NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1815902158|ref|WP_163070468|]
View 

hypothetical protein, partial [Acinetobacter baumannii]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Mfd super family cl34175
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 1-91 1.16e-46

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


The actual alignment was detected with superfamily member COG1197:

Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 158.69  E-value: 1.16e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1815902158    1 AEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKePESEVPEVEVDLNL 80
Cdd:COG1197    912 AEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIAEVGFDLYLQMLEEAVAALKGGK-EPEEEWEPEINLGV 990

                           90
                   ....*....|.
gi 1815902158   81 DAYLPTEYIAN 91
Cdd:COG1197    991 PALIPEDYIPD 1001
 
Name Accession Description Interval E-value
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 1-91 1.16e-46

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 158.69  E-value: 1.16e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1815902158    1 AEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKePESEVPEVEVDLNL 80
Cdd:COG1197    912 AEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIAEVGFDLYLQMLEEAVAALKGGK-EPEEEWEPEINLGV 990

                           90
                   ....*....|.
gi 1815902158   81 DAYLPTEYIAN 91
Cdd:COG1197    991 PALIPEDYIPD 1001
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
 1-91 4.20e-36

transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 128.24  E-value: 4.20e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1815902158   1 AEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKePESEVPEVEVDLNL 80
Cdd:TIGR00580 777 AQKRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGK-PPKLEEETDIELPY 855

                          90
                  ....*....|.
gi 1815902158  81 DAYLPTEYIAN 91
Cdd:TIGR00580 856 SAFIPDDYIAD 866
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
 1-89 1.18e-16

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 72.86  E-value: 1.18e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1815902158    1 AEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVN---EKRGIKEPESEVPEVEVD 77
Cdd:PRK10689   926 AQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELLENAVDalkAGREPSLEDLTSQQTEVE 1005

                           90
                   ....*....|..
gi 1815902158   78 LNLDAYLPTEYI 89
Cdd:PRK10689  1006 LRMPSLLPDDFI 1017
RecG_dom3_C pfam19833
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ...
 17-49 9.45e-04

ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.


Pssm-ID: 437665 [Multi-domain]  Cd Length: 87  Bit Score: 34.76  E-value: 9.45e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1815902158 17 GFKIAMRDLNIRGAGNLLGKQQHGfidtVGFDL 49
Cdd:pfam19833  4 GFEIAEADLKLRGPGDLEGTQQSG----IAFDL 32
 
Name Accession Description Interval E-value
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 1-91 1.16e-46

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 158.69  E-value: 1.16e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1815902158    1 AEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKePESEVPEVEVDLNL 80
Cdd:COG1197    912 AEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIAEVGFDLYLQMLEEAVAALKGGK-EPEEEWEPEINLGV 990

                           90
                   ....*....|.
gi 1815902158   81 DAYLPTEYIAN 91
Cdd:COG1197    991 PALIPEDYIPD 1001
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
 1-91 4.20e-36

transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 128.24  E-value: 4.20e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1815902158   1 AEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKePESEVPEVEVDLNL 80
Cdd:TIGR00580 777 AQKRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGK-PPKLEEETDIELPY 855

                          90
                  ....*....|.
gi 1815902158  81 DAYLPTEYIAN 91
Cdd:TIGR00580 856 SAFIPDDYIAD 866
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
 1-89 1.18e-16

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 72.86  E-value: 1.18e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1815902158    1 AEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVN---EKRGIKEPESEVPEVEVD 77
Cdd:PRK10689   926 AQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELLENAVDalkAGREPSLEDLTSQQTEVE 1005

                           90
                   ....*....|..
gi 1815902158   78 LNLDAYLPTEYI 89
Cdd:PRK10689  1006 LRMPSLLPDDFI 1017
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 1-57 4.23e-09

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 51.30  E-value: 4.23e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1815902158   1 AEDRLQAIKEFTelgSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLY--SQMLEEA 57
Cdd:PRK10917  594 ARERLKIMRETN---DGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVrdEELLEEA 649
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
1-43 1.33e-08

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 50.05  E-value: 1.33e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1815902158   1 AEDRLQAIKEFTelgSGFKIAMRDLNIRGAGNLLGKQQHGFID 43
Cdd:COG1200   592 ARERLEVMRETN---DGFEIAEEDLELRGPGEFLGTRQSGLPD 631
RecG_dom3_C pfam19833
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ...
 17-49 9.45e-04

ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.


Pssm-ID: 437665 [Multi-domain]  Cd Length: 87  Bit Score: 34.76  E-value: 9.45e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1815902158 17 GFKIAMRDLNIRGAGNLLGKQQHGfidtVGFDL 49
Cdd:pfam19833  4 GFEIAEADLKLRGPGDLEGTQQSG----IAFDL 32
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH