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Conserved domains on  [gi|38704147|ref|NP_312087|]
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transcript cleavage factor [Escherichia coli O157:H7 str. Sakai]

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
 1-157 1.04e-92

transcription elongation factor GreA; Reviewed


:

Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 265.43  E-value: 1.04e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147    1 MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKM 80
Cdd:PRK00226   2 MKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38704147   81 PnNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEY 157
Cdd:PRK00226  82 S-GGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVEY 157
 
Name Accession Description Interval E-value
greA PRK00226
transcription elongation factor GreA; Reviewed
 1-157 1.04e-92

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 265.43  E-value: 1.04e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147    1 MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKM 80
Cdd:PRK00226   2 MKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38704147   81 PnNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEY 157
Cdd:PRK00226  82 S-GGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVEY 157
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-156 4.52e-81

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 236.18  E-value: 4.52e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147   1 MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKM 80
Cdd:COG0782   2 MKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSKL 81

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 38704147  81 pNNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVE 156
Cdd:COG0782  82 -DTDKVFFGATVTLEDLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 5-156 6.92e-76

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: 222.88  E-value: 6.92e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147     5 PMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKMPNNg 84
Cdd:TIGR01462   1 PLTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLSTD- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 38704147    85 RVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVE 156
Cdd:TIGR01462  80 VVGFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDSVEVQTPKGEKEYEILKIE 151
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 4-74 5.35e-35

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 116.71  E-value: 5.35e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38704147     4 IPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQV 74
Cdd:pfam03449   1 IPLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
 
Name Accession Description Interval E-value
greA PRK00226
transcription elongation factor GreA; Reviewed
 1-157 1.04e-92

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 265.43  E-value: 1.04e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147    1 MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKM 80
Cdd:PRK00226   2 MKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38704147   81 PnNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEY 157
Cdd:PRK00226  82 S-GGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTTPGGEYEYEILSVEY 157
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-156 4.52e-81

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 236.18  E-value: 4.52e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147   1 MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKM 80
Cdd:COG0782   2 MKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSKL 81

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 38704147  81 pNNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVE 156
Cdd:COG0782  82 -DTDKVFFGATVTLEDLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGDEVEVTTPGGEREYEILEIE 156
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 5-156 6.92e-76

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: 222.88  E-value: 6.92e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147     5 PMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKMPNNg 84
Cdd:TIGR01462   1 PLTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLSTD- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 38704147    85 RVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVE 156
Cdd:TIGR01462  80 VVGFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDSVEVQTPKGEKEYEILKIE 151
greB PRK01885
transcription elongation factor GreB; Reviewed
 6-157 4.15e-45

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 144.99  E-value: 4.15e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147    6 MTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDvTKMPNNGR 85
Cdd:PRK01885   7 ITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVD-YSPQQEGK 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 38704147   86 VIFGATVTVLNlDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEY 157
Cdd:PRK01885  86 VFFGAWVEIEN-EDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEY 156
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 4-74 5.35e-35

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 116.71  E-value: 5.35e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38704147     4 IPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQV 74
Cdd:pfam03449   1 IPLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
GreA_GreB pfam01272
Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.
 83-157 7.15e-34

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


Pssm-ID: 426171 [Multi-domain]  Cd Length: 77  Bit Score: 113.77  E-value: 7.15e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 38704147    83 NGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEY 157
Cdd:pfam01272   3 ADVVTFGSTVTLEDLDTGEEETYTIVGPDEADPSKGKISVLSPLGKALLGKKVGDTVEVTAPGGKIKYEILKIEY 77
PRK14720 PRK14720
transcription elongation factor GreA;
7-156 1.76e-31

transcription elongation factor GreA;


Pssm-ID: 184804 [Multi-domain]  Cd Length: 906  Bit Score: 118.33  E-value: 1.76e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147    7 TLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKMpNNGRV 86
Cdd:PRK14720 753 TRRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIDSAKILDLTDV-KTSKV 831

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147   87 IFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVE 156
Cdd:PRK14720 832 GFGTKVKLKNEDTGEEESYSILGPWESDPEEGIISYQSPLGKSLLGKKEGDSLEFVINDTETRYTVLKIE 901
PRK06342 PRK06342
transcription elongation factor GreA;
31-153 2.04e-16

transcription elongation factor GreA;


Pssm-ID: 180535 [Multi-domain]  Cd Length: 160  Bit Score: 71.67  E-value: 2.04e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147   31 AAIAEAREHGDLKENAEYHAAREQQGfcEGRIKDI---EAKLSNAQVIDVTkmPNNGRVIFGATVTvLNLDSDEEQTYRI 107
Cdd:PRK06342  41 DQLAQARAAYEAAQAIEDVNERRRQM--ARPLRDLrylAARRRTAQLMPDP--ASTDVVAFGSTVT-FSRDDGRVQTYRI 115

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 38704147  108 VGDDEADFKQNLISVNSPIARGLIGKEEDDVVVikTPGGEVEFEVI 153
Cdd:PRK06342 116 VGEDEADPKAGSISYVSPVARALMGKAVGDVVS--VGGQELEIIAI 159
PRK06330 PRK06330
transcript cleavage factor/unknown domain fusion protein; Validated
 7-142 4.29e-10

transcript cleavage factor/unknown domain fusion protein; Validated


Pssm-ID: 235780 [Multi-domain]  Cd Length: 718  Bit Score: 57.07  E-value: 4.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147    7 TLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIdvTKmpnngRV 86
Cdd:PRK06330 570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFALEKRARLQEEIRVLSEEINRARIL--TK-----DD 642

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38704147   87 IFGATVTV-----LNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIK 142
Cdd:PRK06330 643 VFTDKVGVgckvvLEDDQGDKVCYTILGPWDADPDNKILSLKSKLAQEMLGKKVGDSVQFQ 703
PRK05753 PRK05753
nucleoside diphosphate kinase regulator; Provisional
 66-157 4.27e-08

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180236 [Multi-domain]  Cd Length: 137  Bit Score: 49.18  E-value: 4.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147   66 EAKLSNAQVIDVTKMPNNgRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPG 145
Cdd:PRK05753  36 NAELDRAQVVPPAEMPAD-VVTMNSRVRFRDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLGLSVGQSIDWPLPG 114

                         90
                 ....*....|...
gi 38704147  146 GEV-EFEVIKVEY 157
Cdd:PRK05753 115 GKEtHLEVLEVEY 127
PRK05892 PRK05892
nucleoside diphosphate kinase regulator; Provisional
 14-155 8.11e-07

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180307 [Multi-domain]  Cd Length: 158  Bit Score: 45.92  E-value: 8.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704147   14 LREELDFLKSvRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQvidvTKMPNNGRVIFGATVT 93
Cdd:PRK05892  16 LEAELARLRA-RRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDDRINELDRRLRTGP----TPWSGSETLPGGTEVT 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 38704147   94 vLNLDSDEEQTYRIVG-DDEADF--KQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKV 155
Cdd:PRK05892  91 -LRFPDGEVETMHVISvVEETPVgrEAETLTADSPLGQALAGHQAGDTVTYSTPQGPAQVELLAV 154
DDR_swiveling pfam18427
DD-reactivating factor swiveling domain; AdoCbl-dependent diol dehydratase (DD) (EC 4.2.1.28) ...
 93-148 9.76e-04

DD-reactivating factor swiveling domain; AdoCbl-dependent diol dehydratase (DD) (EC 4.2.1.28) is one of the enzymes that catalyzes the conversion of 1,2-propanediol, 1,2-ethanediol, and glycerol to the corresponding aldehydes. A DD-reactivating factor (DDR) is responsible for the rapid reactivation of the inactivated holoDD in the presence of AdoCbl, ATP, and Mg2+. DDR exists as a dimer of heterodimer (alpha-beta)2. The alpha subunit has four domains: ATPase domain, swiveling domain, linker domain, and insert domain. The beta subunit, composed of a single domain, has a similar fold to the beta subunit of diol dehydratase (DD). This entry describes the swiveling domain of DDR, which structurally connects the beta subunit and the ATPase domain of the other alpha subunit. Furthermore, the beta subunit moves with the swiveling domain while the linker domain acts as a flat spring or a hinge for the domain movement of the swiveling domain.


Pssm-ID: 465763  Cd Length: 162  Bit Score: 37.49  E-value: 9.76e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 38704147    93 TVLNLDSDEeqTYRIVgddeadfkqnlisvnsPIARGLIGKEEddVVVIKTPGGEV 148
Cdd:pfam18427 127 TVFGLSPEE--TKQIV----------------PVARALIGNRS--AVVIKTPAGDV 162
 
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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