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Conserved domains on  [gi|446779488|ref|WP_000856744|]
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MULTISPECIES: transcription elongation factor GreB [Enterobacteriaceae]

Protein Classification

transcription elongation factor GreB( domain architecture ID 11479724)

transcription elongation factor GreB induces cleavage of the nascent transcript to allow the resumption of elongation from the new 3' terminus; releases sequences of up to 9 nucleotides in length

Gene Symbol:  greB
Gene Ontology:  GO:0003677|GO:0070063|GO:0006354
PubMed:  17917675|31103420

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
greB PRK01885
transcription elongation factor GreB; Reviewed
 1-156 2.39e-111

transcription elongation factor GreB; Reviewed


:

Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 312.55  E-value: 2.39e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   1 MKTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQ 80
Cdd:PRK01885   2 MKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQ 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446779488  81 QEGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYV 156
Cdd:PRK01885  82 QEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
 
Name Accession Description Interval E-value
greB PRK01885
transcription elongation factor GreB; Reviewed
 1-156 2.39e-111

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 312.55  E-value: 2.39e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   1 MKTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQ 80
Cdd:PRK01885   2 MKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQ 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446779488  81 QEGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYV 156
Cdd:PRK01885  82 QEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
greB TIGR01461
transcription elongation factor GreB; The GreA and GreB transcription elongation factors ...
 2-157 5.92e-100

transcription elongation factor GreB; The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB. [Transcription, Transcription factors]


Pssm-ID: 130528 [Multi-domain]  Cd Length: 156  Bit Score: 284.08  E-value: 5.92e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488    2 KTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQQ 81
Cdd:TIGR01461   1 KTPLITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446779488   82 EGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYVK 157
Cdd:TIGR01461  81 EGKVFFGAWVELENDDGVTHRFRIVGYDEIDGRKNYISIDSPLARALLKKEVGDEVVVNTPAGEASWYVNAIEYVK 156
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-154 2.88e-72

Transcription elongation factor, GreA/GreB family [Transcription];


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 213.84  E-value: 2.88e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   1 MKTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQ 80
Cdd:COG0782    2 MKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446779488  81 QEGKVFFGAWVEIEN-DDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIE 154
Cdd:COG0782   82 DTDKVFFGATVTLEDlEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 5-74 1.67e-28

Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 100.15  E-value: 1.67e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488    5 LVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKI 74
Cdd:pfam03449   2 PLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
 
Name Accession Description Interval E-value
greB PRK01885
transcription elongation factor GreB; Reviewed
 1-156 2.39e-111

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 312.55  E-value: 2.39e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   1 MKTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQ 80
Cdd:PRK01885   2 MKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQ 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446779488  81 QEGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYV 156
Cdd:PRK01885  82 QEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
greB TIGR01461
transcription elongation factor GreB; The GreA and GreB transcription elongation factors ...
 2-157 5.92e-100

transcription elongation factor GreB; The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB. [Transcription, Transcription factors]


Pssm-ID: 130528 [Multi-domain]  Cd Length: 156  Bit Score: 284.08  E-value: 5.92e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488    2 KTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQQ 81
Cdd:TIGR01461   1 KTPLITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446779488   82 EGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYVK 157
Cdd:TIGR01461  81 EGKVFFGAWVELENDDGVTHRFRIVGYDEIDGRKNYISIDSPLARALLKKEVGDEVVVNTPAGEASWYVNAIEYVK 156
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-154 2.88e-72

Transcription elongation factor, GreA/GreB family [Transcription];


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 213.84  E-value: 2.88e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   1 MKTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQ 80
Cdd:COG0782    2 MKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446779488  81 QEGKVFFGAWVEIEN-DDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIE 154
Cdd:COG0782   82 DTDKVFFGATVTLEDlEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greA PRK00226
transcription elongation factor GreA; Reviewed
 2-155 1.29e-43

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 141.40  E-value: 1.29e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   2 KTPLvTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQQ 81
Cdd:PRK00226   4 KIPM-TQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKLS 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446779488  82 EGKVFFGAWVEIEN-DDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEY 155
Cdd:PRK00226  83 GGKVKFGSTVTLKDlDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVEY 157
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 6-154 5.36e-40

transcription elongation factor GreA; The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreA differs functionally in that it releases smaller oligonucleotides. Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (TIGR01461) forms a plausible outgroup and the remainder of the GreA/B family, included in this model, is designated GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein. [Transcription, Transcription factors]


Pssm-ID: 273638 [Multi-domain]  Cd Length: 151  Bit Score: 131.97  E-value: 5.36e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488    6 VTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQQEGKV 85
Cdd:TIGR01462   2 LTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLSTDVV 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   86 FFGAWVEIEN-DDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIE 154
Cdd:TIGR01462  82 GFGSTVTIKDlDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDSVEVQTPKGEKEYEILKIE 151
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 5-74 1.67e-28

Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 100.15  E-value: 1.67e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488    5 LVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKI 74
Cdd:pfam03449   2 PLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
GreA_GreB pfam01272
Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.
 80-155 1.16e-26

Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.


Pssm-ID: 426171 [Multi-domain]  Cd Length: 77  Bit Score: 95.66  E-value: 1.16e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446779488   80 QQEGKVFFGAWVEIEN-DDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEY 155
Cdd:pfam01272   1 LPADVVTFGSTVTLEDlDTGEEETYTIVGPDEADPSKGKISVLSPLGKALLGKKVGDTVEVTAPGGKIKYEILKIEY 77
PRK14720 PRK14720
transcription elongation factor GreA;
5-154 8.36e-16

transcription elongation factor GreA;


Pssm-ID: 184804 [Multi-domain]  Cd Length: 906  Bit Score: 73.65  E-value: 8.36e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   5 LVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQQEGK 84
Cdd:PRK14720 751 LVTRRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIDSAKILDLTDVKTSK 830

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446779488  85 VFFGAWVEIENDD-GVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIE 154
Cdd:PRK14720 831 VGFGTKVKLKNEDtGEEESYSILGPWESDPEEGIISYQSPLGKSLLGKKEGDSLEFVINDTETRYTVLKIE 901
PRK06342 PRK06342
transcription elongation factor GreA;
60-145 4.72e-13

transcription elongation factor GreA;


Pssm-ID: 180535 [Multi-domain]  Cd Length: 160  Bit Score: 62.81  E-value: 4.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488  60 RRVRYLTKCMENLKIVDySPQQEGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDlaVV 139
Cdd:PRK06342  71 RDLRYLAARRRTAQLMP-DPASTDVVAFGSTVTFSRDDGRVQTYRIVGEDEADPKAGSISYVSPVARALMGKAVGD--VV 147


                 ....*.
gi 446779488 140 NTPAGE 145
Cdd:PRK06342 148 SVGGQE 153
PRK05892 PRK05892
nucleoside diphosphate kinase regulator; Provisional
 2-146 1.77e-09

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180307 [Multi-domain]  Cd Length: 158  Bit Score: 53.24  E-value: 1.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   2 KTPLVTREGYEKLKQELNYLwREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSpqq 81
Cdd:PRK05892   4 KSKGLAPAARDHLEAELARL-RARRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDDRINELDRRLRTGPTPWSG--- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446779488  82 EGKVFFGAWVEIENDDGVTHRFRIVGY-DEIFGRKDY--ISIDSPMARALLKKEVGDLAVVNTPAGEA 146
Cdd:PRK05892  80 SETLPGGTEVTLRFPDGEVETMHVISVvEETPVGREAetLTADSPLGQALAGHQAGDTVTYSTPQGPA 147
PRK06330 PRK06330
transcript cleavage factor/unknown domain fusion protein; Validated
 7-135 6.53e-08

transcript cleavage factor/unknown domain fusion protein; Validated


Pssm-ID: 235780 [Multi-domain]  Cd Length: 718  Bit Score: 50.52  E-value: 6.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446779488   7 TREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCMENLKIVDYSPQQEGKVF 86
Cdd:PRK06330 570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFALEKRARLQEEIRVLSEEINRARILTKDDVFTDKVG 649

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446779488  87 FGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGD 135
Cdd:PRK06330 650 VGCKVVLEDDQGDKVCYTILGPWDADPDNKILSLKSKLAQEMLGKKVGD 698
 
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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