NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|19172949|ref|NP_579881|]
View 

nucleocapsid [Human immunodeficiency virus 1]

Protein Classification

CCHC-type zinc finger protein( domain architecture ID 1000253)

CCHC-type zinc finger protein similar to human cellular nucleic acid-binding protein, a single-stranded DNA-binding protein that preferentially binds to the sterol regulatory element (SRE) sequence 5'-GTGCGGTG-3', and thereby mediates transcriptional repression

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 7-52 7.69e-06

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: 39.79  E-value: 7.69e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 19172949    7 RNQRKIVKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTER 52
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
 
Name Accession Description Interval E-value
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 7-52 7.69e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 7.69e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 19172949    7 RNQRKIVKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTER 52
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 14-52 2.00e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 33.67  E-value: 2.00e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 19172949  14 KCFNCGKEGHTARNCRAprkKGCWKCGKEGHQMKDCTER 52
Cdd:COG5082  62 VCFNCGQNGHLRRDCPH---SICYNCSWDGHRSNHCPKP 97
 
Name Accession Description Interval E-value
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 7-52 7.69e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 7.69e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 19172949    7 RNQRKIVKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTER 52
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 15-53 7.67e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.09  E-value: 7.67e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 19172949   15 CFNCGKEGHTARNCRAPRKKG----CWKCGKEGHQMKDCTERQ 53
Cdd:PTZ00368  30 CYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHLSRECPEAP 72
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 13-49 8.17e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.09  E-value: 8.17e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 19172949   13 VKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDC 49
Cdd:PTZ00368  78 RSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISRDC 119
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 15-55 2.32e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 35.94  E-value: 2.32e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 19172949   15 CFNCGKEGHTARNCRAPRKKG----CWKCGKEGHQMKDCTERQAN 55
Cdd:PTZ00368  55 CYNCGKTGHLSRECPEAPPGSgprsCYNCGQTGHISRECPNRAKG 99
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 15-53 7.61e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 34.40  E-value: 7.61e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 19172949   15 CFNCGKEGHTARNCRAPRKKG------CWKCGKEGHQMKDCTERQ 53
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGaakarpCYKCGEPGHLSRECPSAP 47
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 14-52 2.00e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 33.67  E-value: 2.00e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 19172949  14 KCFNCGKEGHTARNCRAprkKGCWKCGKEGHQMKDCTER 52
Cdd:COG5082  62 VCFNCGQNGHLRRDCPH---SICYNCSWDGHRSNHCPKP 97
 
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