NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|158257802|dbj|BAF84874|]
View 

unnamed protein product [Homo sapiens]

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
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 18-117 1.36e-03

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.04  E-value: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158257802  18 DPGRRPHPDQGRTHDRPRDRPGDPRRKRSSDGNRRRDGDRDPERDQERDGNRDRNRDRERERERERDPDRGPRRDTHRDA 97
Cdd:PRK12678 168 ERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDR 247

                         90       100
                 ....*....|....*....|...
gi 158257802  98 GPRAGEHGVW---EKPRQSRTRD 117
Cdd:PRK12678 248 GDRDGDDGEGrggRRGRRFRDRD 270
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 18-117 1.36e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.04  E-value: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158257802  18 DPGRRPHPDQGRTHDRPRDRPGDPRRKRSSDGNRRRDGDRDPERDQERDGNRDRNRDRERERERERDPDRGPRRDTHRDA 97
Cdd:PRK12678 168 ERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDR 247

                         90       100
                 ....*....|....*....|...
gi 158257802  98 GPRAGEHGVW---EKPRQSRTRD 117
Cdd:PRK12678 248 GDRDGDDGEGrggRRGRRFRDRD 270
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 18-65 2.53e-03

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 39.90  E-value: 2.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 158257802   18 DPGRRPHPDQGRTHDRPRDRPGDPRRKRSSDGNRRRDgdRDPERDQER 65
Cdd:TIGR01622  14 SSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRD--RDYYRGRER 59
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 18-117 1.36e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.04  E-value: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158257802  18 DPGRRPHPDQGRTHDRPRDRPGDPRRKRSSDGNRRRDGDRDPERDQERDGNRDRNRDRERERERERDPDRGPRRDTHRDA 97
Cdd:PRK12678 168 ERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDR 247

                         90       100
                 ....*....|....*....|...
gi 158257802  98 GPRAGEHGVW---EKPRQSRTRD 117
Cdd:PRK12678 248 GDRDGDDGEGrggRRGRRFRDRD 270
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 18-65 2.53e-03

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 39.90  E-value: 2.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 158257802   18 DPGRRPHPDQGRTHDRPRDRPGDPRRKRSSDGNRRRDgdRDPERDQER 65
Cdd:TIGR01622  14 SSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRD--RDYYRGRER 59
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 21-162 3.90e-03

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 39.52  E-value: 3.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158257802   21 RRPHPDQGRTHDRPRDRPGDPRRKRSSDGNRRRDGDRDPERDqerdgnrdrnrdRererererdpdrgpRRDTHRDAGPR 100
Cdd:TIGR01622   1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRS------------R--------------RRDRHRDRDYY 54

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158257802  101 AGEHGVwEKPRQSRTRDGARGLTWDAAAPPGPAPWEAPEPPQPQRKGDpgrRRPESEPPSER 162
Cdd:TIGR01622  55 RGRERR-SRSRRPNRRYRPREKRRRRGDSYRRRRDDRRSRREKPRARD---GTPEPLTEDER 112
 
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