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Conserved domains on  [gi|515666951|ref|WP_017099551|]
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MULTISPECIES: transcription elongation factor GreB [Vibrio]

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
 1-157 1.50e-106

transcription elongation factor GreB; Reviewed


:

Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 300.61  E-value: 1.50e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   1 MKTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQ 80
Cdd:PRK01885   2 MKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQ 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515666951  81 QEGKVFFGAWVEIENDDGEIKKFRIVGPEEIYGdAKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHYV 157
Cdd:PRK01885  82 QEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDG-RKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
 
Name Accession Description Interval E-value
greB PRK01885
transcription elongation factor GreB; Reviewed
 1-157 1.50e-106

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 300.61  E-value: 1.50e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   1 MKTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQ 80
Cdd:PRK01885   2 MKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQ 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515666951  81 QEGKVFFGAWVEIENDDGEIKKFRIVGPEEIYGdAKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHYV 157
Cdd:PRK01885  82 QEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDG-RKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
greB TIGR01461
transcription elongation factor GreB; The GreA and GreB transcription elongation factors ...
 2-157 4.92e-79

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: 231.30  E-value: 4.92e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951    2 KTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQQ 81
Cdd:TIGR01461   1 KTPLITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515666951   82 EGKVFFGAWVEIENDDGEIKKFRIVGPEEIYGdAKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHYV 157
Cdd:TIGR01461  81 EGKVFFGAWVELENDDGVTHRFRIVGYDEIDG-RKNYISIDSPLARALLKKEVGDEVVVNTPAGEASWYVNAIEYV 155
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-155 5.17e-67

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 200.74  E-value: 5.17e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   1 MKTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQ 80
Cdd:COG0782    2 MKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515666951  81 QEGKVFFGAWVEIEN-DDGEIKKFRIVGPEEIYGDaKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIH 155
Cdd:COG0782   82 DTDKVFFGATVTLEDlEDGEEETYTIVGPDEADPK-KGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
GreA_GreB pfam01272
Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.
 80-156 1.92e-27

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


Pssm-ID: 426171 [Multi-domain]  Cd Length: 77  Bit Score: 97.59  E-value: 1.92e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515666951   80 QQEGKVFFGAWVEIEN-DDGEIKKFRIVGPEEIYGDaKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHY 156
Cdd:pfam01272   1 LPADVVTFGSTVTLEDlDTGEEETYTIVGPDEADPS-KGKISVLSPLGKALLGKKVGDTVEVTAPGGKIKYEILKIEY 77
 
Name Accession Description Interval E-value
greB PRK01885
transcription elongation factor GreB; Reviewed
 1-157 1.50e-106

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 300.61  E-value: 1.50e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   1 MKTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQ 80
Cdd:PRK01885   2 MKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQ 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515666951  81 QEGKVFFGAWVEIENDDGEIKKFRIVGPEEIYGdAKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHYV 157
Cdd:PRK01885  82 QEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDG-RKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
greB TIGR01461
transcription elongation factor GreB; The GreA and GreB transcription elongation factors ...
 2-157 4.92e-79

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: 231.30  E-value: 4.92e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951    2 KTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQQ 81
Cdd:TIGR01461   1 KTPLITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515666951   82 EGKVFFGAWVEIENDDGEIKKFRIVGPEEIYGdAKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHYV 157
Cdd:TIGR01461  81 EGKVFFGAWVELENDDGVTHRFRIVGYDEIDG-RKNYISIDSPLARALLKKEVGDEVVVNTPAGEASWYVNAIEYV 155
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-155 5.17e-67

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 200.74  E-value: 5.17e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   1 MKTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQ 80
Cdd:COG0782    2 MKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515666951  81 QEGKVFFGAWVEIEN-DDGEIKKFRIVGPEEIYGDaKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIH 155
Cdd:COG0782   82 DTDKVFFGATVTLEDlEDGEEETYTIVGPDEADPK-KGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greA PRK00226
transcription elongation factor GreA; Reviewed
 1-156 2.41e-43

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 140.63  E-value: 2.41e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   1 MKTKLITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQ 80
Cdd:PRK00226   2 MKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515666951  81 QEGKVFFGAWVEIEN-DDGEIKKFRIVGPEEiyGDAK-GYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHY 156
Cdd:PRK00226  82 SGGKVKFGSTVTLKDlDTDEEETYQIVGSDE--ADPKqGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVEY 157
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 6-154 1.17e-38

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: 128.51  E-value: 1.17e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951    6 ITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQQEGKV 85
Cdd:TIGR01462   2 LTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLSTDVV 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   86 FFGAWVEIEN-DDGEIKKFRIVGPEEiYGDAKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAI 154
Cdd:TIGR01462  82 GFGSTVTIKDlDTGEEETYTIVGSWE-ADPKEGKISIDSPLGKALIGKKVGDSVEVQTPKGEKEYEILKI 150
GreA_GreB pfam01272
Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.
 80-156 1.92e-27

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


Pssm-ID: 426171 [Multi-domain]  Cd Length: 77  Bit Score: 97.59  E-value: 1.92e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515666951   80 QQEGKVFFGAWVEIEN-DDGEIKKFRIVGPEEIYGDaKGYISIDSPMARALLKKEVDDEFTVTTPEGDKEWFINAIHY 156
Cdd:pfam01272   1 LPADVVTFGSTVTLEDlDTGEEETYTIVGPDEADPS-KGKISVLSPLGKALLGKKVGDTVEVTAPGGKIKYEILKIEY 77
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 5-74 1.61e-24

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 89.74  E-value: 1.61e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951    5 LITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTI 74
Cdd:pfam03449   2 PLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
PRK14720 PRK14720
transcription elongation factor GreA;
5-139 1.80e-11

transcription elongation factor GreA;


Pssm-ID: 184804 [Multi-domain]  Cd Length: 906  Bit Score: 60.94  E-value: 1.80e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   5 LITREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSPQQEGK 84
Cdd:PRK14720 751 LVTRRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIDSAKILDLTDVKTSK 830

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515666951  85 VFFGAWVEIENDD-GEIKKFRIVGPEEIYGDaKGYISIDSPMARALLKKEVDDEFT 139
Cdd:PRK14720 831 VGFGTKVKLKNEDtGEEESYSILGPWESDPE-EGIISYQSPLGKSLLGKKEGDSLE 885
PRK06342 PRK06342
transcription elongation factor GreA;
79-154 5.13e-11

transcription elongation factor GreA;


Pssm-ID: 180535 [Multi-domain]  Cd Length: 160  Bit Score: 57.41  E-value: 5.13e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515666951  79 PQQEGKVFFGAWVEIENDDGEIKKFRIVGPEEiyGD-AKGYISIDSPMARALLKKEVDDEFTVttpeGDKEWFINAI 154
Cdd:PRK06342  89 PASTDVVAFGSTVTFSRDDGRVQTYRIVGEDE--ADpKAGSISYVSPVARALMGKAVGDVVSV----GGQELEIIAI 159
PRK05892 PRK05892
nucleoside diphosphate kinase regulator; Provisional
 13-147 4.69e-08

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180307 [Multi-domain]  Cd Length: 158  Bit Score: 49.39  E-value: 4.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951  13 KLKAEHDHLWHEkrpeitkiVTWAASLGDRSENADYTFNKRLLRQIDRRVRFLRKFLPDVTIVDYSpqqEGKVFFGAWVE 92
Cdd:PRK05892  22 RLRARRDRLAVE--------VNDRGMIGDHGDQAEAIQRADELARLDDRINELDRRLRTGPTPWSG---SETLPGGTEVT 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 515666951  93 IENDDGEIKKFRIVG-PEEI-YGDAKGYISIDSPMARALLKKEVDDEFTVTTPEGDK 147
Cdd:PRK05892  91 LRFPDGEVETMHVISvVEETpVGREAETLTADSPLGQALAGHQAGDTVTYSTPQGPA 147
PRK06330 PRK06330
transcript cleavage factor/unknown domain fusion protein; Validated
 7-157 1.05e-07

transcript cleavage factor/unknown domain fusion protein; Validated


Pssm-ID: 235780 [Multi-domain]  Cd Length: 718  Bit Score: 50.13  E-value: 1.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515666951   7 TREGYNKLKAEHDHLWHEKRPEITKIVTWAASLGDRSENADYTF----NKRL---LRQIDRRVRFLRKFLPDVTIVDysp 79
Cdd:PRK06330 570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFalekRARLqeeIRVLSEEINRARILTKDDVFTD--- 646

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515666951  80 qqegKVFFGAWVEIENDDGEIKKFRIVGPEEIYGDaKGYISIDSPMARALLKKEVDDEFTVTtpegDKEWFINAIHYV 157
Cdd:PRK06330 647 ----KVGVGCKVVLEDDQGDKVCYTILGPWDADPD-NKILSLKSKLAQEMLGKKVGDSVQFQ----GKKYKISRIQSI 715
 
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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