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Conserved domains on  [gi|1417949060|gb|AWY56397|]
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transcription elongation factor GreB [Burkholderia gladioli pv. gladioli]

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
 25-182 9.85e-106

transcription elongation factor GreB; Reviewed


:

Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 299.84  E-value: 9.85e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  25 AGAKNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASR 104
Cdd:PRK01885    1 AMKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1417949060 105 QEsADQVFFGATVDYATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRYP 182
Cdd:PRK01885   81 QQ-EGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
 
Name Accession Description Interval E-value
greB PRK01885
transcription elongation factor GreB; Reviewed
 25-182 9.85e-106

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 299.84  E-value: 9.85e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  25 AGAKNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASR 104
Cdd:PRK01885    1 AMKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1417949060 105 QEsADQVFFGATVDYATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRYP 182
Cdd:PRK01885   81 QQ-EGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
28-180 1.37e-69

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 208.44  E-value: 1.37e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  28 KNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASrQES 107
Cdd:COG0782     4 KNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPS-KLD 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1417949060 108 ADQVFFGATVDYA-TEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVR 180
Cdd:COG0782    83 TDKVFFGATVTLEdLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greB TIGR01461
transcription elongation factor GreB; The GreA and GreB transcription elongation factors ...
 28-182 1.41e-69

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: 208.19  E-value: 1.41e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  28 KNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASRQEs 107
Cdd:TIGR01461   2 TPLITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQ- 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1417949060 108 ADQVFFGATVDYATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRYP 182
Cdd:TIGR01461  81 EGKVFFGAWVELENDDGVTHRFRIVGYDEIDGRKNYISIDSPLARALLKKEVGDEVVVNTPAGEASWYVNAIEYV 155
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 29-99 1.46e-29

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 103.61  E-value: 1.46e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1417949060  29 NYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEV 99
Cdd:pfam03449   1 IPLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
 
Name Accession Description Interval E-value
greB PRK01885
transcription elongation factor GreB; Reviewed
 25-182 9.85e-106

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 299.84  E-value: 9.85e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  25 AGAKNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASR 104
Cdd:PRK01885    1 AMKTNYITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1417949060 105 QEsADQVFFGATVDYATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRYP 182
Cdd:PRK01885   81 QQ-EGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEYV 157
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
28-180 1.37e-69

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 208.44  E-value: 1.37e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  28 KNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASrQES 107
Cdd:COG0782     4 KNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPS-KLD 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1417949060 108 ADQVFFGATVDYA-TEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVR 180
Cdd:COG0782    83 TDKVFFGATVTLEdLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greB TIGR01461
transcription elongation factor GreB; The GreA and GreB transcription elongation factors ...
 28-182 1.41e-69

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: 208.19  E-value: 1.41e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  28 KNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASRQEs 107
Cdd:TIGR01461   2 TPLITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQ- 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1417949060 108 ADQVFFGATVDYATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRYP 182
Cdd:TIGR01461  81 EGKVFFGAWVELENDDGVTHRFRIVGYDEIDGRKNYISIDSPLARALLKKEVGDEVVVNTPAGEASWYVNAIEYV 155
greA PRK00226
transcription elongation factor GreA; Reviewed
 28-181 3.21e-46

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 149.10  E-value: 3.21e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  28 KNYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASrQES 107
Cdd:PRK00226    4 KIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPS-KLS 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1417949060 108 ADQVFFGATVD-YATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRY 181
Cdd:PRK00226   83 GGKVKFGSTVTlKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVEY 157
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 30-179 2.70e-37

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: 126.19  E-value: 2.70e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  30 YITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASRQESaD 109
Cdd:TIGR01462   1 PLTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLST-D 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1417949060 110 QVFFGATVDYATED-GEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDV 179
Cdd:TIGR01462  80 VVGFGSTVTIKDLDtGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDSVEVQTPKGEKEYEILKI 150
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 29-99 1.46e-29

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 103.61  E-value: 1.46e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1417949060  29 NYITPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEV 99
Cdd:pfam03449   1 IPLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
GreA_GreB pfam01272
Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.
 106-181 1.17e-25

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


Pssm-ID: 426171 [Multi-domain]  Cd Length: 77  Bit Score: 94.12  E-value: 1.17e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1417949060 106 ESADQVFFGATVDYA-TEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRY 181
Cdd:pfam01272   1 LPADVVTFGSTVTLEdLDTGEEETYTIVGPDEADPSKGKISVLSPLGKALLGKKVGDTVEVTAPGGKIKYEILKIEY 77
PRK06342 PRK06342
transcription elongation factor GreA;
29-179 3.46e-15

transcription elongation factor GreA;


Pssm-ID: 180535 [Multi-domain]  Cd Length: 160  Bit Score: 69.36  E-value: 3.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  29 NYITPAGHKRLRDELlhliDEERpevvklVSWAASNGDRSENGDYIYGKRRLREIdrriRFLTKRLDLAEVVDasRQESA 108
Cdd:PRK06342   29 NLVTEAGLKALEDQL----AQAR------AAYEAAQAIEDVNERRRQMARPLRDL----RYLAARRRTAQLMP--DPAST 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1417949060 109 DQVFFGATVDYATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVtlmtPAGPQPIDVLDV 179
Cdd:PRK06342   93 DVVAFGSTVTFSRDDGRVQTYRIVGEDEADPKAGSISYVSPVARALMGKAVGDVV----SVGGQELEIIAI 159
PRK05892 PRK05892
nucleoside diphosphate kinase regulator; Provisional
 31-182 5.26e-14

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180307 [Multi-domain]  Cd Length: 158  Bit Score: 65.95  E-value: 5.26e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  31 ITPAGHKRLRDELLHLiDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEvvdaSRQESADQ 110
Cdd:PRK05892    8 LAPAARDHLEAELARL-RARRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDDRINELDRRLRTGP----TPWSGSET 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1417949060 111 VFFGATVDYATEDGED---HTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQPIDVLDVRYP 182
Cdd:PRK05892   83 LPGGTEVTLRFPDGEVetmHVISVVEETPVGREAETLTADSPLGQALAGHQAGDTVTYSTPQGPAQVELLAVKLP 157
PRK05753 PRK05753
nucleoside diphosphate kinase regulator; Provisional
 94-186 6.51e-11

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180236 [Multi-domain]  Cd Length: 137  Bit Score: 57.26  E-value: 6.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  94 LDLAEVVDASRQeSADQVFFGATVDY-ATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTLMTPAGPQ 172
Cdd:PRK05753   39 LDRAQVVPPAEM-PADVVTMNSRVRFrDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLGLSVGQSIDWPLPGGKE 117

                          90
                  ....*....|....*
gi 1417949060 173 -PIDVLDVRYPAPAA 186
Cdd:PRK05753  118 tHLEVLEVEYQPEAA 132
PRK06330 PRK06330
transcript cleavage factor/unknown domain fusion protein; Validated
 32-165 5.46e-09

transcript cleavage factor/unknown domain fusion protein; Validated


Pssm-ID: 235780 [Multi-domain]  Cd Length: 718  Bit Score: 54.76  E-value: 5.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  32 TPAGHKRLRDELLHLIDEERPEVVKLVSWAASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDLAEVVDASRQESaDQV 111
Cdd:PRK06330  570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFALEKRARLQEEIRVLSEEINRARILTKDDVFT-DKV 648

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1417949060 112 FFGATVDYATEDGEDHTITIVGVDEVDLDHGHVSWVSPIARALLKARIGDTVTL 165
Cdd:PRK06330  649 GVGCKVVLEDDQGDKVCYTILGPWDADPDNKILSLKSKLAQEMLGKKVGDSVQF 702
Flagellar_rod pfam05149
Paraflagellar rod protein; This family consists of several eukaryotic paraflagellar rod ...
 33-97 4.56e-03

Paraflagellar rod protein; This family consists of several eukaryotic paraflagellar rod component proteins. The eukaryotic flagellum represents one of the most complex macromolecular structures found in any organizm and contains more than 250 proteins. In addition to its locomotive role, the flagellum is probably involved in nutrient uptake since receptors for host low-density lipoproteins are localized on the flagellar membrane as well as on the flagellar pocket membrane.


Pssm-ID: 368306 [Multi-domain]  Cd Length: 287  Bit Score: 36.57  E-value: 4.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417949060  33 PAGHKRLRDELLHLIDEERPEVVK----LVSWAasngdrsenGDYIYGK-RRLREIDRRIRFLTKRLDLA 97
Cdd:pfam05149 145 PAKQDKLRNALNELLDAVRKEFLEafraLYLTL---------GELTYKKeRRLEELDRQIRLYHHQRESA 205
 
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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