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Conserved domains on  [gi|490533906|ref|WP_004399078|]
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MULTISPECIES: transcription elongation factor GreA [Bacillaceae]

Protein Classification

transcription elongation factor GreA( domain architecture ID 11478349)

transcription elongation factor GreA induces cleavage of the nascent transcript to allow the resumption of elongation from the new 3' terminus; releases sequences of 2 to 3 nucleotides

Gene Symbol:  greA
Gene Ontology:  GO:0006354|GO:0070063|GO:0003677
PubMed:  23251328|31103420
SCOP:  4000597|4001068

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
greA PRK00226
transcription elongation factor GreA; Reviewed
 4-157 6.06e-81

transcription elongation factor GreA; Reviewed


:

Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 235.77  E-value: 6.06e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   4 EKVFPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIEDDGG 83
Cdd:PRK00226   2 MKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490533906  84 SN-VVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:PRK00226  82 SGgKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVE 156
 
Name Accession Description Interval E-value
greA PRK00226
transcription elongation factor GreA; Reviewed
 4-157 6.06e-81

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 235.77  E-value: 6.06e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   4 EKVFPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIEDDGG 83
Cdd:PRK00226   2 MKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490533906  84 SN-VVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:PRK00226  82 SGgKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVE 156
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
3-157 1.38e-75

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 222.31  E-value: 1.38e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   3 QEKVFPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIE-DD 81
Cdd:COG0782    1 MMKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDpSK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490533906  82 GGSNVVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:COG0782   81 LDTDKVFFGATVTLEDLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 8-157 8.05e-72

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: 212.48  E-value: 8.05e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906    8 PMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIEDDG-GSNV 86
Cdd:TIGR01462   1 PLTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKlSTDV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490533906   87 VGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:TIGR01462  81 VGFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDSVEVQTPKGEKEYEILKIE 151
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 7-77 1.51e-35

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 117.86  E-value: 1.51e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490533906    7 FPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKI 77
Cdd:pfam03449   1 IPLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
 
Name Accession Description Interval E-value
greA PRK00226
transcription elongation factor GreA; Reviewed
 4-157 6.06e-81

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 235.77  E-value: 6.06e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   4 EKVFPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIEDDGG 83
Cdd:PRK00226   2 MKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490533906  84 SN-VVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:PRK00226  82 SGgKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVE 156
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
3-157 1.38e-75

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 222.31  E-value: 1.38e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   3 QEKVFPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIE-DD 81
Cdd:COG0782    1 MMKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDpSK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490533906  82 GGSNVVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:COG0782   81 LDTDKVFFGATVTLEDLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 8-157 8.05e-72

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: 212.48  E-value: 8.05e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906    8 PMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIEDDG-GSNV 86
Cdd:TIGR01462   1 PLTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKlSTDV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490533906   87 VGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:TIGR01462  81 VGFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDSVEVQTPKGEKEYEILKIE 151
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 7-77 1.51e-35

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 117.86  E-value: 1.51e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490533906    7 FPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKI 77
Cdd:pfam03449   1 IPLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
greB PRK01885
transcription elongation factor GreB; Reviewed
 9-157 9.81e-33

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 113.41  E-value: 9.81e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   9 MTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIEDD-GGSNVV 87
Cdd:PRK01885   7 ITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSpQQEGKV 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906  88 GLGKTVTfVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:PRK01885  87 FFGAWVE-IENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIE 155
GreA_GreB pfam01272
Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.
 84-157 1.37e-29

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


Pssm-ID: 426171 [Multi-domain]  Cd Length: 77  Bit Score: 102.98  E-value: 1.37e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490533906   84 SNVVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:pfam01272   3 ADVVTFGSTVTLEDLDTGEEETYTIVGPDEADPSKGKISVLSPLGKALLGKKVGDTVEVTAPGGKIKYEILKIE 76
PRK14720 PRK14720
transcription elongation factor GreA;
4-157 1.39e-29

transcription elongation factor GreA;


Pssm-ID: 184804 [Multi-domain]  Cd Length: 906  Bit Score: 112.94  E-value: 1.39e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   4 EKVFPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIIE-DDG 82
Cdd:PRK14720 747 EIGFLVTRRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIDSAKILDlTDV 826

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490533906  83 GSNVVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKIS 157
Cdd:PRK14720 827 KTSKVGFGTKVKLKNEDTGEEESYSILGPWESDPEEGIISYQSPLGKSLLGKKEGDSLEFVINDTETRYTVLKIE 901
PRK06330 PRK06330
transcript cleavage factor/unknown domain fusion protein; Validated
 10-143 9.15e-20

transcript cleavage factor/unknown domain fusion protein; Validated


Pssm-ID: 235780 [Multi-domain]  Cd Length: 718  Bit Score: 84.80  E-value: 9.15e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906  10 TAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKII-EDDGGSNVVG 88
Cdd:PRK06330 570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFALEKRARLQEEIRVLSEEINRARILtKDDVFTDKVG 649

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490533906  89 LGKTVTfVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQ 143
Cdd:PRK06330 650 VGCKVV-LEDDQGDKVCYTILGPWDADPDNKILSLKSKLAQEMLGKKVGDSVQFQ 703
PRK06342 PRK06342
transcription elongation factor GreA;
72-157 2.03e-16

transcription elongation factor GreA;


Pssm-ID: 180535 [Multi-domain]  Cd Length: 160  Bit Score: 71.67  E-value: 2.03e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906  72 IRNAKIIEDDGGSNVVGLGKTVTFvELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVqtPGGEmlV 151
Cdd:PRK06342  80 RRTAQLMPDPASTDVVAFGSTVTF-SRDDGRVQTYRIVGEDEADPKAGSISYVSPVARALMGKAVGDVVSV--GGQE--L 154


                 ....*.
gi 490533906 152 KIVKIS 157
Cdd:PRK06342 155 EIIAIA 160
PRK05892 PRK05892
nucleoside diphosphate kinase regulator; Provisional
 8-156 6.48e-12

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180307 [Multi-domain]  Cd Length: 158  Bit Score: 59.79  E-value: 6.48e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490533906   8 PMTAEGKQKLEQELEYLKTvKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEGRVTTLENMIRNAKIieDDGGSNVV 87
Cdd:PRK05892   7 GLAPAARDHLEAELARLRA-RRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDDRINELDRRLRTGPT--PWSGSETL 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490533906  88 GLGKTVTfVELPDGDEESYTIVGSAEADPfEGK----ISNDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKI 156
Cdd:PRK05892  84 PGGTEVT-LRFPDGEVETMHVISVVEETP-VGReaetLTADSPLGQALAGHQAGDTVTYSTPQGPAQVELLAV 154
PRK05753 PRK05753
nucleoside diphosphate kinase regulator; Provisional
 84-150 3.13e-09

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180236 [Multi-domain]  Cd Length: 137  Bit Score: 52.26  E-value: 3.13e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490533906  84 SNVVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKISNDSPIAKSLLGKKVDEEVTVQTPGGEML 150
Cdd:PRK05753  52 ADVVTMNSRVRFRDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLGLSVGQSIDWPLPGGKET 118
 
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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