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Conserved domains on  [gi|1125209279|gb|OLB60506|]
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hypothetical protein AUI13_00010 [Gemmatimonadetes bacterium 13_2_20CM_2_69_23]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
2-360 2.08e-121

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 375.98  E-value: 2.08e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADETEIgvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:PRK00405   915 DIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEEI--------------------------------- 961

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:PRK00405       --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  162 kaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:PRK00405   962 ------------------------------------------------KELLEEAGLPEDGKTTLYDGRTGEPFDRPVTV 993

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVYEA 321
Cdd:PRK00405   994 GYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEA 1073

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1125209279  322 IVKGQNLPKPGIPESFNVLVKELQALGLKVTLGTTEDVE 360
Cdd:PRK00405  1074 IVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDGNE 1112
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 2-360 2.08e-121

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 375.98  E-value: 2.08e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADETEIgvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:PRK00405   915 DIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEEI--------------------------------- 961

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:PRK00405       --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  162 kaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:PRK00405   962 ------------------------------------------------KELLEEAGLPEDGKTTLYDGRTGEPFDRPVTV 993

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVYEA 321
Cdd:PRK00405   994 GYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEA 1073

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1125209279  322 IVKGQNLPKPGIPESFNVLVKELQALGLKVTLGTTEDVE 360
Cdd:PRK00405  1074 IVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDGNE 1112
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-353 4.81e-107

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: 335.93  E-value: 4.81e-107
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADETEIgvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:COG0085    806 DIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEI--------------------------------- 852

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:COG0085        --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  162 kaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:COG0085    853 ------------------------------------------------RELLEKAGLPPDGKEVLYDGRTGEPFDNPVTV 884

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVYEA 321
Cdd:COG0085    885 GYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEA 964

                          330       340       350
                   ....*....|....*....|....*....|..
gi 1125209279  322 IVKGQNLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:COG0085    965 IVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 2-353 3.12e-100

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: 318.92  E-value: 3.12e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    2 DIVLNPLGVPSRMNVGQILETHLGWAARILGF---EAKTPVFQGADETEIgvllrlagltwaadalqlgvrlpeldpetv 78
Cdd:TIGR02013  872 DIVLNPLGVPSRMNIGQILETHLGWAGKRLGRkgvPIATPVFDGASEEEI------------------------------ 921

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   79 rrivkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlp 158
Cdd:TIGR02013      --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  159 ktdkaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSD 238
Cdd:TIGR02013  922 ---------------------------------------------------KEYLEKAGLPRDGKVRLYDGRTGEQFDRP 950

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  239 VTVGSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRV 318
Cdd:TIGR02013  951 VTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKA 1030

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1125209279  319 YEAIVKGQNLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:TIGR02013 1031 YEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-353 3.17e-75

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: 248.64  E-value: 3.17e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADETEIGvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:cd00653   665 DIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDIS-------------------------------- 712

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:cd00653       --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 162 kaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravnEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:cd00653   713 -------------------------------------------------ELLGEAGLNYYGKEVLYDGRTGEPLEAPIFV 743

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVYEA 321
Cdd:cd00653   744 GPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCG 823

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1125209279 322 IV----------KGQNLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:cd00653   824 IIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-278 8.16e-38

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: 139.20  E-value: 8.16e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADEteigvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:pfam00562 254 DIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAST------------------------------------ 297

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:pfam00562     --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 162 kaafkaglkEIEKFlehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:pfam00562 298 ---------EVEDI----------------------------------GELLEKAGYNYYGKEVLYDGRTGEPFEAPIFV 334

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1125209279 242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQ 278
Cdd:pfam00562 335 GPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 2-360 2.08e-121

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 375.98  E-value: 2.08e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADETEIgvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:PRK00405   915 DIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEEI--------------------------------- 961

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:PRK00405       --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  162 kaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:PRK00405   962 ------------------------------------------------KELLEEAGLPEDGKTTLYDGRTGEPFDRPVTV 993

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVYEA 321
Cdd:PRK00405   994 GYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEA 1073

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1125209279  322 IVKGQNLPKPGIPESFNVLVKELQALGLKVTLGTTEDVE 360
Cdd:PRK00405  1074 IVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDGNE 1112
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-353 4.81e-107

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: 335.93  E-value: 4.81e-107
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADETEIgvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:COG0085    806 DIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEI--------------------------------- 852

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:COG0085        --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  162 kaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:COG0085    853 ------------------------------------------------RELLEKAGLPPDGKEVLYDGRTGEPFDNPVTV 884

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVYEA 321
Cdd:COG0085    885 GYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEA 964

                          330       340       350
                   ....*....|....*....|....*....|..
gi 1125209279  322 IVKGQNLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:COG0085    965 IVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 2-353 3.12e-100

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: 318.92  E-value: 3.12e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    2 DIVLNPLGVPSRMNVGQILETHLGWAARILGF---EAKTPVFQGADETEIgvllrlagltwaadalqlgvrlpeldpetv 78
Cdd:TIGR02013  872 DIVLNPLGVPSRMNIGQILETHLGWAGKRLGRkgvPIATPVFDGASEEEI------------------------------ 921

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   79 rrivkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlp 158
Cdd:TIGR02013      --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  159 ktdkaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSD 238
Cdd:TIGR02013  922 ---------------------------------------------------KEYLEKAGLPRDGKVRLYDGRTGEQFDRP 950

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  239 VTVGSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRV 318
Cdd:TIGR02013  951 VTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKA 1030

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1125209279  319 YEAIVKGQNLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:TIGR02013 1031 YEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-353 3.17e-75

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: 248.64  E-value: 3.17e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADETEIGvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:cd00653   665 DIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDIS-------------------------------- 712

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:cd00653       --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 162 kaafkaglkeiekflehdkpaevleavgfpalaallgpkseadvdravnEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:cd00653   713 -------------------------------------------------ELLGEAGLNYYGKEVLYDGRTGEPLEAPIFV 743

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVYEA 321
Cdd:cd00653   744 GPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCG 823

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1125209279 322 IV----------KGQNLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:cd00653   824 IIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-361 6.65e-75

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 252.24  E-value: 6.65e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    1 MDIVLNPLGVPSRMNVGQILETHLGWAARILGfEAKTPVFQGADETEIGVLLRLAGLTwAADALQLGVRLpeLDPETVRR 80
Cdd:PRK14844  1115 VDIILNPLGVPSRMNVGQILETHVGWACKKLG-EKVGNILDEINKIKSAFCKGIRSLN-DDNFTKFAAAY--LDNKKIEN 1190

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   81 IVKDlrqlpsgnggrpEVATAGIGVLGHRALSQETRDVYHRVVDFLKAAAKQLAERELEQHRAEREAHQARlEADDLPKT 160
Cdd:PRK14844  1191 IDDD------------EITASVLNTPNKNALNDELNELVENYLNSCKSAYSNLRNFLIEVYSCGSNVSICN-NIRDISDN 1257

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  161 DKAAFKAGLKEiekflehdkpaevleavGFPALAALL-GPKseadvDRAVNEVLKAAGLSPMGKARLRDGRSGEFFSSDV 239
Cdd:PRK14844  1258 NLIEFARKLRD-----------------GIPVAAPVFeGPK-----DEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKV 1315

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  240 TVGSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVY 319
Cdd:PRK14844  1316 TVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIY 1395

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 1125209279  320 EAIVKGQNLPKPGIPESFNVLVKELQALGLKVTLGTTEDVEE 361
Cdd:PRK14844  1396 ESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLKQNDVVIE 1437
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 222-361 5.24e-67

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 228.44  E-value: 5.24e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  222 GKARLRDGRSGEFFSSDVTVGSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTL 301
Cdd:CHL00207   919 GKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTL 998

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  302 QEILTVKSDDVNGRSRVYEAIVKGQNLPKPGIPESFNVLVKELQALGLKVTLGTTEDVEE 361
Cdd:CHL00207   999 KELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAYKIENFLE 1058
rpoB CHL00001
RNA polymerase beta subunit
 222-349 2.23e-66

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 226.71  E-value: 2.23e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  222 GKARLRDGRSGEFFSSDVTVGSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTL 301
Cdd:CHL00001   923 GKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYIL 1002

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1125209279  302 QEILTVKSDDVNGRSRVYEAIVKGQNLPKP-GIPESFNVLVKELQALGL 349
Cdd:CHL00001  1003 QEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLAL 1051
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-358 2.17e-63

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 219.02  E-value: 2.17e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279    1 MDIVLNPLGVPSRMNVGQILETHLGWAARILGfeaktpvfqgadeteigvllrlagltwaadalqlgvrlpeldpETVRR 80
Cdd:PRK09603  1122 VDIVLNPLGVPSRMNIGQILEMHLGLVGKEFG-------------------------------------------KQIAS 1158

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   81 IvkdlrqlpsgnggrpevatagigvlghraLSQETRDvyhrvvdFLKAAAKQLAEReleqhraereahqarleADDLPKT 160
Cdd:PRK09603  1159 M-----------------------------LEDKTKD-------FAKELRAKMLEI-----------------ANAINEK 1185

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  161 DKAafkaglkeIEKFLEHDKPAEVLE-AVGFPALAALLGPKSEADVDRAVNEVLKAAGLSPMGKARLRDGRSGEFFSSDV 239
Cdd:PRK09603  1186 DPL--------TIHALENCSDEELLEyAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERV 1257

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  240 TVGSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRVY 319
Cdd:PRK09603  1258 NVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAY 1337

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 1125209279  320 EAIVKGQNLPKPGIPESFNVLVKELQALGLKVTL-GTTED 358
Cdd:PRK09603  1338 RAIAKGEQVGESEIPETFYVLTKELQSLALDINIfGDDVD 1377
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-278 8.16e-38

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: 139.20  E-value: 8.16e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279   2 DIVLNPLGVPSRMNVGQILETHLGWAARILGFEAKTPVFQGADEteigvllrlagltwaadalqlgvrlpeldpetvrri 81
Cdd:pfam00562 254 DIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAST------------------------------------ 297

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  82 vkdlrqlpsgnggrpevatagigvlghralsqetrdvyhrvvdflkaaakqlaereleqhraereahqarleaddlpktd 161
Cdd:pfam00562     --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 162 kaafkaglkEIEKFlehdkpaevleavgfpalaallgpkseadvdravNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTV 241
Cdd:pfam00562 298 ---------EVEDI----------------------------------GELLEKAGYNYYGKEVLYDGRTGEPFEAPIFV 334

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1125209279 242 GSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQ 278
Cdd:pfam00562 335 GPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 280-353 2.37e-35

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: 124.24  E-value: 2.37e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 280 GGQRFGEMEVWALEAYGAAHTLQEILTVKSD----DVNGRSRVYEA-----IVKGQNLPKPG-IPESFNVLVKELQALGL 349
Cdd:pfam04560   1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80


                  ....
gi 1125209279 350 KVTL 353
Cdd:pfam04560  81 DPRL 84
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 182-353 4.56e-27

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 112.74  E-value: 4.56e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  182 AEVLEAVGFPAlAALLG------PKSEADVDRaVNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTVGSIYMMKLSHLVDD 255
Cdd:PRK08565   906 GQLLESIAGKV-AALEGrfvdatPFYGEPEEE-LRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279  256 KIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV--------------NGRSRVYEA 321
Cdd:PRK08565   984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTtiyvcelcghiawyDRRKNKYVC 1063

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1125209279  322 IVKGQ--NLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:PRK08565  1064 PIHGDkgNISPVEVSYAFKLLLQELMSMGISPRL 1097
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 182-353 4.25e-26

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: 109.35  E-value: 4.25e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 182 AEVLEAVGfPALAALLG------PKSEADVDRaVNEVLKAAGLSPMGKARLRDGRSGEFFSSDVTVGSIYMMKLSHLVDD 255
Cdd:TIGR03670 402 GQLLEMIA-GKVAALEGrrvdgtPFEGEPEEE-LRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVAD 479

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 256 KIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV--------------NGRSRVYEA 321
Cdd:TIGR03670 480 KIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYvvyvcencghiaweDKRKGTAYC 559

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1125209279 322 IVKGQ--NLPKPGIPESFNVLVKELQALGLKVTL 353
Cdd:TIGR03670 560 PVCGEtgDISPVEMSYAFKLLLDELKSLGISPRL 593
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 211-349 1.84e-24

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 104.66  E-value: 1.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209279 211 EVLKAAGLSPMGKARLRDGRSGEFFSSDVTVGSIYMMKLSHLVDDKIHARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVW 290
Cdd:PRK07225  441 EALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERD 520

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1125209279 291 ALEAYGAAHTLQEILTVKSDDVN---------------GRSRVYEAIVKGQ-NLPKPGIPESFNVLVKELQALGL 349
Cdd:PRK07225  521 VLIGHGAAMLLKERLLDESDKVEiyvcakcgmiaiydkKRNRKYCPICGEEtDIYPVEMSYAFKLLLDELKSLGI 595
 
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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