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Conserved domains on  [gi|503781109|ref|WP_014015103|]
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MULTISPECIES: transcription elongation factor GreA [Megasphaera]

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 1.27e-69

transcription elongation factor GreA; Reviewed


:

Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 207.27  E-value: 1.27e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   1 MTNETLITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETD 80
Cdd:PRK00226   1 MMKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503781109  81 DGSDKVRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVIDTanpaIVTVKAPAGEIKYRIL 157
Cdd:PRK00226  81 LSGGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGD----TVEVTTPGGEYEYEIL 153
 
Name Accession Description Interval E-value
greA PRK00226
transcription elongation factor GreA; Reviewed
 1-157 1.27e-69

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 207.27  E-value: 1.27e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   1 MTNETLITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETD 80
Cdd:PRK00226   1 MMKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503781109  81 DGSDKVRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVIDTanpaIVTVKAPAGEIKYRIL 157
Cdd:PRK00226  81 LSGGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGD----TVEVTTPGGEYEYEIL 153
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-157 1.34e-67

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 202.28  E-value: 1.34e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   1 MTNETLITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETD 80
Cdd:COG0782    1 MMKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503781109  81 DGSDKVRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVIDTanpaIVTVKAPAGEIKYRIL 157
Cdd:COG0782   81 LDTDKVFFGATVTLEDLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGD----EVEVTTPGGEREYEIL 153
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 7-157 2.13e-57

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: 176.27  E-value: 2.13e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109    7 ITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETDDGSDKV 86
Cdd:TIGR01462   2 LTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLSTDVV 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503781109   87 RLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVIDTAnpaiVTVKAPAGEIKYRIL 157
Cdd:TIGR01462  82 GFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDS----VEVQTPKGEKEYEIL 148
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 6-75 6.48e-32

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 109.00  E-value: 6.48e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109    6 LITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKI 75
Cdd:pfam03449   2 PLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
 
Name Accession Description Interval E-value
greA PRK00226
transcription elongation factor GreA; Reviewed
 1-157 1.27e-69

transcription elongation factor GreA; Reviewed


Pssm-ID: 234693 [Multi-domain]  Cd Length: 157  Bit Score: 207.27  E-value: 1.27e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   1 MTNETLITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETD 80
Cdd:PRK00226   1 MMKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503781109  81 DGSDKVRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVIDTanpaIVTVKAPAGEIKYRIL 157
Cdd:PRK00226  81 LSGGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGD----TVEVTTPGGEYEYEIL 153
GreA COG0782
Transcription elongation factor, GreA/GreB family [Transcription];
1-157 1.34e-67

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


Pssm-ID: 440545 [Multi-domain]  Cd Length: 156  Bit Score: 202.28  E-value: 1.34e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   1 MTNETLITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETD 80
Cdd:COG0782    1 MMKKNYLTPEGYEKLKAELEELKTVERPEIAEAIAEARAEGDLSENAEYDAAKEEQGFIEGRIRELEKRLANAEVIDPSK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503781109  81 DGSDKVRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVIDTanpaIVTVKAPAGEIKYRIL 157
Cdd:COG0782   81 LDTDKVFFGATVTLEDLEDGEEETYTIVGPDEADPKKGKISIESPLGRALLGKKVGD----EVEVTTPGGEREYEIL 153
greA TIGR01462
transcription elongation factor GreA; The GreA and GreB transcription elongation factors ...
 7-157 2.13e-57

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: 176.27  E-value: 2.13e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109    7 ITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETDDGSDKV 86
Cdd:TIGR01462   2 LTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLSTDVV 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503781109   87 RLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVIDTAnpaiVTVKAPAGEIKYRIL 157
Cdd:TIGR01462  82 GFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDS----VEVQTPKGEKEYEIL 148
GreA_GreB_N pfam03449
Transcription elongation factor, N-terminal; This domain adopts a long alpha-hairpin structure.
 6-75 6.48e-32

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


Pssm-ID: 460920 [Multi-domain]  Cd Length: 71  Bit Score: 109.00  E-value: 6.48e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109    6 LITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKI 75
Cdd:pfam03449   2 PLTREGYEKLKEELEHLKTVERPEIAEAIAEAREHGDLSENAEYDAAKEEQAFIEARIRELEDKLANAEV 71
PRK14720 PRK14720
transcription elongation factor GreA;
6-132 5.02e-26

transcription elongation factor GreA;


Pssm-ID: 184804 [Multi-domain]  Cd Length: 906  Bit Score: 102.93  E-value: 5.02e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   6 LITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETDDGSDK 85
Cdd:PRK14720 751 LVTRRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIDSAKILDLTDVKTSK 830

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 503781109  86 VRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILG 132
Cdd:PRK14720 831 VGFGTKVKLKNEDTGEEESYSILGPWESDPEEGIISYQSPLGKSLLG 877
greB PRK01885
transcription elongation factor GreB; Reviewed
 6-157 6.38e-26

transcription elongation factor GreB; Reviewed


Pssm-ID: 179345 [Multi-domain]  Cd Length: 157  Bit Score: 96.07  E-value: 6.38e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   6 LITQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETDDGSDK 85
Cdd:PRK01885   6 YITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQEGK 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503781109  86 VRLGSKVILEDvETGDRFEYTVVGTAEADPFNGRISNESPVGKAILG-QVIDTanpaiVTVKAPAGEIKYRIL 157
Cdd:PRK01885  86 VFFGAWVEIEN-EDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKkEVGDE-----VTVNTPAGEAEWYVN 152
GreA_GreB pfam01272
Transcription elongation factor, GreA/GreB, C-term; This domain has an FKBP-like fold.
 83-157 4.19e-23

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


Pssm-ID: 426171 [Multi-domain]  Cd Length: 77  Bit Score: 86.80  E-value: 4.19e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503781109   83 SDKVRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILG-QVIDTanpaiVTVKAPAGEIKYRIL 157
Cdd:pfam01272   3 ADVVTFGSTVTLEDLDTGEEETYTIVGPDEADPSKGKISVLSPLGKALLGkKVGDT-----VEVTAPGGKIKYEIL 73
PRK06330 PRK06330
transcript cleavage factor/unknown domain fusion protein; Validated
 8-135 9.78e-19

transcript cleavage factor/unknown domain fusion protein; Validated


Pssm-ID: 235780 [Multi-domain]  Cd Length: 718  Bit Score: 82.10  E-value: 9.78e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   8 TQEGLQKLKDELNELKSVRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIIKETDDGSDKVR 87
Cdd:PRK06330 570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFALEKRARLQEEIRVLSEEINRARILTKDDVFTDKVG 649

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 503781109  88 LGSKVILEDvETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVI 135
Cdd:PRK06330 650 VGCKVVLED-DQGDKVCYTILGPWDADPDNKILSLKSKLAQEMLGKKV 696
PRK06342 PRK06342
transcription elongation factor GreA;
6-135 6.42e-10

transcription elongation factor GreA;


Pssm-ID: 180535 [Multi-domain]  Cd Length: 160  Bit Score: 54.72  E-value: 6.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109   6 LITQEGLQKLKDELNELKsvrrieisqrikeaialgdlsenAEYDAAKNEQGIIEGRIAE---------LEAKIRTAKII 76
Cdd:PRK06342  30 LVTEAGLKALEDQLAQAR-----------------------AAYEAAQAIEDVNERRRQMarplrdlryLAARRRTAQLM 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 503781109  77 kETDDGSDKVRLGSKVILEDvETGDRFEYTVVGTAEADPFNGRISNESPVGKAILGQVI 135
Cdd:PRK06342  87 -PDPASTDVVAFGSTVTFSR-DDGRVQTYRIVGEDEADPKAGSISYVSPVARALMGKAV 143
PRK05892 PRK05892
nucleoside diphosphate kinase regulator; Provisional
 15-157 3.91e-05

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180307 [Multi-domain]  Cd Length: 158  Bit Score: 41.68  E-value: 3.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503781109  15 LKDELNELKSvRRIEISQRIKEAIALGDLSENAEYDAAKNEQGIIEGRIAELEAKIRTAKIikeTDDGSDKVRLGSKVIL 94
Cdd:PRK05892  16 LEAELARLRA-RRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDDRINELDRRLRTGPT---PWSGSETLPGGTEVTL 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503781109  95 EdVETGDRFEYTVVGTAEADPFNGR---ISNESPVGKAILG-QVIDTanpaiVTVKAPAGEIKYRIL 157
Cdd:PRK05892  92 R-FPDGEVETMHVISVVEETPVGREaetLTADSPLGQALAGhQAGDT-----VTYSTPQGPAQVELL 152
PRK05753 PRK05753
nucleoside diphosphate kinase regulator; Provisional
 65-132 2.28e-04

nucleoside diphosphate kinase regulator; Provisional


Pssm-ID: 180236 [Multi-domain]  Cd Length: 137  Bit Score: 39.16  E-value: 2.28e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503781109  65 ELEAKIRTAKIIKETDDGSDKVRLGSKVILEDVETGDRFEYTVVGTAEADPFNGRISNESPVGKAILG 132
Cdd:PRK05753  34 ALNAELDRAQVVPPAEMPADVVTMNSRVRFRDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLG 101
 
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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