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DNA-directed RNA polymerase [Saccharomyces cerevisiae S288C]
Protein Classification
similar to DNA-directed RNA polymerase ( domain architecture ID 11473812 )
protein similar to DNA-directed RNA polymerase
List of domain hits
Name
Accession
Description
Interval
E-value
RNA_pol
pfam00940 DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
855-1351
0e+00
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
Pssm-ID: 460006
Cd Length: 411
Bit Score: 743.56
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 855 K K LG PS GL K WLKIHL S NL F GFDK LP L KD RVAF T E SH L Q DI K DSAENPL T G D RWW TT A DK PWQ A LA T CFEL NEVMKMDN PE 934
Cdd:pfam00940 1 K P LG ER GL R WLKIHL A NL Y GFDK AS L DE RVAF V E DN L E DI L DSAENPL D G R RWW LK A ED PWQ C LA A CFEL ANALRSPD PE 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 935 E FI SH Q PVHQDG T CNGLQHYAALGGD V EGA T QVNLVPSD K PQDVY AH VA R LV QKRL E IA A E KG D E N AK I LK D KITRKVVK 1014
Cdd:pfam00940 81 E YV SH L PVHQDG S CNGLQHYAALGGD E EGA K QVNLVPSD R PQDVY SG VA E LV EEKI E KD A A KG N E I AK L LK G KITRKVVK 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1015 QTVMTNVYGVT YV GA TF QI A KQL SP I F D D -- RKESLDF S K YL T K HV F SA I R ELF HS AH L IQDWLGE S AKRI S KS IRLDV d 1092
Cdd:pfam00940 161 QTVMTNVYGVT FI GA RE QI E KQL KE I G D F pg EEDLYKA S S YL A K KI F DS I G ELF TG AH E IQDWLGE C AKRI A KS VPPEQ - 239
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1093 eksfkngnkpd F MS S VIWTTPLGLP I VQPYR EES KKQV E TNLQ T V F ISDP FAVN PV NA R R Q KAGL PPNFIHSLDA S HM L L 1172
Cdd:pfam00940 240 ----------- S MS P VIWTTPLGLP V VQPYR KSK KKQV K TNLQ S V S ISDP NDTD PV DK R K Q LQAF PPNFIHSLDA T HM M L 308
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1173 S A AE C GKQ GL D FA S VHDS Y WTHA S D I D T MN VV LREQF I KLH EV D LVL RL K EEF DQ RYK NYVKIG K LKRSTD L AQ kiirir 1252
Cdd:pfam00940 309 T A LA C DEA GL T FA A VHDS F WTHA C D V D E MN KI LREQF V KLH SE D ILE RL R EEF KE RYK GSLQLA K IPKDSP L TP ------ 382
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1253 kdlsrklgrsttladeiyfekkrqellnspliedrnvgekmvttvslfeditdldalelenggdensgms V L LPL RL PE I 1332
Cdd:pfam00940 383 ---------------------------------------------------------------------- V W LPL TF PE V 392
490
....*....|....*....
gi 14318482 1333 P P KGDFD VTVLRN S Q YFFS 1351
Cdd:pfam00940 393 P K KGDFD LNRVLD S K YFFS 411
PHA00452 super family
cl42978 T3/T7-like RNA polymerase
415-1228
1.63e-157
T3/T7-like RNA polymerase
PHA00452 :Pssm-ID: 222797 [Multi-domain]
Cd Length: 807
Bit Score: 494.16
E-value: 1.63e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 415 R Q KV LE NR A TEAAR ER WKHDF E EAKAR G DIS ie K N LNVK lw KWYNEM LP L V K E E I N hcrsllsekls DK K GLN K VDTNRL 494
Cdd:PHA00452 8 E Q LQ LE EE A YGEGE ER FRKAL E RQLEA G EAD -- D N PVAR -- RLLATL LP P V A E A I D ----------- AW K EEY K KRGRAA 72
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 495 GYGPY L T L I DP GKMC VIT ILEL L - K L N S tggvi EGMR TA R AV IS - V G K AIE M E F R SEQ vlksesqa FR D V N K K S pe FKK L 572
Cdd:PHA00452 73 KARGL L R L V DP EVLA VIT LKVT L d M L L S ----- KETP TA Q AV AT a I G R AIE D E I R FGR -------- IE D L N P K Y -- FKK V 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 573 V QNA K -------------- S V FRSSQIEQSKIL WP QSIRARI G SV L ISM LI Q vakv S VQG V DP V T kakvhgeapa FAH G Y 638
Cdd:PHA00452 138 V EYL K rsrtgsvyhiafmm V V EADMVLLGEWDP WP KEDYIHV G KW L LEA LI E ---- S TGL V EL V R ---------- HTG G N 203
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 639 QYHNGSK L GVL - KIHKT L IRQL nge RLI A SVQ P QLL PM L V E PKPW VNWRS GGYH YTQS --- TL L RT K DSP eqv A YLKA as 714
Cdd:PHA00452 204 GGKDHEY L ELS e EAVEL L QDIA --- AAA A GIS P MYQ PM V V P PKPW TSIVG GGYH TEGR rpl AP L VR K TKK --- A LRRY -- 275
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 715 DNGDIDR VY DGL N V L GR T P W TV N RK V FD VV SQ V W N K G E -- GF L D IP GAQ demvl P P AP P KNS D -- PSILR AWK LQVKTIA 790
Cdd:PHA00452 276 RQKQMPE VY KAV N A L QN T A W RI N KD V LA VV NE V V N W G P vg DV L G IP RRP ----- L P PK P EFL D en EEAFK AWK RAAAAWY 350
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 791 N K FSSDR S N R CDTNYK L EI A RA F LGE K - L YFP H N L D F RGR A Y P l SPHF N HL G N D MSRG LL I F WH GK K LG PS GL K WLK I H L 869
Cdd:PHA00452 351 T K EKERV S K R RRLEFM L RV A NK F ADY K a I YFP Y N M D W RGR V Y A - VSML N PQ G S D LQKA LL R F AE GK P LG KR GL Y WLK V H G 429
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 870 S N LF G F DK LPLKD R V A FTESHLQD I KDS AE N PL TGD r WW TT AD K P WQA LA T CFE LNEVM km DNPEEFI S HQ PV HQ DGTC N 949
Cdd:PHA00452 430 A N CY G V DK VTFDE R A A WVDENHDN I LAA AE D PL NNT - WW AE AD S P LCF LA A CFE YAAAV -- HSGTSYV S GL PV AM DGTC S 506
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 950 GLQH YA A LGG D VE G ATQ VNL V PSDKPQD V Y AH VA RL V QKR LE IA A EK G DE N AKI L KDK ----- ITR KVV K QT VMT NV YG V 1024
Cdd:PHA00452 507 GLQH FS A MLR D EV G GRA VNL L PSDKPQD I Y GI VA EV V NEK LE RD A IN G TD N TRA L ARL wlayg ITR SLT K RP VMT LP YG S 586
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1025 T YVGATFQ I AKQ L - S P IF D DRKESLDFSK --- Y LT K HVFS AI R E LFHS A HLIQD WL GES AK RISKS irldvdeksfkn G N 1100
Cdd:PHA00452 587 T RFSCRDY I LED L l Q P GI D EGDGAMFTNQ aas Y MA K LIWD AI S E TVPA A VEAMN WL QQA AK LLAAK ------------ G A 654
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1101 KP dfmss VI WTTP L G L P IV Q P YR EESK K Q V ETN L QT V F - ISDPFAVNPVN AR RQKA G LP PNF I HSLDASH ML L SAAE C - G 1178
Cdd:PHA00452 655 EA ----- LH WTTP T G F P VW Q E YR KPEE K R V RLR L MG V A r VQLYVNTDTID AR KHAS G IA PNF V HSLDASH LR L TVVA C a E 729
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|.
gi 14318482 1179 K QGLD FA SV HDS YW THA S D I D TMNVVL RE Q F IKLH E - V D LVLRLKEE F DQR 1228
Cdd:PHA00452 730 K GIES FA VI HDS FG THA A D A D NLHRAI RE T F VEMY E e N D VLADFADQ F GDQ 780
Name
Accession
Description
Interval
E-value
RNA_pol
pfam00940 DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
855-1351
0e+00
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
Pssm-ID: 460006
Cd Length: 411
Bit Score: 743.56
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 855 K K LG PS GL K WLKIHL S NL F GFDK LP L KD RVAF T E SH L Q DI K DSAENPL T G D RWW TT A DK PWQ A LA T CFEL NEVMKMDN PE 934
Cdd:pfam00940 1 K P LG ER GL R WLKIHL A NL Y GFDK AS L DE RVAF V E DN L E DI L DSAENPL D G R RWW LK A ED PWQ C LA A CFEL ANALRSPD PE 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 935 E FI SH Q PVHQDG T CNGLQHYAALGGD V EGA T QVNLVPSD K PQDVY AH VA R LV QKRL E IA A E KG D E N AK I LK D KITRKVVK 1014
Cdd:pfam00940 81 E YV SH L PVHQDG S CNGLQHYAALGGD E EGA K QVNLVPSD R PQDVY SG VA E LV EEKI E KD A A KG N E I AK L LK G KITRKVVK 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1015 QTVMTNVYGVT YV GA TF QI A KQL SP I F D D -- RKESLDF S K YL T K HV F SA I R ELF HS AH L IQDWLGE S AKRI S KS IRLDV d 1092
Cdd:pfam00940 161 QTVMTNVYGVT FI GA RE QI E KQL KE I G D F pg EEDLYKA S S YL A K KI F DS I G ELF TG AH E IQDWLGE C AKRI A KS VPPEQ - 239
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1093 eksfkngnkpd F MS S VIWTTPLGLP I VQPYR EES KKQV E TNLQ T V F ISDP FAVN PV NA R R Q KAGL PPNFIHSLDA S HM L L 1172
Cdd:pfam00940 240 ----------- S MS P VIWTTPLGLP V VQPYR KSK KKQV K TNLQ S V S ISDP NDTD PV DK R K Q LQAF PPNFIHSLDA T HM M L 308
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1173 S A AE C GKQ GL D FA S VHDS Y WTHA S D I D T MN VV LREQF I KLH EV D LVL RL K EEF DQ RYK NYVKIG K LKRSTD L AQ kiirir 1252
Cdd:pfam00940 309 T A LA C DEA GL T FA A VHDS F WTHA C D V D E MN KI LREQF V KLH SE D ILE RL R EEF KE RYK GSLQLA K IPKDSP L TP ------ 382
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1253 kdlsrklgrsttladeiyfekkrqellnspliedrnvgekmvttvslfeditdldalelenggdensgms V L LPL RL PE I 1332
Cdd:pfam00940 383 ---------------------------------------------------------------------- V W LPL TF PE V 392
490
....*....|....*....
gi 14318482 1333 P P KGDFD VTVLRN S Q YFFS 1351
Cdd:pfam00940 393 P K KGDFD LNRVLD S K YFFS 411
PHA00452
PHA00452 T3/T7-like RNA polymerase
415-1228
1.63e-157
T3/T7-like RNA polymerase
Pssm-ID: 222797 [Multi-domain]
Cd Length: 807
Bit Score: 494.16
E-value: 1.63e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 415 R Q KV LE NR A TEAAR ER WKHDF E EAKAR G DIS ie K N LNVK lw KWYNEM LP L V K E E I N hcrsllsekls DK K GLN K VDTNRL 494
Cdd:PHA00452 8 E Q LQ LE EE A YGEGE ER FRKAL E RQLEA G EAD -- D N PVAR -- RLLATL LP P V A E A I D ----------- AW K EEY K KRGRAA 72
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 495 GYGPY L T L I DP GKMC VIT ILEL L - K L N S tggvi EGMR TA R AV IS - V G K AIE M E F R SEQ vlksesqa FR D V N K K S pe FKK L 572
Cdd:PHA00452 73 KARGL L R L V DP EVLA VIT LKVT L d M L L S ----- KETP TA Q AV AT a I G R AIE D E I R FGR -------- IE D L N P K Y -- FKK V 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 573 V QNA K -------------- S V FRSSQIEQSKIL WP QSIRARI G SV L ISM LI Q vakv S VQG V DP V T kakvhgeapa FAH G Y 638
Cdd:PHA00452 138 V EYL K rsrtgsvyhiafmm V V EADMVLLGEWDP WP KEDYIHV G KW L LEA LI E ---- S TGL V EL V R ---------- HTG G N 203
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 639 QYHNGSK L GVL - KIHKT L IRQL nge RLI A SVQ P QLL PM L V E PKPW VNWRS GGYH YTQS --- TL L RT K DSP eqv A YLKA as 714
Cdd:PHA00452 204 GGKDHEY L ELS e EAVEL L QDIA --- AAA A GIS P MYQ PM V V P PKPW TSIVG GGYH TEGR rpl AP L VR K TKK --- A LRRY -- 275
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 715 DNGDIDR VY DGL N V L GR T P W TV N RK V FD VV SQ V W N K G E -- GF L D IP GAQ demvl P P AP P KNS D -- PSILR AWK LQVKTIA 790
Cdd:PHA00452 276 RQKQMPE VY KAV N A L QN T A W RI N KD V LA VV NE V V N W G P vg DV L G IP RRP ----- L P PK P EFL D en EEAFK AWK RAAAAWY 350
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 791 N K FSSDR S N R CDTNYK L EI A RA F LGE K - L YFP H N L D F RGR A Y P l SPHF N HL G N D MSRG LL I F WH GK K LG PS GL K WLK I H L 869
Cdd:PHA00452 351 T K EKERV S K R RRLEFM L RV A NK F ADY K a I YFP Y N M D W RGR V Y A - VSML N PQ G S D LQKA LL R F AE GK P LG KR GL Y WLK V H G 429
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 870 S N LF G F DK LPLKD R V A FTESHLQD I KDS AE N PL TGD r WW TT AD K P WQA LA T CFE LNEVM km DNPEEFI S HQ PV HQ DGTC N 949
Cdd:PHA00452 430 A N CY G V DK VTFDE R A A WVDENHDN I LAA AE D PL NNT - WW AE AD S P LCF LA A CFE YAAAV -- HSGTSYV S GL PV AM DGTC S 506
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 950 GLQH YA A LGG D VE G ATQ VNL V PSDKPQD V Y AH VA RL V QKR LE IA A EK G DE N AKI L KDK ----- ITR KVV K QT VMT NV YG V 1024
Cdd:PHA00452 507 GLQH FS A MLR D EV G GRA VNL L PSDKPQD I Y GI VA EV V NEK LE RD A IN G TD N TRA L ARL wlayg ITR SLT K RP VMT LP YG S 586
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1025 T YVGATFQ I AKQ L - S P IF D DRKESLDFSK --- Y LT K HVFS AI R E LFHS A HLIQD WL GES AK RISKS irldvdeksfkn G N 1100
Cdd:PHA00452 587 T RFSCRDY I LED L l Q P GI D EGDGAMFTNQ aas Y MA K LIWD AI S E TVPA A VEAMN WL QQA AK LLAAK ------------ G A 654
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1101 KP dfmss VI WTTP L G L P IV Q P YR EESK K Q V ETN L QT V F - ISDPFAVNPVN AR RQKA G LP PNF I HSLDASH ML L SAAE C - G 1178
Cdd:PHA00452 655 EA ----- LH WTTP T G F P VW Q E YR KPEE K R V RLR L MG V A r VQLYVNTDTID AR KHAS G IA PNF V HSLDASH LR L TVVA C a E 729
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|.
gi 14318482 1179 K QGLD FA SV HDS YW THA S D I D TMNVVL RE Q F IKLH E - V D LVLRLKEE F DQR 1228
Cdd:PHA00452 730 K GIES FA VI HDS FG THA A D A D NLHRAI RE T F VEMY E e N D VLADFADQ F GDQ 780
RPOL_N
pfam14700 DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
415-731
1.52e-130
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex.
Pssm-ID: 464270
Cd Length: 286
Bit Score: 403.15
E-value: 1.52e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 415 RQ KV LE NRAT EAA R ERW KHD FEE AKA RG D - ISIE K N LN VK LW K WY NEM LP LV KEEI NHCRSLLSEKLSD K kglnkv D TN R 493
Cdd:pfam14700 1 RQ LR LE RDSV EAA V ERW REE FEE LQK RG L n TNLP K S LN AL LW Q WY EAL LP AI KEEI ELLKAAEAKPKKT K ------ D KE R 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 494 LG YGPYL T L ID P G K MCV ITILELL K L N STGGV IE GM RTA R AV IS V GKA I E M E F R SE Q V LK S E SQ afrdvnkkspefkklv 573
Cdd:pfam14700 75 CE YGPYL R L LP P E K LAA ITILELL S L L STGGV DK GM KVS R LA IS I GKA V E D E Y R AQ Q L LK K E KK ---------------- 138
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 574 qnaksvfrss Q I EQS KI L WPQ SI RA RI G S VL I S M LI QV AKV S V QGV DP V T KA KV HGEA PAF A H G YQY HN G S K L GV L K I H K 653
Cdd:pfam14700 139 ---------- K I KKK KI P WPQ EV RA KV G A VL L S L LI ET AKV P V TAE DP E T GE KV IQPQ PAF Y H S YQY KR G K K V GV I K P H P 208
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 14318482 654 T L IRQ L NG E RLIASVQ P QL LPMLV E PKPW VNWRS GGY HYTQ S T L L RTKD SP EQ V AYLKAAS DN GD I D R V Y DGL N VLG R 731
Cdd:pfam14700 209 E L VKL L LR E PARDTLT P RH LPMLV P PKPW TSYNK GGY LLSP S K L M RTKD GD EQ R AYLKAAS ER GD L D Q V F DGL D VLG N 286
RPO41
COG5108 Mitochondrial DNA-directed RNA polymerase [Transcription];
414-1225
1.48e-126
Mitochondrial DNA-directed RNA polymerase [Transcription];
Pssm-ID: 444054 [Multi-domain]
Cd Length: 826
Bit Score: 412.00
E-value: 1.48e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 414 D RQ KV LE NRAT EA A R E R WKHDF E E A KA RG DI S IEKNLNVKL wkwy NEMLP L VK E E I nhcrsllse KLSDKKGLNKVDT N R 493
Cdd:COG5108 12 A RQ IA LE EEMA EA G R S R FVERI E K A RK RG EE S GTQYGRRII ---- SDAVE L LA E A I --------- EATIDESSSGGAG N W 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 494 LGYGP YL TLI D PGKMCVITILEL L KLNSTGGVIE gmrta RAV I SVGKAI E M E F R S E QVLKSESQAFRDVN KK SPEFKKLV 573
Cdd:COG5108 79 HTAYA YL REL D AEVLAYLALRQC L DAVTQRHTLQ ----- AVA I RIASMV E D E V R G E AIREAFKDFYPRGK KK IESRTSRA 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 574 QNA K SV F RSSQIEQSKIL -- WP Q S IRARI G SV LI SMLIQ vakv S VQG V DPVTKAKVHGEA P A F ahgyqyhngsklgv LKI 651
Cdd:COG5108 154 VRY K DD F ERRVKNAVAKE ed WP V S DKIHV G FK LI ELVVE ---- S TGL V EIARDTEGINDT P V F -------------- VRP 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 652 HK T LIRQLNGER L IAS - VQ P QL LPM L V E P KP W VNWRS GGY HYTQSTL L RTKDSPEQ v A YL KAA s D NGD IDR VY DGL N V L G 730
Cdd:COG5108 216 TE T TLEWIAEAN L RMA m LS P AY LPM V V P P RN W TTPFR GGY LSGEVRR L PLVKTRNR - K YL EEL - K NGD MPE VY AAV N A L Q 293
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 731 R TPWT V NR K V FD V VSQV W NKGEG f L DI P GA q DEMVL P PA P PKNS D PSILRAWKLQV K TI A N K FSSDRSNR C DTNYK ---- 806
Cdd:COG5108 294 Q TPWT I NR Y V LA V MKWL W ERDLD - L GL P QR - EPITP P IK P ENRE D ITTNQVARKRW K KA A R K IYIANAKL C SKRVQ frrd 371
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 807 L EI A RA F - LGEKL YFP HN LDFRGR A Y PLSPHF N HL G N D MSR GLL I F WH GK KL G PS G L KWL K IH LS N LF G F DK LP L KD RV A 885
Cdd:COG5108 372 L NE A ER F s DYREF YFP YQ LDFRGR V Y AVPAFL N PQ G Q D HAK GLL M F AD GK PI G DG G A KWL A IH GA N VW G Y DK AS L EE RV K 451
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 886 FT E SHLQD I KDS A EN pl TGDRW W TT ADKPWQ A LA T C F E LNEVMK md NP E EFI S HQ P VHQ DG T C N GLQHY A A LGG D VE G AT 965
Cdd:COG5108 452 WV E DNYEA I LAA A AD -- YVAEF W SK ADKPWQ F LA F C R E WYGYDQ -- HG E GYV S GL P IAM DG S C S GLQHY S A MLR D EV G GA 527
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 966 Q VNLVPSDKPQD V YA H VA RLVQKRL ------------ EI AAEKG D ENAKI L KDK ITRKV V K QT VMT NV YG V T YV G ATF Q I 1033
Cdd:COG5108 528 A VNLVPSDKPQD I YA F VA EVDINLA qrigcpdelttn EI LNGIM D MAHNW L AFG ITRKV T K RN VMT LP YG S T EY G FRD Q V 607
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1034 akq LSPIFDDR KE SLD --------- FS K -- Y L T K HVFS AI R E LFHS A HLIQ DWL GES A KRIS K S irldvdeksfkng NK P 1102
Cdd:COG5108 608 --- REDMITRK KE EEG epfpfggdg FS A am W L A K LIWD AI G E VVVA A RRGM DWL QDL A GIAA K E ------------- GL P 671
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1103 dfmss VIWTTPLG L P IV Q P YR EESKKQVE T NLQT V FI -- SDPFAVNPVNA R R QK A G LP PNF I HS L DA S H MLLSAAECGKQ 1180
Cdd:COG5108 672 ----- VIWTTPLG F P VM Q D YR SSKARRIN T TTRK V RV rl TLREEQDTIDK R K QK Q G IA PNF V HS M DA T H LMMTVNRSNEY 746
810 820 830 840
....*....|....*....|....*....|....*....|....*..
gi 14318482 1181 G L - D FA S VHDS YW T H A SDIDT M NVV LR EQ FI K L H - E V D LVLRL K E E F 1225
Cdd:COG5108 747 G A s S FA L VHDS FG T D A GSAEL M LDC LR KA FI E L Y e E S D VLEDF K S E I 793
Name
Accession
Description
Interval
E-value
RNA_pol
pfam00940 DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
855-1351
0e+00
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
Pssm-ID: 460006
Cd Length: 411
Bit Score: 743.56
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 855 K K LG PS GL K WLKIHL S NL F GFDK LP L KD RVAF T E SH L Q DI K DSAENPL T G D RWW TT A DK PWQ A LA T CFEL NEVMKMDN PE 934
Cdd:pfam00940 1 K P LG ER GL R WLKIHL A NL Y GFDK AS L DE RVAF V E DN L E DI L DSAENPL D G R RWW LK A ED PWQ C LA A CFEL ANALRSPD PE 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 935 E FI SH Q PVHQDG T CNGLQHYAALGGD V EGA T QVNLVPSD K PQDVY AH VA R LV QKRL E IA A E KG D E N AK I LK D KITRKVVK 1014
Cdd:pfam00940 81 E YV SH L PVHQDG S CNGLQHYAALGGD E EGA K QVNLVPSD R PQDVY SG VA E LV EEKI E KD A A KG N E I AK L LK G KITRKVVK 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1015 QTVMTNVYGVT YV GA TF QI A KQL SP I F D D -- RKESLDF S K YL T K HV F SA I R ELF HS AH L IQDWLGE S AKRI S KS IRLDV d 1092
Cdd:pfam00940 161 QTVMTNVYGVT FI GA RE QI E KQL KE I G D F pg EEDLYKA S S YL A K KI F DS I G ELF TG AH E IQDWLGE C AKRI A KS VPPEQ - 239
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1093 eksfkngnkpd F MS S VIWTTPLGLP I VQPYR EES KKQV E TNLQ T V F ISDP FAVN PV NA R R Q KAGL PPNFIHSLDA S HM L L 1172
Cdd:pfam00940 240 ----------- S MS P VIWTTPLGLP V VQPYR KSK KKQV K TNLQ S V S ISDP NDTD PV DK R K Q LQAF PPNFIHSLDA T HM M L 308
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1173 S A AE C GKQ GL D FA S VHDS Y WTHA S D I D T MN VV LREQF I KLH EV D LVL RL K EEF DQ RYK NYVKIG K LKRSTD L AQ kiirir 1252
Cdd:pfam00940 309 T A LA C DEA GL T FA A VHDS F WTHA C D V D E MN KI LREQF V KLH SE D ILE RL R EEF KE RYK GSLQLA K IPKDSP L TP ------ 382
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1253 kdlsrklgrsttladeiyfekkrqellnspliedrnvgekmvttvslfeditdldalelenggdensgms V L LPL RL PE I 1332
Cdd:pfam00940 383 ---------------------------------------------------------------------- V W LPL TF PE V 392
490
....*....|....*....
gi 14318482 1333 P P KGDFD VTVLRN S Q YFFS 1351
Cdd:pfam00940 393 P K KGDFD LNRVLD S K YFFS 411
PHA00452
PHA00452 T3/T7-like RNA polymerase
415-1228
1.63e-157
T3/T7-like RNA polymerase
Pssm-ID: 222797 [Multi-domain]
Cd Length: 807
Bit Score: 494.16
E-value: 1.63e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 415 R Q KV LE NR A TEAAR ER WKHDF E EAKAR G DIS ie K N LNVK lw KWYNEM LP L V K E E I N hcrsllsekls DK K GLN K VDTNRL 494
Cdd:PHA00452 8 E Q LQ LE EE A YGEGE ER FRKAL E RQLEA G EAD -- D N PVAR -- RLLATL LP P V A E A I D ----------- AW K EEY K KRGRAA 72
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 495 GYGPY L T L I DP GKMC VIT ILEL L - K L N S tggvi EGMR TA R AV IS - V G K AIE M E F R SEQ vlksesqa FR D V N K K S pe FKK L 572
Cdd:PHA00452 73 KARGL L R L V DP EVLA VIT LKVT L d M L L S ----- KETP TA Q AV AT a I G R AIE D E I R FGR -------- IE D L N P K Y -- FKK V 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 573 V QNA K -------------- S V FRSSQIEQSKIL WP QSIRARI G SV L ISM LI Q vakv S VQG V DP V T kakvhgeapa FAH G Y 638
Cdd:PHA00452 138 V EYL K rsrtgsvyhiafmm V V EADMVLLGEWDP WP KEDYIHV G KW L LEA LI E ---- S TGL V EL V R ---------- HTG G N 203
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 639 QYHNGSK L GVL - KIHKT L IRQL nge RLI A SVQ P QLL PM L V E PKPW VNWRS GGYH YTQS --- TL L RT K DSP eqv A YLKA as 714
Cdd:PHA00452 204 GGKDHEY L ELS e EAVEL L QDIA --- AAA A GIS P MYQ PM V V P PKPW TSIVG GGYH TEGR rpl AP L VR K TKK --- A LRRY -- 275
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 715 DNGDIDR VY DGL N V L GR T P W TV N RK V FD VV SQ V W N K G E -- GF L D IP GAQ demvl P P AP P KNS D -- PSILR AWK LQVKTIA 790
Cdd:PHA00452 276 RQKQMPE VY KAV N A L QN T A W RI N KD V LA VV NE V V N W G P vg DV L G IP RRP ----- L P PK P EFL D en EEAFK AWK RAAAAWY 350
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 791 N K FSSDR S N R CDTNYK L EI A RA F LGE K - L YFP H N L D F RGR A Y P l SPHF N HL G N D MSRG LL I F WH GK K LG PS GL K WLK I H L 869
Cdd:PHA00452 351 T K EKERV S K R RRLEFM L RV A NK F ADY K a I YFP Y N M D W RGR V Y A - VSML N PQ G S D LQKA LL R F AE GK P LG KR GL Y WLK V H G 429
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 870 S N LF G F DK LPLKD R V A FTESHLQD I KDS AE N PL TGD r WW TT AD K P WQA LA T CFE LNEVM km DNPEEFI S HQ PV HQ DGTC N 949
Cdd:PHA00452 430 A N CY G V DK VTFDE R A A WVDENHDN I LAA AE D PL NNT - WW AE AD S P LCF LA A CFE YAAAV -- HSGTSYV S GL PV AM DGTC S 506
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 950 GLQH YA A LGG D VE G ATQ VNL V PSDKPQD V Y AH VA RL V QKR LE IA A EK G DE N AKI L KDK ----- ITR KVV K QT VMT NV YG V 1024
Cdd:PHA00452 507 GLQH FS A MLR D EV G GRA VNL L PSDKPQD I Y GI VA EV V NEK LE RD A IN G TD N TRA L ARL wlayg ITR SLT K RP VMT LP YG S 586
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1025 T YVGATFQ I AKQ L - S P IF D DRKESLDFSK --- Y LT K HVFS AI R E LFHS A HLIQD WL GES AK RISKS irldvdeksfkn G N 1100
Cdd:PHA00452 587 T RFSCRDY I LED L l Q P GI D EGDGAMFTNQ aas Y MA K LIWD AI S E TVPA A VEAMN WL QQA AK LLAAK ------------ G A 654
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1101 KP dfmss VI WTTP L G L P IV Q P YR EESK K Q V ETN L QT V F - ISDPFAVNPVN AR RQKA G LP PNF I HSLDASH ML L SAAE C - G 1178
Cdd:PHA00452 655 EA ----- LH WTTP T G F P VW Q E YR KPEE K R V RLR L MG V A r VQLYVNTDTID AR KHAS G IA PNF V HSLDASH LR L TVVA C a E 729
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|.
gi 14318482 1179 K QGLD FA SV HDS YW THA S D I D TMNVVL RE Q F IKLH E - V D LVLRLKEE F DQR 1228
Cdd:PHA00452 730 K GIES FA VI HDS FG THA A D A D NLHRAI RE T F VEMY E e N D VLADFADQ F GDQ 780
RPOL_N
pfam14700 DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
415-731
1.52e-130
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex.
Pssm-ID: 464270
Cd Length: 286
Bit Score: 403.15
E-value: 1.52e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 415 RQ KV LE NRAT EAA R ERW KHD FEE AKA RG D - ISIE K N LN VK LW K WY NEM LP LV KEEI NHCRSLLSEKLSD K kglnkv D TN R 493
Cdd:pfam14700 1 RQ LR LE RDSV EAA V ERW REE FEE LQK RG L n TNLP K S LN AL LW Q WY EAL LP AI KEEI ELLKAAEAKPKKT K ------ D KE R 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 494 LG YGPYL T L ID P G K MCV ITILELL K L N STGGV IE GM RTA R AV IS V GKA I E M E F R SE Q V LK S E SQ afrdvnkkspefkklv 573
Cdd:pfam14700 75 CE YGPYL R L LP P E K LAA ITILELL S L L STGGV DK GM KVS R LA IS I GKA V E D E Y R AQ Q L LK K E KK ---------------- 138
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 574 qnaksvfrss Q I EQS KI L WPQ SI RA RI G S VL I S M LI QV AKV S V QGV DP V T KA KV HGEA PAF A H G YQY HN G S K L GV L K I H K 653
Cdd:pfam14700 139 ---------- K I KKK KI P WPQ EV RA KV G A VL L S L LI ET AKV P V TAE DP E T GE KV IQPQ PAF Y H S YQY KR G K K V GV I K P H P 208
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 14318482 654 T L IRQ L NG E RLIASVQ P QL LPMLV E PKPW VNWRS GGY HYTQ S T L L RTKD SP EQ V AYLKAAS DN GD I D R V Y DGL N VLG R 731
Cdd:pfam14700 209 E L VKL L LR E PARDTLT P RH LPMLV P PKPW TSYNK GGY LLSP S K L M RTKD GD EQ R AYLKAAS ER GD L D Q V F DGL D VLG N 286
RPO41
COG5108 Mitochondrial DNA-directed RNA polymerase [Transcription];
414-1225
1.48e-126
Mitochondrial DNA-directed RNA polymerase [Transcription];
Pssm-ID: 444054 [Multi-domain]
Cd Length: 826
Bit Score: 412.00
E-value: 1.48e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 414 D RQ KV LE NRAT EA A R E R WKHDF E E A KA RG DI S IEKNLNVKL wkwy NEMLP L VK E E I nhcrsllse KLSDKKGLNKVDT N R 493
Cdd:COG5108 12 A RQ IA LE EEMA EA G R S R FVERI E K A RK RG EE S GTQYGRRII ---- SDAVE L LA E A I --------- EATIDESSSGGAG N W 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 494 LGYGP YL TLI D PGKMCVITILEL L KLNSTGGVIE gmrta RAV I SVGKAI E M E F R S E QVLKSESQAFRDVN KK SPEFKKLV 573
Cdd:COG5108 79 HTAYA YL REL D AEVLAYLALRQC L DAVTQRHTLQ ----- AVA I RIASMV E D E V R G E AIREAFKDFYPRGK KK IESRTSRA 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 574 QNA K SV F RSSQIEQSKIL -- WP Q S IRARI G SV LI SMLIQ vakv S VQG V DPVTKAKVHGEA P A F ahgyqyhngsklgv LKI 651
Cdd:COG5108 154 VRY K DD F ERRVKNAVAKE ed WP V S DKIHV G FK LI ELVVE ---- S TGL V EIARDTEGINDT P V F -------------- VRP 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 652 HK T LIRQLNGER L IAS - VQ P QL LPM L V E P KP W VNWRS GGY HYTQSTL L RTKDSPEQ v A YL KAA s D NGD IDR VY DGL N V L G 730
Cdd:COG5108 216 TE T TLEWIAEAN L RMA m LS P AY LPM V V P P RN W TTPFR GGY LSGEVRR L PLVKTRNR - K YL EEL - K NGD MPE VY AAV N A L Q 293
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 731 R TPWT V NR K V FD V VSQV W NKGEG f L DI P GA q DEMVL P PA P PKNS D PSILRAWKLQV K TI A N K FSSDRSNR C DTNYK ---- 806
Cdd:COG5108 294 Q TPWT I NR Y V LA V MKWL W ERDLD - L GL P QR - EPITP P IK P ENRE D ITTNQVARKRW K KA A R K IYIANAKL C SKRVQ frrd 371
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 807 L EI A RA F - LGEKL YFP HN LDFRGR A Y PLSPHF N HL G N D MSR GLL I F WH GK KL G PS G L KWL K IH LS N LF G F DK LP L KD RV A 885
Cdd:COG5108 372 L NE A ER F s DYREF YFP YQ LDFRGR V Y AVPAFL N PQ G Q D HAK GLL M F AD GK PI G DG G A KWL A IH GA N VW G Y DK AS L EE RV K 451
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 886 FT E SHLQD I KDS A EN pl TGDRW W TT ADKPWQ A LA T C F E LNEVMK md NP E EFI S HQ P VHQ DG T C N GLQHY A A LGG D VE G AT 965
Cdd:COG5108 452 WV E DNYEA I LAA A AD -- YVAEF W SK ADKPWQ F LA F C R E WYGYDQ -- HG E GYV S GL P IAM DG S C S GLQHY S A MLR D EV G GA 527
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 966 Q VNLVPSDKPQD V YA H VA RLVQKRL ------------ EI AAEKG D ENAKI L KDK ITRKV V K QT VMT NV YG V T YV G ATF Q I 1033
Cdd:COG5108 528 A VNLVPSDKPQD I YA F VA EVDINLA qrigcpdelttn EI LNGIM D MAHNW L AFG ITRKV T K RN VMT LP YG S T EY G FRD Q V 607
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1034 akq LSPIFDDR KE SLD --------- FS K -- Y L T K HVFS AI R E LFHS A HLIQ DWL GES A KRIS K S irldvdeksfkng NK P 1102
Cdd:COG5108 608 --- REDMITRK KE EEG epfpfggdg FS A am W L A K LIWD AI G E VVVA A RRGM DWL QDL A GIAA K E ------------- GL P 671
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318482 1103 dfmss VIWTTPLG L P IV Q P YR EESKKQVE T NLQT V FI -- SDPFAVNPVNA R R QK A G LP PNF I HS L DA S H MLLSAAECGKQ 1180
Cdd:COG5108 672 ----- VIWTTPLG F P VM Q D YR SSKARRIN T TTRK V RV rl TLREEQDTIDK R K QK Q G IA PNF V HS M DA T H LMMTVNRSNEY 746
810 820 830 840
....*....|....*....|....*....|....*....|....*..
gi 14318482 1181 G L - D FA S VHDS YW T H A SDIDT M NVV LR EQ FI K L H - E V D LVLRL K E E F 1225
Cdd:COG5108 747 G A s S FA L VHDS FG T D A GSAEL M LDC LR KA FI E L Y e E S D VLEDF K S E I 793
Blast search parameters
Data Source:
Precalculated data, version = cdd.v.3.21
Preset Options: Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
