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Conserved domains on  [gi|4867893|emb|CAB43087|]
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RNA polymerase II, partial [Sanango racemosum]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 10089863)

DNA-directed RNA polymerase subunit B family protein similar to Frog virus 3DNA-directed RNA polymerase II subunit RPB2 homolog and to Homo sapiens interphase nucleus and mitotic apparatus associated protein (INMAP), a novel interphase nucleus and mitotic apparatus protein that is involved in spindle formation and cell cycle progression

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 10-256 3.76e-152

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


:

Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 445.47  E-value: 3.76e-152
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   10 QAARY*KRDHSTSLRHSETGIVDQVLLTT---NADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVE 86
Cdd:cd00653 581 GEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTED 660

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   87 GISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSM 166
Cdd:cd00653 661 GIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAP 740

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893  167 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICE 246
Cdd:cd00653 741 IFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCV 820

                       250
                ....*....|
gi 4867893  247 RCGLIAIANL 256
Cdd:cd00653 821 KCGIILSANL 830
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 10-256 3.76e-152

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 445.47  E-value: 3.76e-152
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   10 QAARY*KRDHSTSLRHSETGIVDQVLLTT---NADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVE 86
Cdd:cd00653 581 GEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTED 660

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   87 GISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSM 166
Cdd:cd00653 661 GIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAP 740

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893  167 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICE 246
Cdd:cd00653 741 IFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCV 820

                       250
                ....*....|
gi 4867893  247 RCGLIAIANL 256
Cdd:cd00653 821 KCGIILSANL 830
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 16-259 2.88e-135

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 407.81  E-value: 2.88e-135
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     16 KRDHSTSLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVN 95
Cdd:PRK08565  816 RRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIIN 895

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     96 P*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPTYYQ 175
Cdd:PRK08565  896 PHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQ 975

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    176 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICERCGLIAIAN 255
Cdd:PRK08565  976 KLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYD 1055


                  ....
gi 4867893    256 LK*N 259
Cdd:PRK08565 1056 RRKN 1059
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 16-259 6.66e-132

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 385.15  E-value: 6.66e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     16 KRDHSTSLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVN 95
Cdd:TIGR03670 312 RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIIN 391

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     96 P*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPTYYQ 175
Cdd:TIGR03670 392 PHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQ 471

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    176 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICERCGLIAIAN 255
Cdd:TIGR03670 472 KLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWED 551


                  ....
gi 4867893    256 LK*N 259
Cdd:TIGR03670 552 KRKG 555
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 9-253 9.44e-104

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 322.83  E-value: 9.44e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     9 GQAARY*KRDHSTSLRHSETGIVDQVLLTTNADG-------LRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDM 81
Cdd:COG0085  718 GEKARE-VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDM 796

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    82 PWTVEGISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 161
Cdd:COG0085  797 PFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGE 876

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   162 RLTSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYr 241
Cdd:COG0085  877 PFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV- 955

                        250
                 ....*....|..
gi 4867893   242 ihicerCGLIAI 253
Cdd:COG0085  956 ------CGRVKV 961
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 16-206 2.89e-103

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 304.45  E-value: 2.89e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     16 KRDHSTSLRHSETGIVDQVLL-TTNADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIV 94
Cdd:pfam00562 178 VKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIIL 257

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     95 NP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT--DVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPT 172
Cdd:pfam00562 258 NPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPI 337

                         170       180       190
                  ....*....|....*....|....*....|....
gi 4867893    173 YYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSR 206
Cdd:pfam00562 338 YYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 10-256 3.76e-152

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 445.47  E-value: 3.76e-152
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   10 QAARY*KRDHSTSLRHSETGIVDQVLLTT---NADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVE 86
Cdd:cd00653 581 GEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTED 660

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   87 GISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSM 166
Cdd:cd00653 661 GIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAP 740

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893  167 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICE 246
Cdd:cd00653 741 IFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCV 820

                       250
                ....*....|
gi 4867893  247 RCGLIAIANL 256
Cdd:cd00653 821 KCGIILSANL 830
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 16-259 2.88e-135

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 407.81  E-value: 2.88e-135
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     16 KRDHSTSLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVN 95
Cdd:PRK08565  816 RRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIIN 895

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     96 P*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPTYYQ 175
Cdd:PRK08565  896 PHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQ 975

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    176 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICERCGLIAIAN 255
Cdd:PRK08565  976 KLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYD 1055


                  ....
gi 4867893    256 LK*N 259
Cdd:PRK08565 1056 RRKN 1059
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 16-259 6.66e-132

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 385.15  E-value: 6.66e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     16 KRDHSTSLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVN 95
Cdd:TIGR03670 312 RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIIN 391

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     96 P*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPTYYQ 175
Cdd:TIGR03670 392 PHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQ 471

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    176 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICERCGLIAIAN 255
Cdd:TIGR03670 472 KLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWED 551


                  ....
gi 4867893    256 LK*N 259
Cdd:TIGR03670 552 KRKG 555
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 16-259 2.45e-129

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 378.92  E-value: 2.45e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    16 KRDHSTSLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVN 95
Cdd:PRK07225 318 RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIIN 397

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    96 P*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPTYYQ 175
Cdd:PRK07225 398 PHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQ 477

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   176 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICERCGLIAIAN 255
Cdd:PRK07225 478 KLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYD 557


                 ....
gi 4867893   256 LK*N 259
Cdd:PRK07225 558 KKRN 561
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 9-253 9.44e-104

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 322.83  E-value: 9.44e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     9 GQAARY*KRDHSTSLRHSETGIVDQVLLTTNADG-------LRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDM 81
Cdd:COG0085  718 GEKARE-VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDM 796

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    82 PWTVEGISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 161
Cdd:COG0085  797 PFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGE 876

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893   162 RLTSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYr 241
Cdd:COG0085  877 PFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV- 955

                        250
                 ....*....|..
gi 4867893   242 ihicerCGLIAI 253
Cdd:COG0085  956 ------CGRVKV 961
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 16-206 2.89e-103

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 304.45  E-value: 2.89e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     16 KRDHSTSLRHSETGIVDQVLL-TTNADGLRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIV 94
Cdd:pfam00562 178 VKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIIL 257

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     95 NP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT--DVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPT 172
Cdd:pfam00562 258 NPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPI 337

                         170       180       190
                  ....*....|....*....|....*....|....
gi 4867893    173 YYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSR 206
Cdd:pfam00562 338 YYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 17-238 1.73e-52

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 182.94  E-value: 1.73e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893      17 RDHSTSLRHSETGIVDQVLLTTNADG-------LRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGIS 89
Cdd:TIGR02013  791 RDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTP 870

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893      90 PDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGD--ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSM 166
Cdd:TIGR02013  871 VDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRP 950

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4867893     167 IFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 238
Cdd:TIGR02013  951 VTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 46-238 7.70e-44

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 158.33  E-value: 7.70e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     46 VKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGD 125
Cdd:CHL00207  800 IRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFK 879

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    126 ATPFTDVTVDNISKAL-HKCGYQ---MRGFETMYN-----------GHTGRRLTSMIFLGPTYYQRLKHMVDDKIHSRGR 190
Cdd:CHL00207  880 ILPFDEMYGSEYSRILiNNKLNQasiKNNEYWLFNsyhpgkmvlrdGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTT 959

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 4867893    191 GPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 238
Cdd:CHL00207  960 GPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD 1007
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 17-238 6.07e-43

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 155.64  E-value: 6.07e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     17 RDhsTSLR--HSETGIV-DQVLLTTNADG-------LRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVE 86
Cdd:PRK00405  833 KD--TSLRvpHGEEGTViDVKVFTRIEQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLED 910

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     87 GISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGdATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTS 165
Cdd:PRK00405  911 GTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDR 989

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4867893    166 MIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 238
Cdd:PRK00405  990 PVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1062
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
43-238 7.50e-36

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 135.44  E-value: 7.50e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     43 LRFVKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGK 122
Cdd:PRK09603 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGK 1154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    123 EGD---------------------------------------------------------ATP-FTDVTVDNISKALHKC 144
Cdd:PRK09603 1155 QIAsmledktkdfakelrakmleianainekdpltihalencsdeelleyakdwskgvkmAIPvFEGISQEKFYKLFELA 1234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    145 GYQMRGFETMYNGHTGRRLTSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHG 224
Cdd:PRK09603 1235 KIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYG 1314

                         250
                  ....*....|....
gi 4867893    225 AAHFLKERLFDQSD 238
Cdd:PRK09603 1315 AAHTLKEMLTIKSD 1328
rpoB CHL00001
RNA polymerase beta subunit
 57-244 2.36e-31

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 121.93  E-value: 2.36e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     57 QIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDN 136
Cdd:CHL00001  815 QVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQE 894

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    137 ISKA-----LHKCGYQMRG---FETMY-------NGHTGRRLTSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPA 201
Cdd:CHL00001  895 ASRKlvfseLYEASKQTANpwvFEPEYpgksrlfDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPL 974

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 4867893    202 EGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDayriHI 244
Cdd:CHL00001  975 RGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD----HI 1013
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 208-255 4.79e-28

RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.


Pssm-ID: 461355 [Multi-domain]  Cd Length: 87  Bit Score: 102.67  E-value: 4.79e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 4867893    208 GGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRIHICERCGLIAIAN 255
Cdd:pfam04560   1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYN 48
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
46-238 2.43e-23

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 98.93  E-value: 2.43e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893     46 VKVRVRSVRIPQIGD*FSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVNP*AIPSRMTIGQLIECIMGKVAAHMGKEG- 124
Cdd:PRK14844 1071 VKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVg 1150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    125 ---------------------------------DATPFTDVTVDNISKAL------------------------------ 141
Cdd:PRK14844 1151 nildeinkiksafckgirslnddnftkfaaaylDNKKIENIDDDEITASVlntpnknalndelnelvenylnscksaysn 1230

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4867893    142 --------HKCG---------------------YQMR------------------------------GFETMYNGHTGRR 162
Cdd:PRK14844 1231 lrnflievYSCGsnvsicnnirdisdnnliefaRKLRdgipvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEK 1310

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4867893    163 LTSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 238
Cdd:PRK14844 1311 FDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
 
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

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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