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Conserved domains on  [gi|612487316|gb|AHX02977|]
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RNA polymerase beta subunit, partial [Acinetobacter sp. CC-LY182]

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;
85-288 2.01e-102

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: 322.44  E-value: 2.01e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   85 KLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILE 164
Cdd:PRK00405  855 RIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILE 934

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  165 THLGMAAKGLGDQIdkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPVFDGAEEGQIK 244
Cdd:PRK00405  935 THLGWAAKGLGIKF----------------------------------------------------ATPVFDGAKEEEIK 962

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 612487316  245 ELLELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:PRK00405  963 ELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVD 1006
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 85-288 2.01e-102

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 322.44  E-value: 2.01e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   85 KLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILE 164
Cdd:PRK00405  855 RIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILE 934

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  165 THLGMAAKGLGDQIdkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPVFDGAEEGQIK 244
Cdd:PRK00405  935 THLGWAAKGLGIKF----------------------------------------------------ATPVFDGAKEEEIK 962

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 612487316  245 ELLELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:PRK00405  963 ELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVD 1006
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 89-288 7.13e-86

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: 277.31  E-value: 7.13e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316    89 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLG 168
Cdd:TIGR02013  816 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLG 895

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   169 MAAKGLGdqidkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlRKGVPLATPVFDGAEEGQIKELLE 248
Cdd:TIGR02013  896 WAGKRLG-------------------------------------------------RKGVPIATPVFDGASEEEIKEYLE 926

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 612487316   249 LAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:TIGR02013  927 KAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVD 966
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 89-288 1.95e-81

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: 264.28  E-value: 1.95e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   89 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLG 168
Cdd:COG0085   750 GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLG 829

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  169 MAAKGLGDQIdkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPVFDGAEEGQIKELLE 248
Cdd:COG0085   830 WAAALLGRRV----------------------------------------------------ATPVFDGAPEEEIRELLE 857

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 612487316  249 LAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:COG0085   858 KAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVD 897
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 91-288 2.08e-76

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: 237.04  E-value: 2.08e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   91 ELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMA 170
Cdd:pfam00562 200 ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKA 279

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  171 AKGlgdqidkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrKGVPLATPVFDGA--EEGQIKELLE 248
Cdd:pfam00562 280 AAL----------------------------------------------------LGVFVDATPFDGAstEVEDIGELLE 307

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 612487316  249 LAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:pfam00562 308 KAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVD 347
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 88-288 1.59e-66

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: 222.44  E-value: 1.59e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  88 TGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHL 167
Cdd:cd00653  608 FSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316 168 GMAAKGLGDQIDkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPvFDGAEEGQIKELL 247
Cdd:cd00653  688 GKAGALLGKFGD---------------------------------------------------ATP-FDGAEEEDISELL 715

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 612487316 248 ELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:cd00653  716 GEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVD 756
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 85-288 2.01e-102

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 322.44  E-value: 2.01e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   85 KLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILE 164
Cdd:PRK00405  855 RIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILE 934

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  165 THLGMAAKGLGDQIdkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPVFDGAEEGQIK 244
Cdd:PRK00405  935 THLGWAAKGLGIKF----------------------------------------------------ATPVFDGAKEEEIK 962

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 612487316  245 ELLELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:PRK00405  963 ELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVD 1006
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 89-288 7.13e-86

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: 277.31  E-value: 7.13e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316    89 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLG 168
Cdd:TIGR02013  816 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLG 895

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   169 MAAKGLGdqidkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlRKGVPLATPVFDGAEEGQIKELLE 248
Cdd:TIGR02013  896 WAGKRLG-------------------------------------------------RKGVPIATPVFDGASEEEIKEYLE 926

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 612487316   249 LAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:TIGR02013  927 KAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVD 966
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 89-288 1.95e-81

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: 264.28  E-value: 1.95e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   89 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLG 168
Cdd:COG0085   750 GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLG 829

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  169 MAAKGLGDQIdkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPVFDGAEEGQIKELLE 248
Cdd:COG0085   830 WAAALLGRRV----------------------------------------------------ATPVFDGAPEEEIRELLE 857

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 612487316  249 LAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:COG0085   858 KAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVD 897
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 91-288 2.08e-76

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: 237.04  E-value: 2.08e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   91 ELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMA 170
Cdd:pfam00562 200 ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKA 279

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  171 AKGlgdqidkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrKGVPLATPVFDGA--EEGQIKELLE 248
Cdd:pfam00562 280 AAL----------------------------------------------------LGVFVDATPFDGAstEVEDIGELLE 307

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 612487316  249 LAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:pfam00562 308 KAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVD 347
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
25-288 6.95e-73

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 243.29  E-value: 6.95e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   25 GGTTKRGDKLSEELLSGLELVDLLD-IQPSDEAIAERLTQIQVFLKEKSLEIDEKFAEKKRKLSTGDELTTGVLKVVKVY 103
Cdd:PRK09603 1002 GKDYKEGDQIPKEEIASINRFTLASlVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLY 1081

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  104 LAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQIDKMLK 183
Cdd:PRK09603 1082 IATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLE 1161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  184 EQRtvlelRDFLDKIYNKV-----------GGQQEDLDSLTDEEILKLSGNLRKGVPLATPVFDGAEEGQIKELLELAGL 252
Cdd:PRK09603 1162 DKT-----KDFAKELRAKMleianainekdPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKI 1236

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 612487316  253 SRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:PRK09603 1237 AMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVD 1272
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
36-288 2.31e-68

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 230.28  E-value: 2.31e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   36 EELLSGLELVDLLDIQPSDEAIAERLTQIQVFLKEKSLEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 115
Cdd:PRK14844 1007 REKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDK 1086

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  116 MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQIDKML------------- 182
Cdd:PRK14844 1087 MAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILdeinkiksafckg 1166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  183 --------------------------------------------KEQRTVLE------------LRDFLDKIYNKVGGQQ 206
Cdd:PRK14844 1167 irslnddnftkfaaayldnkkienidddeitasvlntpnknalnDELNELVEnylnscksaysnLRNFLIEVYSCGSNVS 1246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  207 --EDLDSLTDEEILKLSGNLRKGVPLATPVFDGAEEGQIKELLELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLN 284
Cdd:PRK14844 1247 icNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLH 1326


                  ....
gi 612487316  285 HLVD 288
Cdd:PRK14844 1327 HLVD 1330
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 88-288 1.59e-66

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: 222.44  E-value: 1.59e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  88 TGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHL 167
Cdd:cd00653  608 FSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316 168 GMAAKGLGDQIDkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPvFDGAEEGQIKELL 247
Cdd:cd00653  688 GKAGALLGKFGD---------------------------------------------------ATP-FDGAEEEDISELL 715

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 612487316 248 ELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:cd00653  716 GEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVD 756
rpoB CHL00001
RNA polymerase beta subunit
 90-288 2.36e-48

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 172.39  E-value: 2.36e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   90 DELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGM 169
Cdd:CHL00001  794 KGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGL 873

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  170 AAkglgdqidKMLKEQRTVLElrdfLDKIYnkvggQQEDLDSLTDEEILKLSgnLRKGVPLatpVFDgaeegqikelLEL 249
Cdd:CHL00001  874 AG--------DLLNRHYRIAP----FDERY-----EQEASRKLVFSELYEAS--KQTANPW---VFE----------PEY 921

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 612487316  250 AGLSRtgqtvLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:CHL00001  922 PGKSR-----LFDGRTGDPFEQPVTIGKAYILKLIHQVD 955
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 69-288 5.44e-46

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 165.65  E-value: 5.44e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   69 KEKSLEIdeKFAEKKRKL-------STGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANG 141
Cdd:CHL00207  764 KDTSLRM--PNGGYGRVIkveifsrSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDG 841

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  142 VPVDIVLNPLGVPSRMNVGQILETHLGMAakglGDQIDKMLKeqrtVLELRDFLDKIYNKVggqqedldsLTDEEILKLS 221
Cdd:CHL00207  842 TPPDIILNPLGVPSRMNVGQLFECLLGLA----GDNLNKRFK----ILPFDEMYGSEYSRI---------LINNKLNQAS 904

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 612487316  222 gnlrkgvplatpvfdgaeegQIKELLELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVD 288
Cdd:CHL00207  905 --------------------IKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVD 951
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 98-287 6.44e-31

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: 121.29  E-value: 6.44e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   98 KVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQ 177
Cdd:TIGR03670 340 KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRR 419

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  178 IDkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPvFDGAEEGQIKELLELAGLSRTGQ 257
Cdd:TIGR03670 420 VD---------------------------------------------------GTP-FEGEPEEELRKELLKLGFKPDGK 447

                         170       180       190
                  ....*....|....*....|....*....|
gi 612487316  258 TVLYDGRTGERFDRPVTVGYMYMLKLNHLV 287
Cdd:TIGR03670 448 EVMYDGITGEKLEAEIFIGVIYYQKLHHMV 477
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 98-287 2.62e-30

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 120.06  E-value: 2.62e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316   98 KVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQ 177
Cdd:PRK08565  844 KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRF 923

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  178 IDkmlkeqrtvlelrdfldkiynkvggqqedldsltdeeilklsgnlrkgvplATPvFDGAEEGQIKELLELAGLSRTGQ 257
Cdd:PRK08565  924 VD---------------------------------------------------ATP-FYGEPEEELRKELLKLGYKPDGT 951

                         170       180       190
                  ....*....|....*....|....*....|
gi 612487316  258 TVLYDGRTGERFDRPVTVGYMYMLKLNHLV 287
Cdd:PRK08565  952 EVMYDGRTGEKIKAPIFIGVVYYQKLHHMV 981
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 98-287 3.10e-28

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 113.52  E-value: 3.10e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316  98 KVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILEThlgmaakglgdq 177
Cdd:PRK07225 346 RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM------------ 413

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612487316 178 idkmlkeqrtvlelrdfldkIYNKVGGqqedldsltdeeilkLSGNLRKGVPlatpvFDGAEEGQIKELLELAGLSRTGQ 257
Cdd:PRK07225 414 --------------------IGGKVGS---------------LEGRRVDGTA-----FSGEDEEDLREALEKLGFEHTGK 453

                        170       180       190
                 ....*....|....*....|....*....|
gi 612487316 258 TVLYDGRTGERFDRPVTVGYMYMLKLNHLV 287
Cdd:PRK07225 454 EVMYDGITGEKIEAEIFVGVIYYQKLHHMV 483
 
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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