEFSLSTLLFEILLRSGIESKRVRSELTCNSKAGVCFLCYGRDKYRRSLVEPGEAVGI 160 (447) T ss_pred EECCCCCCCCEEECCCCCEEECCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCHHH T ss_conf 76257223747745998554002214558899999972767378865530261889999999987542132478741102 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEE-EECCCCCEEEEECCCCEEEEECCCCEEEEEEC Q ss_conf 21111007889877642024543222112202401487689721134-65178877897427604664067760000001 Q gi|254780142|r 915 IAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNV-CRNSTNDLISMGRNTTLQILDMSGQEQYSHRI 993 (1398) Q Consensus 915 iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~-~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki 993 (1398) T Consensus 161 IAAQSIGEP~TQmTLnTFH~AGvas~-------nvT~GvPRl~Eil~~~~~~~tp~~~~~~~~~~------~~~~~~~~~ 227 (447) T pfam04998 161 IAAQSIGEPGTQMTLNTFHFAGVASK-------NVTLGVPRLKEIINVAKNNKKPVITVLLIKNI------VSDKARVKK 227 (447) T ss_pred HHHCCCCCCHHHHHHHHHHHCCCCCC-------CCCCCCEEEEEEEEEEEECCEEEEECCCCEEE------ECCCCEEEE T ss_conf 33202467035564776543331012-------33226349985249996154357853785444------323450687 Q ss_pred CCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCE Q ss_conf 10000135678553225078621354311320246368975312783200123023686026775101101221238534 Q gi|254780142|r 994 MYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAI 1073 (1398) Q Consensus 994 ~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~ 1073 (1398) T Consensus 228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~------------~~~~~~~~ 290 (447) T pfam04998 228 QREEKTLLLLKKVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPEEVA-----EEVALAI------------IIIGKRKS 290 (447) T ss_pred EECCCEEEEEEEECEEEEEEECCCCEEEECCEEEEECCCCCCCCHHHH-----CHHHHHH------------HCCCEEEE T ss_conf 722674999998330589997589656623300133331266531221-----2123344------------15616530 Q ss_pred EEECCCC-CEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECC Q ss_conf 7742778-253224788420213778445413676135484222101320245543367732889887525111101113 Q gi|254780142|r 1074 VVTDENG-VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAE 1152 (1398) Q Consensus 1074 ~i~d~~~-~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiise 1152 (1398) T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------------ 334 (447) T pfam04998 291 RKRKKNNLGVAKDEKGLEEEELLLLNKILLVIPGIKVKYGVILT------------------------------------ 334 (447) T ss_pred EEECCCEEEEEECCCCCHHHHCCCCCCHHEECCCCEEEECCCCC------------------------------------ T ss_conf 68336407998537751112125212102001386897223256------------------------------------ Q ss_pred CCCEEEE-EEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHH Q ss_conf 4786786-331279449999836898402689813896589841987740864643899999998752799999999999 Q gi|254780142|r 1153 ISGTIRI-KRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINE 1231 (1398) Q Consensus 1153 i~Giv~i-~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~E 1231 (1398) T Consensus 335 -~~~~~~~~~~~~~~~~~~l~--t~G~nl~~v~~~~----gvid~~k~~--------sn~I~em~~~lGIEAAr~~i~~E 399 (447) T pfam04998 335 -DGRVDPHTILEKLGKEWLLK--TEGNNLQAVMRLQ----GVIDNDKTY--------SNDIREMLKKLGIEAARDSILLE 399 (447) T ss_pred -CCCCCCHHHHCCCCCEEEEE--EEHHHHHHHHHCC----CCCCCCCEE--------EEEHHHHHHHEEEEECCCCHHHH T ss_conf -57776213201368376664--4058999999728----935478168--------98299665225999885121353 Q ss_pred HHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCC Q ss_conf 99999980970061256012476286148941886454566410699999999999972898752012100001453023 Q gi|254780142|r 1232 VQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQT 1311 (1398) Q Consensus 1232 Iq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t 1311 (1398) T Consensus 400 ~~~V~~~~g~~vn~RHl~llaD~MT~~G~l~----------------------------------------gitR~Gl~~ 439 (447) T pfam04998 400 IRNVFKFDGIYVNRRHLALLADLMTFKGELL----------------------------------------GITRAGLNR 439 (447) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEECCEEE----------------------------------------EECHHHHCC T ss_conf 8999988778876999985897462356176----------------------------------------330645166 Q ss_pred --CCHHHH Q ss_conf --107765 Q gi|254780142|r 1312 --KSFISA 1317 (1398) Q Consensus 1312 --~S~Ls~ 1317 (1398) T Consensus 440 ~~~s~l~~ 447 (447) T pfam04998 440 EKSSFILM 447 (447) T ss_pred CCCCCCCC T ss_conf 99886157 |
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. |
| >PRK04309 DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=623.41 Aligned_cols=359 Identities=26% Similarity=0.339 Sum_probs=253.2 Q ss_pred EECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 51786578999999997598402023310003551865788754201785200010146021111007889877642024 Q gi|254780142|r 855 VKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHL 934 (1398) Q Consensus 855 ~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHf 934 (1398) T Consensus 14 ~~~~~~i~e~~~~~i~~~gi~~~~irsvlt------~~~~~Y~rsL-----V~~GEaVGiIAAQSIGEPgTQLTLrTFH~ 82 (381) T PRK04309 14 SELPESLKEELEEKVKKYGLTEEEVEEIIK------EVVREYLRSL-----IEPGEAVGIVAAQSIGEPGTQMTMRTFHY 82 (381) T ss_pred CCCCHHHHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHCCCC-----CCCCCHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 799878999999999886998999999999------9999857157-----67874688887773284788888987635 Q ss_pred CCCCCCCCCCEEEECCCCEEEEEEEEEEE-CCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEE Q ss_conf 54322211220240148768972113465-17887789742760466406776000000110000135678553225078 Q gi|254780142|r 935 GGAVTVMDRSFIESPCDGIVKIKNRNVCR-NSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRI 1013 (1398) Q Consensus 935 AGVAS~~~~~~iknvTlGVPRlkEi~~~~-n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii 1013 (1398) T Consensus 83 gGva~~-------~vT~G~pRl~Ei~~a~k~~~tp~~~i~------l~~~~~~~~~~~~~v~~~i~~~~~~dv~~~~~-- 147 (381) T PRK04309 83 AGVAEI-------NVTLGLPRLIEIVDARKTPSTPMMTIY------LKEEYAYDREKAEEVAKKIEATTLEDLAKDIS-- 147 (381) T ss_pred HCEEEE-------EEECCCCEEEEEEECCCCCCCCEEEEE------ECCCCCCCHHHHHHHHHHCCEEEEEEEEEEEE-- T ss_conf 211000-------055377628999862356664318999------33433443899999875303499573036999-- Q ss_pred EECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEE Q ss_conf 62135431132024636897531278320012302368602677510110122123853477427782532247884202 Q gi|254780142|r 1014 SEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARW 1093 (1398) Q Consensus 1014 ~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~ 1093 (1398) T Consensus 148 --~d~~~~~i~i~~----------~-----~~~~~~~~i~~~~i~------------------------~~i~~~~~--- 183 (381) T PRK04309 148 --VDLANMTIIIEL----------D-----EEQLEERGLTVDKVV------------------------EKIKSKLG--- 183 (381) T ss_pred --EECCCCEEEEEE----------C-----HHHHHHCCCCHHHHH------------------------HHHHHCCC--- T ss_conf --936897699998----------8-----677856389889999------------------------99862158--- Q ss_pred ECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEE Q ss_conf 13778445413676135484222101320245543367732889887525111101113478678633127944999983 Q gi|254780142|r 1094 FLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEP 1173 (1398) Q Consensus 1094 ~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~ 1173 (1398) T Consensus 184 -----------------------~~~~~~~~~~~i~~~~~~v~el~~~~~~~~~~~i~gi~gi~r~~i~~~~-~e~~i~- 238 (381) T PRK04309 184 -----------------------LKVEIEGNTIIVTPKEPSIRELRKLAEKIKDIKIKGIKGIKRVIIRKEG-DEYVIY- 238 (381) T ss_pred -----------------------CEEECCCCEEEEECCCCCHHHHHHHHHCCCCCEEECCCCCEEEEEECCC-CEEEEE- T ss_conf -----------------------4683379879981799888999997630357168457992699997589-789999- Q ss_pred CCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHH Q ss_conf 68984026898138965898419877408646438999999987527999999999999999998097006125601247 Q gi|254780142|r 1174 FEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVR 1253 (1398) Q Consensus 1174 ~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD 1253 (1398) T Consensus 239 -t~G~~l~~~~-------~------~~~vD~~~~~sndi~dIl~i~GiEAar~~iv~Eiq~Vy~~qGv~IndkHIelI~d 304 (381) T PRK04309 239 -TEGSNLKEVL-------K------IEGVDPTRTTTNNIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVAD 304 (381) T ss_pred -ECCCCHHHEE-------E------ECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEE T ss_conf -4474545526-------5------2563344522486899998860999999999998878862886435203103200 Q ss_pred HHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHC Q ss_conf 62861489418864545664106999999999999728987520121000014530231077650402589999997452 Q gi|254780142|r 1254 HMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIA 1333 (1398) Q Consensus 1254 ~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ 1333 (1398) T Consensus 305 ~Mt~~G~~~~------i~r~gi-----------------------------~---~~~~S~lsaASFqeTt~VLt~AAi~ 346 (381) T PRK04309 305 MMTWDGEVRQ------IGRHGI-----------------------------S---GEKASVLARAAFEVTVKHLLDAAIR 346 (381) T ss_pred EHHCCCEEEE------CCCCCC-----------------------------C---CCCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 0303780530------550112-----------------------------6---7887899982227499999999850 Q ss_pred CCEECCCCCCEEEECCCCCCCCCCHHH Q ss_conf 855236653221550730565535466 Q gi|254780142|r 1334 GKVDTLDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1334 ge~D~L~GvSENIIlGqliP~GTG~f~ 1360 (1398) T Consensus 347 Gk~D~L~GlkeNVIvG~liPaGTG~~~ 373 (381) T PRK04309 347 GEVDELKGVVENIIVGQPIPLGTGDVE 373 (381) T ss_pred CCCCCCCCCHHHEECCCCCCCCCCCEE T ss_conf 897778880887334897568866678 |
|
| >cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=571.44 Aligned_cols=356 Identities=25% Similarity=0.320 Sum_probs=239.6 Q ss_pred CCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 57899999999759840202331000355186578875420178520001014602111100788987764202454322 Q gi|254780142|r 860 LILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939 (1398) Q Consensus 860 ~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS 939 (1398) T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~y~~sl-----V~pGEaVGiIAAQSIGEPgTQLTLrTFH~aG~a~ 70 (363) T cd06528 2 LLKEKLEEVLKEHGLTLSEAEEIIK------EVLREYLRSL-----IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAE 70 (363) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHHHCC-----CCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCEEE T ss_conf 5578999999982999999999999------9999987607-----7987388999887327669888898764510001 Q ss_pred CCCCCEEEECCCCEEEEEEEEEEE-CCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCC Q ss_conf 211220240148768972113465-1788778974276046640677600000011000013567855322507862135 Q gi|254780142|r 940 VMDRSFIESPCDGIVKIKNRNVCR-NSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDP 1018 (1398) Q Consensus 940 ~~~~~~iknvTlGVPRlkEi~~~~-n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp 1018 (1398) T Consensus 71 -------~~vt~G~pRl~Ei~~a~k~~~tp~~~i~l~------~~~~~~~~~~~~v~~~i~~~~~~~~~~~i~----id~ 133 (363) T cd06528 71 -------INVTLGLPRLIEIVDARKEPSTPTMTIYLE------EEYKYDREKAEEVARKIEETTLENLAEDIS----IDL 133 (363) T ss_pred -------EEEECCCCEEEEEEECCCCCCCCEEEEEEC------CCCCCCHHHHHHHHHHCCEEEEEEEEEEEE----ECC T ss_conf -------006537432699886004766756999960------544551899998886435189870068999----917 Q ss_pred CCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCC Q ss_conf 43113202463689753127832001230236860267751011012212385347742778253224788420213778 Q gi|254780142|r 1019 HTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVD 1098 (1398) Q Consensus 1019 ~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~ 1098 (1398) T Consensus 134 ~~~~i~i~l~~---------------~~~~~~~-----------------i~----~~~i~~~i~~~-~----------- 165 (363) T cd06528 134 FNMRITIELDE---------------EMLEDRG-----------------IT----VDDVLKAIEKL-K----------- 165 (363) T ss_pred CCCEEEEEECH---------------HHHHHCC-----------------CC----HHHHHHHHHHH-C----------- T ss_conf 87079999884---------------6764249-----------------98----89999998764-3----------- Q ss_pred CEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCC Q ss_conf 44541367613548422210132024554336773288988752511110111347867863312794499998368984 Q gi|254780142|r 1099 ALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGV 1178 (1398) Q Consensus 1099 ~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~ 1178 (1398) T Consensus 166 ------~~~~~~~---------~~~~~~~~~~~~~~~~~l~~~~~~~~~~~i~gi~gi~~~~i~~~~~-e~~i~--t~G~ 227 (363) T cd06528 166 ------KGKVGEE---------GDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEED-EYVIY--TEGS 227 (363) T ss_pred ------CCCEEEC---------CCCCEEEECCCCCCHHHHHHHHHHCCCEEEECCCCEEEEEEEECCC-EEEEE--ECCC T ss_conf ------8877664---------9952797069999989999987442674793679858999996399-99999--5475 Q ss_pred CEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCE Q ss_conf 02689813896589841987740864643899999998752799999999999999999809700612560124762861 Q gi|254780142|r 1179 EPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQK 1258 (1398) Q Consensus 1179 ~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~k 1258 (1398) T Consensus 228 nl~~~l----------~~~~v---D~~~~~tndi~dI~~i~GiEAar~~lv~Ei~~v~~~qGv~In~rHi~li~d~Mt~~ 294 (363) T cd06528 228 NLKAVL----------KVEGV---DPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYD 294 (363) T ss_pred CHHHHE----------ECCCC---CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 567723----------00661---35323358789999886088899999999988886078632057787765344046 Q ss_pred EEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEEC Q ss_conf 48941886454566410699999999999972898752012100001453023107765040258999999745285523 Q gi|254780142|r 1259 VEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDT 1338 (1398) Q Consensus 1259 g~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~ 1338 (1398) T Consensus 295 G~~~~------i~r~g--------------------------------~~~~~~S~ls~ASFqeT~~vLt~AAi~g~~D~ 336 (363) T cd06528 295 GEVRQ------IGRHG--------------------------------IAGEKPSVLARAAFEVTVKHLLDAAVRGEVDE 336 (363) T ss_pred CCEEE------CCHHH--------------------------------HCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 71420------45132--------------------------------23799889997210638999999985389676 Q ss_pred CCCCCEEEECCCCCCCCCCHHH Q ss_conf 6653221550730565535466 Q gi|254780142|r 1339 LDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1339 L~GvSENIIlGqliP~GTG~f~ 1360 (1398) T Consensus 337 L~GlkenVi~G~~ipaGTG~~~ 358 (363) T cd06528 337 LRGVIENIIVGQPIPLGTGDVE 358 (363) T ss_pred CCCCHHHEECCCCCCCCCCCEE T ss_conf 7880888335897568868779 |
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. |
| >cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=605.91 Aligned_cols=401 Identities=21% Similarity=0.228 Sum_probs=259.6 Q ss_pred CCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEE- Q ss_conf 1000355186578875420178520001014602111100788987764202454322211220240148768972113- Q gi|254780142|r 882 ALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN- 960 (1398) Q Consensus 882 ~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~- 960 (1398) T Consensus 2 ~~s~~~~~~~~~~~--~~ky~rslV~pGEaVGiIAAQSIGEPgTQlTLrTFH~gG~as~-------~vT~GipRl~Ei~~ 72 (410) T cd02584 2 RLNKEAFDWILGEI--ETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAK-------NVTLGVPRLKEIIN 72 (410) T ss_pred CCCHHHHHHHHHHH--HHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCHHHH-------CEECCCHHHHHHHH T ss_conf 77889999999999--9999983879875889998873473698898874604013101-------04457405676765 Q ss_pred EEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCC Q ss_conf 46517887789742760466406776000000110000135678553225078621354311320246368975312783 Q gi|254780142|r 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGI 1040 (1398) Q Consensus 961 ~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~ 1040 (1398) T Consensus 73 ~~k~~kt~~~~i~------l~~~~~~~~~~~~~~~~~i~~~~l~d~~~~~~i~~~~~~~~~~i~~~~~~i~~~~~~~~~~ 146 (410) T cd02584 73 VAKNIKTPSLTVY------LEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDED 146 (410) T ss_pred HCCCCCCCEEEEE------ECCCCCCCHHHHHHHHHEEEEEEHHHEEEEEEEEECCCCCCEEEEECCEEEEEEEEECCCC T ss_conf 4057777607999------7577542188887776500155444511245899627777427873140388768833410 Q ss_pred EEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHH Q ss_conf 20012302368602677510110122123853477427782532247884202137784454136761354842221013 Q gi|254780142|r 1041 SVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPI 1120 (1398) Q Consensus 1041 ~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~ 1120 (1398) T Consensus 147 ~---~~~~~~~~~~~~~~~~~~-----~~~~~i~~~~~~~~i-------~~~~~~~~~~~~~~~~~~~---~~~~~r~~~ 208 (410) T cd02584 147 V---EQDRLSPWLLRIELDRKK-----MTDKKLSMEQIAKKI-------KEEFKDDLNVIFSDDNAEK---LVIRIRIIN 208 (410) T ss_pred C---CCCCCCCEEEEEEECHHH-----HCCCCCCHHHHHHHH-------HHHCCCCCEEEECCCCCCE---EEEEEECCC T ss_conf 2---213335437999953355-----303787788889999-------8752898469841577653---699998047 Q ss_pred HHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEE-CCCCEEEEECCCEE Q ss_conf 20245543367732889887525111101113478678633127944999983689840268981-38965898419877 Q gi|254780142|r 1121 SSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFI-PKNKHFYLQDGDHV 1199 (1398) Q Consensus 1121 ~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~i-p~~~~l~v~dgd~V 1199 (1398) T Consensus 209 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~~~l~t~g~n--l~~il~~ 283 (410) T cd02584 209 -DDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIR-EENKKKVDIETGEFK-KREEWVLETDGVN--LREVLSH 283 (410) T ss_pred -CCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCEEEEEEE-ECCCEEEEECCCCCC-CCEEEEEECCCCC--HHHEECC T ss_conf -7655555676245535666336666469764665999989-717279980378767-6507998048832--6333243 Q ss_pred ECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHH Q ss_conf 40864643899999998752799999999999999999809700612560124762861489418864545664106999 Q gi|254780142|r 1200 EKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279 (1398) Q Consensus 1200 ~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~ 1279 (1398) T Consensus 284 ~~vd~~~~~sNdi~eil~~~GiEAar~~iv~Ei~~V~~~~Gv~In~rHi~lI~d~Mt~~G~~~----------------- 346 (410) T cd02584 284 PGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLM----------------- 346 (410) T ss_pred CCCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEE----------------- T ss_conf 575333002576314666414999999988888899984595516999999888872178265----------------- Q ss_pred HHHHHHHHHHCCCCCCCEEEEEECHHHHHH--CCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCC Q ss_conf 999999999728987520121000014530--231077650402589999997452855236653221550730565535 Q gi|254780142|r 1280 VEELNRSLAQQGKKLVSFSPILQGITKASL--QTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTG 1357 (1398) Q Consensus 1280 ~~~~Nr~~~~~g~~pa~~~p~llGITKasl--~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG 1357 (1398) T Consensus 347 -----------------------~itR~gi~k~s~S~isaASFqeTt~vLt~AAi~G~~D~L~GlkenVIvG~lipaGTG 403 (410) T cd02584 347 -----------------------AITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403 (410) T ss_pred -----------------------EECHHHCCCCCCCHHHHHHCHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCCCCCC T ss_conf -----------------------401764466986888872046289999999862896667780887445897578777 Q ss_pred HHH Q ss_conf 466 Q gi|254780142|r 1358 AIL 1360 (1398) Q Consensus 1358 ~f~ 1360 (1398) T Consensus 404 ~fd 406 (410) T cd02584 404 CFD 406 (410) T ss_pred CEE T ss_conf 378 |
RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. |
| >TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''; InterPro: IPR012757 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=568.27 Aligned_cols=339 Identities=27% Similarity=0.364 Sum_probs=224.6 Q ss_pred CCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEEECC-CCCEEEEECCCCEEE Q ss_conf 7852000101460211110078898776420245432221122024014876897211346517-887789742760466 Q gi|254780142|r 902 RGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVCRNS-TNDLISMGRNTTLQI 980 (1398) Q Consensus 902 ~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~~n~-~~~~i~vs~~~~~~i 980 (1398) T Consensus 38 ~~~li~P~EAvGiVAAQSiGEPGTQMTmRTFHYAGv~El-------nVTlGLPRLIEIVDArk~PSTP~MtI------YL 104 (397) T TIGR02389 38 LRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEL-------NVTLGLPRLIEIVDARKTPSTPLMTI------YL 104 (397) T ss_pred HHHHCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHH-------HHHCCCCCCEEEECCCCCCCCCEEEE------EE T ss_conf 764106688610388442188454787776657766788-------76447840145450666789863799------62 Q ss_pred EECCCC----EEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEE Q ss_conf 406776----0000001100001356785532250786213543113202463689753127832001230236860267 Q gi|254780142|r 981 LDMSGQ----EQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRK 1056 (1398) Q Consensus 981 ~d~~~~----~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~ 1056 (1398) T Consensus 105 ~~ey~~dyaydrE~a~~va~kie~t~l~~v~~~i~~----D~~~~~v~i~Ld---------------~~~~~~r~~t~d~ 165 (397) T TIGR02389 105 EDEYEKDYAYDREKAEEVAKKIEATKLEDVAKDISI----DLADMTVIIELD---------------EEKLKERGITVDD 165 (397) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHCEEEE----EEECEEEEEEEC---------------HHHHHHCCCCHHH T ss_conf 788632245667899999987520333252241248----875308999417---------------4886306986689 Q ss_pred EEEHHHCCCCCCCCCCEEEE----CCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCC Q ss_conf 75101101221238534774----27782532247884202137784454136761354842221013202455433677 Q gi|254780142|r 1057 VIDWRFASRSQNLKPAIVVT----DENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGL 1132 (1398) Q Consensus 1057 ~i~~~~~~~~~~~~~~~~i~----d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GL 1132 (1398) T Consensus 166 v~~a-----~~~~~~~~~~~~~~~~~~~-v-------------seGGvkkvivy------~~i~---~~~~------~~~ 211 (397) T TIGR02389 166 VLKA-----IKKAKLGKVIEEVSEDVDN-V-------------SEGGVKKVIVY------STIT---IKAP------PKE 211 (397) T ss_pred HHHH-----HHHHHCCEEEEEECCCCCC-C-------------CCCCEEEEEEE------EEEE---ECCC------CCC T ss_conf 9999-----9987464255664368676-5-------------34761489999------8897---1578------899 Q ss_pred CHHH--HHHHHHCCCCCCEECCCCCEEEEE--EECCCCE--EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEE Q ss_conf 3288--988752511110111347867863--3127944--999983689840268981389658984198774086464 Q gi|254780142|r 1133 PRVA--ELFEARRPKNHAILAEISGTIRIK--RNYKNKS--RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206 (1398) Q Consensus 1133 PrV~--eLFEar~pk~~aiisei~Giv~i~--~~~~~k~--~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt 1206 (1398) T Consensus 212 p~~~sneL~~l~~ki~~~~iKGikgIkrvvir~E~~k~dsyEy~i~--TeGSNL~~VL-------------~~eGVD~tR 276 (397) T TIGR02389 212 PSLKSNELRKLKEKIKNLKIKGIKGIKRVVIRREEEKGDSYEYVIY--TEGSNLKEVL-------------KLEGVDKTR 276 (397) T ss_pred CCCCHHHHHHHHHHHCCEEEEEEECCEEEEEEEECCCCCEEEEEEE--ECCCCHHHHC-------------CCCCCCCCC T ss_conf 8622267898887570415334504328999986688842799998--6063317650-------------889847742 Q ss_pred CCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCE-ECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 389999999875279999999999999999980970-0612560124762861489418864545664106999999999 Q gi|254780142|r 1207 DGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVA-INHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNR 1285 (1398) Q Consensus 1207 ~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~-IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr 1285 (1398) T Consensus 277 T~TNdI~EI~~VLGIEAAR~AII~E~~~tL~EQGL~dVDiRHlmLvAD~MT~~G~V~~------IGRHGi---------- 340 (397) T TIGR02389 277 TTTNDIHEIEEVLGIEAARNAIIEEIKRTLEEQGLDDVDIRHLMLVADLMTWDGEVRQ------IGRHGI---------- 340 (397) T ss_pred CEECCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEE------EEEEEC---------- T ss_conf 0015614455530668999999999999986428860248989888651078854841------012000---------- Q ss_pred HHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH Q ss_conf 99972898752012100001453023107765040258999999745285523665322155073056553546 Q gi|254780142|r 1286 SLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398) Q Consensus 1286 ~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398) T Consensus 341 ----------------------~GeK~SVLARAAFEvTvKhLl~Aa~rGe~d~L~GV~ENIIvG~Pi~lGTG~V 392 (397) T TIGR02389 341 ----------------------SGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVVENIIVGQPIRLGTGSV 392 (397) T ss_pred ----------------------CCCCCCHHHHCCCCCCHHHHHHHHHCCCHHHCCCEEEEEECCCCCCCCCCEE T ss_conf ----------------------3547853420012022346887520371214676799997077852154258 |
7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. |
| >cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=560.80 Aligned_cols=293 Identities=27% Similarity=0.380 Sum_probs=203.6 Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEE-EEECCCCCEEEEECCCCEE Q ss_conf 178520001014602111100788987764202454322211220240148768972113-4651788778974276046 Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN-VCRNSTNDLISMGRNTTLQ 979 (1398) Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~-~~~n~~~~~i~vs~~~~~~ 979 (1398) T Consensus 2 y~~slv~pGEaVGiIAAQSIGEPgTQlTLrTFH~aGvas~-------~vT~GvpRl~El~~a~k~~~tp~i~~~l~---- 70 (300) T cd02736 2 YMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASM-------NITLGVPRIKEIINASKNISTPIITAKLE---- 70 (300) T ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCCE-------EEECCCCEEEEEEECCCCCCCCEEEEEEE---- T ss_conf 5415279986378776773386488888885635220030-------35437651799886555677877999974---- Q ss_pred EEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEE Q ss_conf 64067760000001100001356785532250786213543113202463689753127832001230236860267751 Q gi|254780142|r 980 ILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVID 1059 (1398) Q Consensus 980 i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~ 1059 (1398) T Consensus 71 --~--~~~~~~~~~v~~~i~k~~l~~v~~~~~~~~~~~~~~~~i~~~~-------------------------------- 114 (300) T cd02736 71 --N--DRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDK-------------------------------- 114 (300) T ss_pred --C--CCCHHHHHEECCEEEEEEEECCCCEEEEEECCCCEEEEEEECH-------------------------------- T ss_conf --2--5325432201146889985201122799988983489998467-------------------------------- Q ss_pred HHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHH Q ss_conf 01101221238534774277825322478842021377844541367613548422210132024554336773288988 Q gi|254780142|r 1060 WRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELF 1139 (1398) Q Consensus 1060 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLF 1139 (1398) T Consensus 115 -~~i~~-~---------------------------------------------------------------~l~~~~~~~ 129 (300) T cd02736 115 -KIIEK-L---------------------------------------------------------------QLSKSNLYF 129 (300) T ss_pred -HHHHH-C---------------------------------------------------------------CCCHHHHHH T ss_conf -67753-3---------------------------------------------------------------787477888 Q ss_pred HHHCCCC---CCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHH Q ss_conf 7525111---1011134786786331279449999836898402689813896589841987740864643899999998 Q gi|254780142|r 1140 EARRPKN---HAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDIL 1216 (1398) Q Consensus 1140 Ear~pk~---~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl 1216 (1398) T Consensus 130 ~~~~~~~~l~~v~i~Gi~~i~~----------~~i~~-~~~~~~~~~~~~g~~l~~v~~~~~vd~~~~~---sn~i~~i~ 195 (300) T cd02736 130 LLQSLKRKLPDVVVSGIPEVKR----------AVINK-DKKKGKYKLLVEGYGLRAVMNTPGVIGTRTT---SNHIMEVE 195 (300) T ss_pred HHHHHHHHCCCEEEECCCCCCE----------EEEEE-CCCCCEEEEEECCCCCEEEECCCCEECCEEC---CCCHHHHH T ss_conf 8888884458559946678547----------99960-2788538999538771024313867323412---37888888 Q ss_pred HHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC Q ss_conf 75279999999999999999980970061256012476286148941886454566410699999999999972898752 Q gi|254780142|r 1217 RIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVS 1296 (1398) Q Consensus 1217 ~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~ 1296 (1398) T Consensus 196 ~~lGiEAar~~ii~Ei~~v~~~~Gv~in~rHi~li~d~Mt~~g~~----------------------------------- 240 (300) T cd02736 196 KVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEV----------------------------------- 240 (300) T ss_pred HHHHHHHHHEEEEECCCEEEECCCCEECHHHHHHHCCEEEECCEE----------------------------------- T ss_conf 774366532156411520330365100034476534430574789----------------------------------- Q ss_pred EEEEEECHHHHHHC--CCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH Q ss_conf 01210000145302--3107765040258999999745285523665322155073056553546 Q gi|254780142|r 1297 FSPILQGITKASLQ--TKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398) Q Consensus 1297 ~~p~llGITKasl~--t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398) T Consensus 241 -----~~itr~gl~~~~~S~ls~ASFeeT~~vLt~AAi~g~~D~L~GlkenVi~G~~ip~GTG~F 300 (300) T cd02736 241 -----LGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300) T ss_pred -----EEECHHHCCCCCCCHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHEECCCCCCCCCCCC T ss_conf -----610143176799998897031879999999997189776788288665289767886889 |
Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. |
| >cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=540.69 Aligned_cols=303 Identities=22% Similarity=0.313 Sum_probs=195.8 Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECCCCE Q ss_conf 17852000101460211110078898776420245432221122024014876897211--3465178877897427604 Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRNTTL 978 (1398) Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~~~~ 978 (1398) T Consensus 2 y~~slV~pGEaVGiIAAQSIGEPgTQlTLrTFH~aGv~~-------~~vT~GvpRl~EIl~~~sk~~ktp~~~v~l~--- 71 (309) T cd02735 2 YMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGE-------MNVTLGIPRLREILMTASKNIKTPSMTLPLK--- 71 (309) T ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-------EEEEECCCCEEEEEEECCCCCCCCEEEEEEE--- T ss_conf 200447997689999988638558888887663076045-------1145156631677752378887876999961--- Q ss_pred EEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEE Q ss_conf 66406776000000110000135678553225078621354311320246368975312783200123023686026775 Q gi|254780142|r 979 QILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVI 1058 (1398) Q Consensus 979 ~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i 1058 (1398) T Consensus 72 ---~~~--~~~~~~~~~~~~~~~~l~dv~~~i~i~~i~~~------------------------------~~~~------ 110 (309) T cd02735 72 ---NGK--SAERAETLKKRLSRVTLSDVVEKVEVTEILKT------------------------------IERV------ 110 (309) T ss_pred ---CCC--CHHHHHHHHHHCCCEEEEEECCCEEEEEEHHH------------------------------HHHH------ T ss_conf ---783--07899999862373999871472799995232------------------------------0001------ Q ss_pred EHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHH Q ss_conf 10110122123853477427782532247884202137784454136761354842221013202455433677328898 Q gi|254780142|r 1059 DWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAEL 1138 (1398) Q Consensus 1059 ~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eL 1138 (1398) T Consensus 111 ----------~~~~---~~---~~--------~~~~--------~-------------~~~----------~~~~~~~~~ 135 (309) T cd02735 111 ----------FKKL---LG---KW--------CEVT--------I-------------KLP----------LSSPKLLLL 135 (309) T ss_pred ----------EECC---CC---CE--------EEEE--------E-------------EEC----------CCCCHHHHH T ss_conf ----------0013---48---53--------8999--------9-------------816----------888402677 Q ss_pred HHHHCCCCCCEECCCCCEEEEEEECCCCE-EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHH Q ss_conf 87525111101113478678633127944-99998368984026898138965898419877408646438999999987 Q gi|254780142|r 1139 FEARRPKNHAILAEISGTIRIKRNYKNKS-RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILR 1217 (1398) Q Consensus 1139 FEar~pk~~aiisei~Giv~i~~~~~~k~-~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~ 1217 (1398) T Consensus 136 ~~~~~~~~~~~i~~i~gI~~~~~~~~~~~~~~~~~~~t~g~n~~~~~---------~~~~~id~~~~~---sndi~di~~ 203 (309) T cd02735 136 SIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALW---------KFSDILDVNRIY---TNDIHAMLN 203 (309) T ss_pred HHHHHHHHHCEEECCCCEEEEEEEECCCCCEEEEEECCCCCCHHHHC---------CCCCEECCCCCC---CCCHHHHHH T ss_conf 88876541038967899179999703798138999546872276610---------137767677555---688999998 Q ss_pred HHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCE Q ss_conf 52799999999999999999809700612560124762861489418864545664106999999999999728987520 Q gi|254780142|r 1218 IKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSF 1297 (1398) Q Consensus 1218 vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~ 1297 (1398) T Consensus 204 ~~GIEAar~~li~Ei~~V~~~~Gv~in~rHi~li~d~Mt~~G~~~~------~~R~g----------------------- 254 (309) T cd02735 204 TYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRP------FNRIG----------------------- 254 (309) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCEEE------CCHHC----------------------- T ss_conf 7579999999999999997435865674776657665000685731------01221----------------------- Q ss_pred EEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHH Q ss_conf 121000014530231077650402589999997452855236653221550730565535466 Q gi|254780142|r 1298 SPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1298 ~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~ 1360 (1398) T Consensus 255 ------i~~----~~s~L~~aSFeet~~vL~~AAi~g~~D~l~Gl~enVi~G~~ip~GTG~~~ 307 (309) T cd02735 255 ------MES----STSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFD 307 (309) T ss_pred ------CCC----CCCHHHHHHCHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCCCCCCCEE T ss_conf ------025----98898984267599999999863896777880776442898778776435 |
RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. |
| >pfam04997 RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=587.93 Aligned_cols=310 Identities=41% Similarity=0.581 Sum_probs=235.3 Q ss_pred CCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 64053689845886788501448971755425456875688733621368566772156641563448835675788530 Q gi|254780142|r 15 DRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVT 94 (1398) Q Consensus 15 ~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~ 94 (1398) T Consensus 1 ~k~i~~i~f~l~S~eeI~k~Sv~eVt~~~t~~~~~~~P~~gGL~D~rlG~~~~~---------------~~C~TCg~~~~ 65 (330) T pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGTIKKK---------------SICETCGVEVT 65 (330) T ss_pred CCCCCEEEEEECCHHHHHHHCEEEECCCCCEECCCCCCCCCCCCCCCCCCCCCC---------------CCCCCCCCCCC T ss_conf 974163899817899999744799837566638999747899865001799999---------------86889999877 Q ss_pred CCCCCCCCCCCCCCCCCCEEECHHHHHHH---HHHHHHCCCHHHHHHHHHHCCEEEECC-CCCCHHHHCCCCHHH-HHHH Q ss_conf 47757876772002776220130122578---999980999656301332111232178-865104322369999-9886 Q gi|254780142|r 95 LSSVRRDRMAHIDLASPVAHPWFLKSLPS---RISTLLGMSLRDVERVLYFESYVVVDP-GLSSLEKYQILTEEE-YVEA 169 (1398) Q Consensus 95 ~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~---~i~~~l~~~~~~~~~v~y~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~ 169 (1398) T Consensus 66 ~Cp---GHfGhIeL~~PV~h~~f~~~i~~iL~~iC~~C~~~ll~~~~~~~~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~ 141 (330) T pfam04997 66 ECP---GHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESVKYFF-LKVVIDPKGKNSKKRLKKINNLCKKKSI 141 (330) T ss_pred CCC---CCCEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 179---856268865312019899999999999875065503656678899-9988621678878999999999977654 Q ss_pred HHHCCC--------------CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 763585--------------550611552677888772674889999998731032203478864477888666634898 Q gi|254780142|r 170 VSQFGQ--------------DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNN 235 (1398) Q Consensus 170 ~~~~~~--------------~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ 235 (1398) T Consensus 142 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ilk~I~~~d~~llg~~~~~~~ 220 (330) T pfam04997 142 CSKCGEDNGGLKAFEGCGKYQPKISKDGAEAIKALLKNIEIEE-LKEKLRKLNPEKVLQIFKKISKEDEEILGFNPSGNR 220 (330) T ss_pred HHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHH-HHHHHHHCCHHHHHHHHHHCCHHHHHHHCCCCCCCC T ss_conf 0146601343110378666787045507999999986275166-678875358999999998556989998577677999 Q ss_pred CCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 51128630450762235138846973131003789999999869999998739835677769999999888874277678 Q gi|254780142|r 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK 315 (1398) Q Consensus 236 Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~ 315 (1398) T Consensus 221 Pe~mil~~lPVpPp~~RP~v~~~~~~~~edDlt~~~~~Ii~~N~~L~~~~~~~~~~~~i~~~~~~LQ~~V~~lidn~~~~ 300 (330) T pfam04997 221 PEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLEEGAPSHIIREEKRLLQEHVATLFDNDIPG 300 (330) T ss_pred CCEEEEEECCCCCCCCCCCEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 77688775358989999977719985206831799999999999999999749968899999999999999995499889 Q ss_pred CCC-CCCCCCHHHHHHHHHCCCCCCEEECC Q ss_conf 772-47876506789986102378200034 Q gi|254780142|r 316 RVV-TGANRRPLKSLSDMLKGKQGRFRTNL 344 (1398) Q Consensus 316 ~~~-~~~~~rp~ks~~~rlkgK~GrfR~nl 344 (1398) T Consensus 301 ~~~~~~~~~kp~k~i~qrLkgKeGrfR~NL 330 (330) T pfam04997 301 QPPALQKSGRPLKSISQRLKGKEGRFRGNL 330 (330) T ss_pred CCCCCCCCCCCCCCHHHHHCCCCCCCCCCC T ss_conf 986668897914329999678877578899 |
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand. |
| >cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=537.33 Aligned_cols=166 Identities=63% Similarity=0.929 Sum_probs=158.2 Q ss_pred CCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEE Q ss_conf 43367732889887525111101113478678633127944999983689840268981389658984198774086464 Q gi|254780142|r 1127 DITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206 (1398) Q Consensus 1127 DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt 1206 (1398) T Consensus 37 ~it~Glpri~ei~~ar~~-------------------------------------------------------------- 54 (204) T cd02655 37 DITQGLPRVEELFEARKI-------------------------------------------------------------- 54 (204) T ss_pred CCCCCCCCHHHHHHCCCC-------------------------------------------------------------- T ss_conf 233575208999864189-------------------------------------------------------------- Q ss_pred CCCCCHHHHHHH--HCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHH Q ss_conf 389999999875--279999999999999999980970061256012476286148941886454566410699999999 Q gi|254780142|r 1207 DGNPVPQDILRI--KGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELN 1284 (1398) Q Consensus 1207 ~Gsid~~eIl~v--lGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~N 1284 (1398) T Consensus 55 ----~~~~il~~~~~~~~~~~~~iv~eIq~vY~~qGV~I~dKHiEiIvrqm~~kV~I~~~Gdt~~l~Ge~v~~~~i~~~n 130 (204) T cd02655 55 ----NPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEEN 130 (204) T ss_pred ----CCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCEECCCEEEEEEEEECCEEEEEECCCCCCCCCCEEEHHHHHHHH T ss_conf ----9478777651069999999999999999986970245778988544023489975898635777635199999999 Q ss_pred HHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH Q ss_conf 99997289875201210000145302310776504025899999974528552366532215507305655354 Q gi|254780142|r 1285 RSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358 (1398) Q Consensus 1285 r~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~ 1358 (1398) T Consensus 131 ~~~~~~~~~~~~~~~~vLGITr~~l~~~S~Ls~ASFeeT~~~L~~AAi~g~~D~L~Gv~EnIIiG~~Ip~GTGl 204 (204) T cd02655 131 KRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204) T ss_pred HHHHHCCCCCCCCCHHHHHHHHHHHCCCCHHHHCCHHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCC T ss_conf 99997058885411143301045424788054311799999999998638975348823440207854688798 |
Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations. |
| >cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=485.27 Aligned_cols=351 Identities=16% Similarity=0.109 Sum_probs=200.0 Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEE-ECCCCCE--EEEECCCCEEEEECCC Q ss_conf 101460211110078898776420245432221122024014876897211346-5178877--8974276046640677 Q gi|254780142|r 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVC-RNSTNDL--ISMGRNTTLQILDMSG 985 (1398) Q Consensus 909 Ge~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~-~n~~~~~--i~vs~~~~~~i~d~~~ 985 (1398) T Consensus 1 GE~VG~IAAQSIGEPaTQMTLnTFH~agts-------------~vpRlkEIl~~~~~~~~~~~t~~~~l~~~~~~~~~~~ 67 (381) T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS-------------PLELLKEVLECRSKSKSKENDRRVILSLHLCKCDHGF 67 (381) T ss_pred CCCCHHHHHHHCCCHHHCCCCCCCCCCCCC-------------CCHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCHHH T ss_conf 972126676744727754112251336456-------------6277888863102678999873589840323320116 Q ss_pred CEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEEC--CCCEEHHHHHCCCCCEEEEEEEHHHC Q ss_conf 6000000110000135678553225078621354311320246368975312--78320012302368602677510110 Q gi|254780142|r 986 QEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLV--DGISVIESIGESTGIAKRKVIDWRFA 1063 (1398) Q Consensus 986 ~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~--~~~~~~~~~~~~t~~~~~~~i~~~~~ 1063 (1398) T Consensus 68 e~~~~A~~Vk~~IE~ttL~div~~~~I~y~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~d~~~~ 147 (381) T cd02737 68 EYERAALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKECQ 147 (381) T ss_pred HHHHHHHHHHHHHHHEEHHHHHEEEEEEECCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHEEEEECHHHH T ss_conf 78999999998764137984010899999488662244031889998875555566776653313673021356405451 Q ss_pred CCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHC Q ss_conf 12212385347742778253224788420213778445413676135484222101320245543367732889887525 Q gi|254780142|r 1064 SRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARR 1143 (1398) Q Consensus 1064 ~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~ 1143 (1398) T Consensus 148 ~--------------------~~~~~---------~-i~~~~~~~~---------------~~~------~~~~l~~l~~ 176 (381) T cd02737 148 K--------------------LSDGP---------C-LTFSVSKEV---------------SKS------SEELLDVLRD 176 (381) T ss_pred C--------------------CCCCC---------E-EEEEECCCC---------------CCH------HHHHHHHHHH T ss_conf 0--------------------24563---------5-999836555---------------700------8999999999 Q ss_pred ---CC-CCCEECCCCCEEEEEE--EC------------CCCEEEEEEECCCCCCEEEEEECCCCEEE-EECCC--EEECC Q ss_conf ---11-1101113478678633--12------------79449999836898402689813896589-84198--77408 Q gi|254780142|r 1144 ---PK-NHAILAEISGTIRIKR--NY------------KNKSRVVIEPFEDGVEPAEYFIPKNKHFY-LQDGD--HVEKG 1202 (1398) Q Consensus 1144 ---pk-~~aiisei~Giv~i~~--~~------------~~k~~~vi~~~~~g~~~~e~~ip~~~~l~-v~dgd--~V~~g 1202 (1398) T Consensus 177 ~i~~~ll~~~ikGi~~i~~v~i~~~~~~~~~~~~~~~~~~~~e~~l~v~~~~~~~----~~~~~~~~~v~~~cl~~ld~V 252 (381) T cd02737 177 RIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCK----KTRGNAWNVVMDACIPVMDLI 252 (381) T ss_pred HHHHHHHCCEECCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEECCCC----CCCCCHHHHHHHHCCCCCCCC T ss_conf 9875652033458766556999840576543112334577754999998403433----014303566654121223443 Q ss_pred CEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHH Q ss_conf 64643899999998752799999999999999999809700612560124762861489418864545664106999999 Q gi|254780142|r 1203 DYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEE 1282 (1398) Q Consensus 1203 d~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~ 1282 (1398) T Consensus 253 D~~RT~sn~i~ei~~~lGIEaar~~i~~e~~~~~~~~g~~v~~rHl~llad~mt~~G~~~~------i~r~G~~~~~--- 323 (381) T cd02737 253 DWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVG------LNAKGYKAQR--- 323 (381) T ss_pred CCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCEEE------EECCCCCCCC--- T ss_conf 5775230879999997709999999999999999852764218889898887335781677------5330201445--- Q ss_pred HHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH-HH Q ss_conf 9999997289875201210000145302310776504025899999974528552366532215507305655354-66 Q gi|254780142|r 1283 LNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA-IL 1360 (1398) Q Consensus 1283 ~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~-f~ 1360 (1398) T Consensus 324 ------------------------~sv~~~~pl~~asfe~t~~~l~~Aa~~~~~d~~~gvs~~i~~G~~~~~GTG~~Fd 378 (381) T cd02737 324 ------------------------RSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFE 378 (381) T ss_pred ------------------------CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCCEE T ss_conf ------------------------5554468888854465999999999847977778989987659988888887641 |
Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena. |
| >pfam00623 RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2 | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=449.16 Aligned_cols=143 Identities=50% Similarity=0.711 Sum_probs=121.5 Q ss_pred CCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHH--------HHHHHHCCCCCC-----CC---CCCCEEE----- Q ss_conf 51004577403412554354620034898776128999--------999998798666-----30---0010012----- Q gi|254780142|r 346 GKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFL--------YAQLEKKGYVST-----VK---QAKKFVE----- 404 (1398) Q Consensus 346 GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~--------~~~L~~~g~~~~-----i~---~~k~~i~----- 404 (1398) T Consensus 1 GKRvd~saRsVItpdP~L~i~evGiP~~iA~~Lt~pe~V~~~N~~~l~~~v~~g~~~~~~~~~~~~~~~~~~~l~~~~~~ 80 (165) T pfam00623 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPGAKYIKRIKGAKRDLEYKKRI 80 (165) T ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCHHHHHHCCCHHEEHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEECCCC T ss_conf 99877489754617998838874697999986281032379899999999972986566650677178858887505631 Q ss_pred -CCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHH Q ss_conf -2488250132666569789975763101114012358994495479731225454678775456997468999999999 Q gi|254780142|r 405 -KERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEAR 483 (1398) Q Consensus 405 -~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~ 483 (1398) T Consensus 81 ~~~l~~g~~v~R~l~dGD~Vl~NRqPTLHr~si~a~~v~i~~~~tirlnp~vc~~fNADFDGDeMnih~pqs~~a~~E~~ 160 (165) T pfam00623 81 AIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRVLEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEAR 160 (165) T ss_pred CHHHCCCHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEECCCEEEECCCCCCCCCCCCCCCEEEEECCCCHHHHHHHH T ss_conf 11212351156576479889992785225142036688996897058776546770588787247876689999999999 Q ss_pred HHHHH Q ss_conf 98767 Q gi|254780142|r 484 VLMLS 488 (1398) Q Consensus 484 ~Lm~~ 488 (1398) T Consensus 161 ~Lm~v 165 (165) T pfam00623 161 ELMLV 165 (165) T ss_pred HHHCC T ss_conf 87249 |
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion. |
| >cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=434.70 Aligned_cols=110 Identities=35% Similarity=0.547 Sum_probs=100.3 Q ss_pred CHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHC Q ss_conf 99999875279999999999999999980970061256012476286148941886454566410699999999999972 Q gi|254780142|r 1211 VPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQ 1290 (1398) Q Consensus 1211 d~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~ 1290 (1398) T Consensus 49 di~eil~vlGIEAaR~~Ii~Ei~~V~~~~Gi~Id~RHi~LIaD~MT~~G~i~~------i~R~Gi~~------------- 109 (158) T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRG------VTRSGFRA------------- 109 (158) T ss_pred CHHHHHHHCCHHHHHHHHHHHHHHHHHHCCEEECHHHHHHHHHHHHCCCCCCC------CCHHHHCC------------- T ss_conf 99999995199999999999999999965935439999999999854786666------72565104------------- Q ss_pred CCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH Q ss_conf 89875201210000145302310776504025899999974528552366532215507305655354 Q gi|254780142|r 1291 GKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358 (1398) Q Consensus 1291 g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~ 1358 (1398) T Consensus 110 -------------------~~~S~L~~ASFE~T~~~L~~AAi~g~~D~L~gvsenIiiG~~ip~GTGs 158 (158) T cd00630 110 -------------------SKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158) T ss_pred -------------------CCCCHHHHCCHHHHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCCCCC T ss_conf -------------------6757888716599999999999818978787819873058987899896 |
RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe |
| >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
Probab=99.68 E-value=8.9e-20 Score=166.75 Aligned_cols=121 Identities=25% Similarity=0.337 Sum_probs=96.8 Q ss_pred ECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCE-ECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHH Q ss_conf 4086464389999999875279999999999999999980970-061256012476286148941886454566410699 Q gi|254780142|r 1200 EKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVA-INHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRI 1278 (1398) Q Consensus 1200 ~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~-IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~ 1278 (1398) T Consensus 619 ~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~~G------~~gv--- 689 (808) T COG0086 619 EEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIG------QQGV--- 689 (808) T ss_pred HCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHH------HHEE--- T ss_conf 4587634577875687621779999999999876667752874023999864362448999999863------3203--- Q ss_pred HHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH Q ss_conf 99999999997289875201210000145302310776504025899999974528552366532215507305655354 Q gi|254780142|r 1279 EVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358 (1398) Q Consensus 1279 ~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~ 1358 (1398) T Consensus 690 -----------------------------~g~r~~~~~~~~Fe~~~~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~Gl 739 (808) T COG0086 690 -----------------------------MGEKISVLARAAFEVTVKH-LEAEGPGESSFLEGLTENEYFGHPIGGRTGL 739 (808) T ss_pred -----------------------------ECCCCCCCCCCCCCCCCCC-CEEEEEEECCCCCCCCCCEEEEECCCCCCCH T ss_conf -----------------------------1257886532222346655-3455456645577997226875057665316 Q ss_pred H Q ss_conf 6 Q gi|254780142|r 1359 I 1359 (1398) Q Consensus 1359 f 1359 (1398) T Consensus 740 v 740 (808) T COG0086 740 V 740 (808) T ss_pred H T ss_conf 8 |
|
| >pfam04983 RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3 | Back alignment and domain information |
|---|
Probab=99.93 E-value=1e-25 Score=211.53 Aligned_cols=133 Identities=37% Similarity=0.574 Sum_probs=114.9 Q ss_pred CCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEECC Q ss_conf 54237887820440258999999873367887446814179999999998889867852365204645667614245217 Q gi|254780142|r 491 NLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKIYDT 570 (1398) Q Consensus 491 niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~~~t 570 (1398) T Consensus 1 NiisP~~G~Pii~~~QD~ilG~y~LT~~~--------~f~~~~e~~~~~~~~~~~~~~~i~~~~~-~------------~ 59 (158) T pfam04983 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRD--------TFFDREEVMQLLMYGIVLPHPAILKPIK-P------------L 59 (158) T ss_pred CCCCCCCCCCEEEEHHHHHHHHHHHHCCC--------CCCCHHHHHHHHHHCCCCCCCCEEECCC-C------------C T ss_conf 93268998936764028989989972898--------6699999999998379877870576376-6------------7 Q ss_pred CCCCCCCCE-------------------------EEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHH Q ss_conf 977511220-------------------------5545875101775110020136669999999808178999875588 Q gi|254780142|r 571 TPGRMIIGE-------------------------ILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLM 625 (1398) Q Consensus 571 t~Gr~~~~~-------------------------ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~ 625 (1398) T Consensus 60 ~tgkq~~s~il~~~~~~~~~~~~~~~~~~~~~~~v~I~~G~l~~G~idk~~~~~~~~~Li~~i~~~~G~~~~~~~ld~i~ 139 (158) T pfam04983 60 WTGKQTFSRLLPNEINPKGKPKTNEETLCENDSYVLINNGELISGVIDKKLGGKSLGSLIHIIYKEYGPEETVKFLDRLQ 139 (158) T ss_pred CEEEEEHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCEEEEEEECCHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHH T ss_conf 23103131102266454757766764457777748985781787453311126528889999999829899999999999 Q ss_pred HHHHHHHHHCCCCCCCCCC Q ss_conf 9999999853986132123 Q gi|254780142|r 626 RLGFRYACSSGISFGKDDI 644 (1398) Q Consensus 626 ~l~~~~l~~~GfSigi~D~ 644 (1398) T Consensus 140 ~l~~~~l~~~GfSvgi~Dl 158 (158) T pfam04983 140 KLGFRYLTKSGFSIGIDDI 158 (158) T ss_pred HHHHHHHHHCCEEEEECCC T ss_conf 9999999977867952059 |
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking. |
| >pfam04998 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
Probab=98.98 E-value=2.6e-10 Score=95.50 Aligned_cols=120 Identities=29% Similarity=0.286 Sum_probs=110.6 Q ss_pred CEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCE Q ss_conf 02689813896589841987740864643899999998752799999999999999999809700612560124762861 Q gi|254780142|r 1179 EPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQK 1258 (1398) Q Consensus 1179 ~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~k 1258 (1398) T Consensus 307 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~t~G~nl~~v~~~~gvid~~k~~sn~I~em~~~ 386 (447) T pfam04998 307 LEEEELLLLNKILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYSNDIREMLKK 386 (447) T ss_pred CHHHHCCCCCCHHEECCCCEEEECCCCCCCCCCCHHHHCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCEEEEEHHHHHHH T ss_conf 11121252121020013868972232565777621320136837666440589999997289354781689829966522 Q ss_pred EEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 4894188645456641069999999999997289875201 Q gi|254780142|r 1259 VEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFS 1298 (1398) Q Consensus 1259 g~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~ 1298 (1398) T Consensus 387 lGIEAAr~~i~~E~~~V~~~~g~~vn~RHl~llaD~MT~~ 426 (447) T pfam04998 387 LGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFK 426 (447) T ss_pred EEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC T ss_conf 5999885121353899998877887699998589746235 |
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. |
| >pfam05000 RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4 | Back alignment and domain information |
|---|
Probab=98.83 E-value=4.7e-10 Score=93.59 Aligned_cols=89 Identities=31% Similarity=0.435 Sum_probs=57.1 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEEECCCCCC Q ss_conf 6678887886423465899999999998761----15654322224688376422555578---4241120010000246 Q gi|254780142|r 674 TRGEKYNKVVDLWGKTTDKVTEEMMARIKRV----EFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAK 746 (1398) Q Consensus 674 t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gk 746 (1398) T Consensus 2 ~~~~~~~~~~~~~~~s~~~~~E~~i~~~l~~~~~~~~~~~~~~~~~~N~~~~Mv~SGsKGs~~Ni~Qi~g~~GQQ~v~g~ 81 (108) T pfam05000 2 TDAERYGKLEDIWGMTLEEVFEALINNILNKARDPAGNIASKSLDLNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGK 81 (108) T ss_pred CCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHHHCCEEECCC T ss_conf 16544885347999988999999999999999999999999865866659999883377654529999986352147782 Q ss_pred CCCCCCCCCCCCHHHC Q ss_conf 4434445666301110 Q gi|254780142|r 747 PSGEIIESPIRSHFKG 762 (1398) Q Consensus 747 p~G~~~~~PV~~sF~~ 762 (1398) T Consensus 82 Ri~~~~~~Rtlp~f~~ 97 (108) T pfam05000 82 RIPFGFSGRTLPHFKK 97 (108) T ss_pred CCCCCCCCCCCCCCCC T ss_conf 1678989987999999 |
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors. |
| >PRK02995 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=96.99 E-value=0.00019 Score=51.36 Aligned_cols=31 Identities=10% Similarity=-0.030 Sum_probs=25.6 Q ss_pred EECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHH Q ss_conf 0061256012476286148941886454566410699 Q gi|254780142|r 1242 AINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRI 1278 (1398) Q Consensus 1242 ~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~ 1278 (1398) T Consensus 1166 ~~n~~~~~~~~~~~~~r~~llG------ITr~~l~t~ 1196 (1291) T PRK02995 1166 AENRRVVAEGGEPASGRPVLMG------ITKASLATE 1196 (1291) T ss_pred HHHHHHHHCCCCCCEEEEEEEE------EEECCCCCC T ss_conf 9999999839971134221466------400431122 |
|
| >PRK05258 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
Probab=96.26 E-value=4.7e-05 Score=55.96 Aligned_cols=30 Identities=10% Similarity=-0.015 Sum_probs=25.6 Q ss_pred EECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCH Q ss_conf 006125601247628614894188645456641069 Q gi|254780142|r 1242 AINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDR 1277 (1398) Q Consensus 1242 ~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr 1277 (1398) T Consensus 1102 ~~n~~~~~~g~~~a~~~~~llG------ITr~~l~t 1131 (1204) T PRK05258 1102 DANKKVLISGGIPATARPVLLG------ITKASLET 1131 (1204) T ss_pred HHHHHHHHCCCCCCEEEEEEEE------EECCCCCC T ss_conf 9999999759976445458877------63165233 |
|
| >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
Probab=95.95 E-value=0.096 Score=31.08 Aligned_cols=39 Identities=26% Similarity=0.340 Sum_probs=21.5 Q ss_pred CEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEE Q ss_conf 046640677600000011000013567855322507862 Q gi|254780142|r 977 TLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE 1015 (1398) Q Consensus 977 ~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~ 1015 (1398) T Consensus 1265 rI~i~D~~~~~~a~Y~~P~~Aii~V~dG~~v~~GDIlAk 1303 (1552) T TIGR02386 1265 RIAILDEKGELVATYAIPADAIISVEDGQKVKPGDILAK 1303 (1552) T ss_pred EEEEEECCCCCCEEEECCCCEEEEECCCCCCCCCCEEEE T ss_conf 489985689831355663010787215875474747886 |
7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. |
| >pfam05183 RdRP RNA dependent RNA polymerase | Back alignment and domain information |
|---|
Probab=90.52 E-value=0.3 Score=27.34 Aligned_cols=52 Identities=27% Similarity=0.379 Sum_probs=31.7 Q ss_pred HHCCCEEEECCCCCCEECCEEEEEEEEECC------------CEEEEECCCCCCCCCCCCCCEEEEE Q ss_conf 656978997576310111401235899449------------5479731225454678775456997 Q gi|254780142|r 417 VVHQHVVLLNRAPSLHRLSMQAFEPKIISG------------KAIQLHPLVCAGYNADFDGDQMAVY 471 (1398) Q Consensus 417 l~~gd~Vl~NRqPsLHr~Simah~~~v~~~------------~t~rln~~vc~pyNADFDGDEMnlH 471 (1398) T Consensus 228 ~~~g~-VlV~RnP~lhPGDiq~~~AV~~p~L~hl~dvIVFp~kG~rpl~~~lS--GgDlDGD~y~V~ 291 (381) T pfam05183 228 VIGGD-VLVTRNPCLHPGDIRVLKAVDVPELRHLKDVIVFPQKGDRPLPSELS--GGDLDGDLYFVI 291 (381) T ss_pred EEEEE-EEEEECCCCCCCCEEEEECCCCHHHHCCCCEEEECCCCCCCCHHHHC--CCCCCCCEEEEE T ss_conf 55003-99983676688854788626765564138789948989988557735--778788657997 |
This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates. |
Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch
Homologous Structures Detected by PSI-BLAST against Nonredundant Database
| Identity | Alignment graph | Length | Definition | E-value |
| Target | 1398 | DNA-directed RNA polymerase subunit beta' [Candidatus L | ||
| 3iyd_D | 1413 | Three-Dimensional Em Structure Of An Intact Activat | 0.0 | |
| 3lu0_D | 1407 | Molecular Model Of Escherichia Coli Core Rna Polyme | 0.0 | |
| 3h0g_A | 1752 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 0.0 | |
| 1i3q_A | 1733 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 0.0 | |
| 2gho_D | 1233 | Recombinant Thermus Aquaticus Rna Polymerase For St | 0.0 | |
| 1hqm_D | 1265 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 0.0 | |
| 1i6v_D | 1264 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 0.0 | |
| 2gho_D | 1233 | Recombinant Thermus Aquaticus Rna Polymerase For St | 4e-96 | |
| 1hqm_D | 1265 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 5e-96 | |
| 1i6v_D | 1264 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 3e-96 | |
| 1iw7_D | 1524 | Crystal Structure Of The Rna Polymerase Holoenzyme | 1e-94 | |
| 1l9u_D | 1524 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 7e-96 | |
| 1iw7_D | 1524 | Crystal Structure Of The Rna Polymerase Holoenzyme | 0.0 | |
| 1l9u_D | 1524 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 0.0 | |
| 1iw7_D | 1524 | Crystal Structure Of The Rna Polymerase Holoenzyme | 1e-80 | |
| 1l9u_D | 1524 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 2e-81 | |
| 2waq_A | 880 | The Complete Structure Of The Archaeal 13-Subunit D | 1e-150 | |
| 2pmz_A | 880 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 1e-148 | |
| 3qqc_A | 436 | Crystal Structure Of Archaeal Spt45 BOUND TO THE RN | 1e-71 | |
| 3qqc_A | 436 | Crystal Structure Of Archaeal Spt45 BOUND TO THE RN | 2e-06 | |
| 2waq_C | 395 | The Complete Structure Of The Archaeal 13-Subunit D | 8e-40 | |
| 2y0s_C | 395 | Crystal Structure Of Sulfolobus Shibatae Rna Polyme | 4e-39 | |
| 2pmz_C | 392 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 4e-38 | |
| 3hkz_C | 395 | The X-Ray Crystal Structure Of Rna Polymerase From | 5e-38 | |
| 2auk_A | 190 | Structure Of E. Coli Rna Polymerase Beta' GG' INSER | 3e-33 |
| >gi|266618718|pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator- Dependent Transcription Initiation Complex Length = 1413 | Back alignment and structure |
Score = 1727 bits (4473), Expect = 0.0, Method: Composition-based stats.
Identities = 743/1372 (54%), Positives = 982/1372 (71%), Gaps = 14/1372 (1%)
Query: 3 QEVMRFFNPWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARI 62
+++++F T FD+++I++ASP I S S+GE+KKPETINYRTFKPERDGLFCARI
Sbjct: 2 KDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARI 61
Query: 63 FGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLP 122
FGP+KDYEC+CGKYKR+K++G+ICEKCGVEVT + VRR+RM HI+LASP AH WFLKSLP
Sbjct: 62 FGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLP 121
Query: 123 SRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMM 182
SRI LL M LRD+ERVLYFESYVV++ G+++LE+ QILTEE+Y++A+ +FG D+F A M
Sbjct: 122 SRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFG-DEFDAKM 180
Query: 183 GADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIR 242
GA+AI LL ++DL+ LR++L++++S +RKK+ KR+K++++F+ SGN P WMI+
Sbjct: 181 GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT 240
Query: 243 KLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQ 302
LPVLPPDLRPLV LD GRFA SDLNDLYRRVI RNNRL RL L AP+II+RNEKRMLQ
Sbjct: 241 VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ 300
Query: 303 ESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPE 362
E+VDAL DNGR R +TG+N+RPLKSL+DM+KGKQGRFR NLLGKRVDYSGRSVI GP
Sbjct: 301 EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY 360
Query: 363 LQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHV 422
L+LHQCGLPK MALELFKPF+Y +LE +G +T+K AKK VE+E VWD+L EV+ +H
Sbjct: 361 LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP 420
Query: 423 VLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEA 482
VLLNRAP+LHRL +QAFEP +I GKAIQLHPLVCA YNADFDGDQMAV+ ++ EAQLEA
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA 480
Query: 483 RVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENK 542
R LM+STNN+L PA+G P+ VPSQD+VLGL Y++ GEGM+ E +
Sbjct: 481 RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG 540
Query: 543 IVTLHSKIRGRYKSVDKDGNS----ISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIK 598
+ +LH++++ R +KD N + + DTT GR I+ I+P+ + + I NQ + K
Sbjct: 541 LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKG--LPYSIVNQALGK 598
Query: 599 KNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEAD 658
K IS M++T YR G K TV F D +M GF YA SG S G DD+++PE K +II+EA+
Sbjct: 599 KAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAE 658
Query: 659 KMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRV---EFDPETGRQKK 715
V E + Q+ GL+T GE+YNKV+D+W D+V++ MM ++ D + +Q
Sbjct: 659 AEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVS 718
Query: 716 MNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVG 775
NSI+MM+ SGARGS Q+RQL GMRGL+AKP G IIE+PI ++F+ GL ++F S G
Sbjct: 719 FNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHG 778
Query: 776 GRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSR 835
RKGL D ++TA+SGYL+RRLVDVAQ+ VV + DC T +G+ +T +++ G V L R
Sbjct: 779 ARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDR 838
Query: 836 VLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLC 895
VLGR +D++ P T + +V L+ E + +E+ + +V++RS ++C++ GVC C
Sbjct: 839 VLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHC 898
Query: 896 YGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG-AVTVMDRSFIESPCDGIV 954
YGRDLARG ++N GEA+GVIAAQSIGEPGTQLTMRTFH+GG A S I+ G +
Sbjct: 899 YGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSI 958
Query: 955 KIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRIS 1014
K+ N NS+ L+ RNT L+++D G+ + S+++ YGA L DG + G+ ++
Sbjct: 959 KLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVA 1018
Query: 1015 EWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDW-RFASRSQNLKPAI 1073
WDPHT P+ITEVSG V F D++DG ++ E TG++ V+D + ++L+PA+
Sbjct: 1019 NWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPAL 1078
Query: 1074 VVTDENGV-VLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGL 1132
+ D G VL A++FLP A++ + G ++S+GD LAR+P S TKDIT GL
Sbjct: 1079 KIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGL 1138
Query: 1133 PRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFY 1192
PRVA+LFEARRPK AILAEISG + + K K R+VI P DG +P E IPK +
Sbjct: 1139 PRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPV-DGSDPYEEMIPKWRQLN 1197
Query: 1193 LQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVV 1252
+ +G+ VE+GD I DG P DILR++GV A+ Y++NEVQ+VYRL+GV IN KHIEV+V
Sbjct: 1198 VFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIV 1257
Query: 1253 RHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTK 1312
R ML+K I + ++++ G+ V+ V+ NR L GK ++S L GITKASL T+
Sbjct: 1258 RQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATE 1317
Query: 1313 SFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKR 1364
SFISAASFQETT+VLTEAA+AGK D L G KENVIVGR IPAGTG H+ R
Sbjct: 1318 SFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDR 1369
|