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Conserved domains on  [gi|22749387|ref|NP_689907|]
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retrotransposon Gag-like protein 3 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Retrotrans_gag super family cl46289
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 237-316 3.33e-10

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


The actual alignment was detected with superfamily member pfam16297:

Pssm-ID: 480629  Cd Length: 112  Bit Score: 57.23  E-value: 3.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387   237 PLQYTLTFSGDSQKLPEFLVQLYSYMRVRGHLYPTEAALVSFVGNCFSGRAGWWFQLLLDIQSPLLEQCESFIPVLQDTF 316
Cdd:pfam16297  24 PIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
PRK10263 super family cl35903
DNA translocase FtsK; Provisional
 70-179 4.15e-05

DNA translocase FtsK; Provisional


The actual alignment was detected with superfamily member PRK10263:

Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 46.23  E-value: 4.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387    70 PPAAWEAQKTPEFKEP-------QKPPEPQDLLPWEPPAAWELQEAPAAPESLAPPATRESQKPPMAHEIPTVLEGQGPA 142
Cdd:PRK10263  356 PTVAWQPVPGPQTGEPviapapeGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYA 435

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 22749387   143 NTQDATIAQEPKNSEPQDPPNIEKPQEAPE--YQETAAQ 179
Cdd:PRK10263  436 PAPEQPVAGNAWQAEEQQSTFAPQSTYQTEqtYQQPAAQ 474
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 419-461 5.35e-04

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 5.35e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 22749387  419 NQPMQAAINCPhiseAEWVRWHKGRLCLYCGYPGHFARDCPVK 461
Cdd:PTZ00368 110 GGEGHISRDCP----NAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
 
Name Accession Description Interval E-value
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 237-316 3.33e-10

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 57.23  E-value: 3.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387   237 PLQYTLTFSGDSQKLPEFLVQLYSYMRVRGHLYPTEAALVSFVGNCFSGRAGWWFQLLLDIQSPLLEQCESFIPVLQDTF 316
Cdd:pfam16297  24 PIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 70-179 4.15e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 46.23  E-value: 4.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387    70 PPAAWEAQKTPEFKEP-------QKPPEPQDLLPWEPPAAWELQEAPAAPESLAPPATRESQKPPMAHEIPTVLEGQGPA 142
Cdd:PRK10263  356 PTVAWQPVPGPQTGEPviapapeGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYA 435

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 22749387   143 NTQDATIAQEPKNSEPQDPPNIEKPQEAPE--YQETAAQ 179
Cdd:PRK10263  436 PAPEQPVAGNAWQAEEQQSTFAPQSTYQTEqtYQQPAAQ 474
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 419-461 5.35e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 5.35e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 22749387  419 NQPMQAAINCPhiseAEWVRWHKGRLCLYCGYPGHFARDCPVK 461
Cdd:PTZ00368 110 GGEGHISRDCP----NAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
ZnF_C2HC smart00343
zinc finger;
445-459 4.64e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.34  E-value: 4.64e-03
                           10
                   ....*....|....*
gi 22749387    445 CLYCGYPGHFARDCP 459
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 443-459 5.52e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.43  E-value: 5.52e-03
                          10
                  ....*....|....*..
gi 22749387   443 RLCLYCGYPGHFARDCP 459
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
 
Name Accession Description Interval E-value
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 237-316 3.33e-10

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 57.23  E-value: 3.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387   237 PLQYTLTFSGDSQKLPEFLVQLYSYMRVRGHLYPTEAALVSFVGNCFSGRAGWWFQLLLDIQSPLLEQCESFIPVLQDTF 316
Cdd:pfam16297  24 PIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 234-380 1.69e-08

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 54.40  E-value: 1.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387   234 TDFPLQYTLTFSG--DSQKLPEFLVQLYSYMRVrgHLYPTEAALVSFVGNCFSGRAGWWFQLLLDIQSPLLEQCESFIPV 311
Cdd:pfam19259   7 PNFMIQVILPFRGrkDVLKLKSFISEIMLQMSM--IFWPNDAERIVFCARHLTGPAAQWFHDFVQEQGILDATFDTFIKA 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 22749387   312 LQDTFDNPENMKDANQCIHQLCQGEGHV---ATHFHLIAQEL---NWDESTLWIQFQEGLASSIQDELSHTSPAT 380
Cdd:pfam19259  85 FKQHFYGKPDINKLFNDIVNLSEAKLGIeryNSHFNRLWDLLppdFLSEKAAIMFYIRGLKPETYIIVRLAKPST 159
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 70-179 4.15e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 46.23  E-value: 4.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387    70 PPAAWEAQKTPEFKEP-------QKPPEPQDLLPWEPPAAWELQEAPAAPESLAPPATRESQKPPMAHEIPTVLEGQGPA 142
Cdd:PRK10263  356 PTVAWQPVPGPQTGEPviapapeGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYA 435

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 22749387   143 NTQDATIAQEPKNSEPQDPPNIEKPQEAPE--YQETAAQ 179
Cdd:PRK10263  436 PAPEQPVAGNAWQAEEQQSTFAPQSTYQTEqtYQQPAAQ 474
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 419-461 5.35e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 5.35e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 22749387  419 NQPMQAAINCPhiseAEWVRWHKGRLCLYCGYPGHFARDCPVK 461
Cdd:PTZ00368 110 GGEGHISRDCP----NAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 420-462 1.00e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.40  E-value: 1.00e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 22749387  420 QPMQAAINCPHISEAEwvrwhKGRLCLYCGYPGHFARDCPVKP 462
Cdd:PTZ00368  35 EPGHLSRECPSAPGGR-----GERSCYNCGKTGHLSRECPEAP 72
PHA03160 PHA03160
hypothetical protein; Provisional
 31-161 1.26e-03

hypothetical protein; Provisional


Pssm-ID: 165431  Cd Length: 499  Bit Score: 41.23  E-value: 1.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22749387   31 AALQAQIPELQKSQAAKEYDL--LRKSSEAKEPQKLPEHMNPPAAWEAQKTPEF--------KEPQKPPEPQDLLPWEPP 100
Cdd:PHA03160 345 SSLYKDVLNLTKNISQLQDDLkdLKQAAINQPNRIIPHHFSNPYSFDPGHAPFFryapygapKNDHHLLPPLACSQQLPM 424

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22749387  101 AAWELQEAPAAPESLAPPatreSQKPPMAHEIPTVLEGQGPANTQDATIAQEPKNSEP---QDP 161
Cdd:PHA03160 425 QPLHVQQAPMQAPHVAPP----PMQPPHVQQPRVLPSTDGASNEAPKPSAQEPVHIDAsfaQDP 484
ZnF_C2HC smart00343
zinc finger;
445-459 4.64e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.34  E-value: 4.64e-03
                           10
                   ....*....|....*
gi 22749387    445 CLYCGYPGHFARDCP 459
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 443-459 5.52e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.43  E-value: 5.52e-03
                          10
                  ....*....|....*..
gi 22749387   443 RLCLYCGYPGHFARDCP 459
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
 
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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