NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|569003995|ref|XP_006526062|]
View 

nucleolar protein 4 isoform X1 [Mus musculus]

Protein Classification

integrase zinc binding domain-containing protein( domain architecture ID 16053682)

integrase zinc binding domain-containing protein;

Gene Ontology:  GO:0008270
PubMed:  11774877|20118915

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
MSCRAMM_ClfA super family cl41352
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 94-255 6.45e-04

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


The actual alignment was detected with superfamily member NF033609:

Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 42.59  E-value: 6.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569003995  94 NSQQDEDESSiESDEFDMSDSTRMSAVNSDLSSNLEERMQSPQTVHGQQDDDSAAESSNGNETLGHSSAASGGAHGREPE 173
Cdd:NF033609 715 DSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 793

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569003995 174 -DSSSDGKTGLEQEEQPLNLSDSPSSAQLTSEfriDDQGSDGKNKYKNLLISDLKMEREArENGSKSPAHSYSSYDSGKN 252
Cdd:NF033609 794 sDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSESDSNSDSESGSN 869


                 ...
gi 569003995 253 ESV 255
Cdd:NF033609 870 NNV 872
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 15-50 8.66e-04

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 37.61  E-value: 8.66e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 569003995   15 HAGQKRTYKAISESYaFLP--REAVTRFLMSCSECQKR 50
Cdd:pfam17921  19 HLGIEKTLARLRRRY-WWPgmRKDVKKYVKSCETCQRR 55
 
Name Accession Description Interval E-value
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 94-255 6.45e-04

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 42.59  E-value: 6.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569003995  94 NSQQDEDESSiESDEFDMSDSTRMSAVNSDLSSNLEERMQSPQTVHGQQDDDSAAESSNGNETLGHSSAASGGAHGREPE 173
Cdd:NF033609 715 DSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 793

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569003995 174 -DSSSDGKTGLEQEEQPLNLSDSPSSAQLTSEfriDDQGSDGKNKYKNLLISDLKMEREArENGSKSPAHSYSSYDSGKN 252
Cdd:NF033609 794 sDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSESDSNSDSESGSN 869


                 ...
gi 569003995 253 ESV 255
Cdd:NF033609 870 NNV 872
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 15-50 8.66e-04

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 37.61  E-value: 8.66e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 569003995   15 HAGQKRTYKAISESYaFLP--REAVTRFLMSCSECQKR 50
Cdd:pfam17921  19 HLGIEKTLARLRRRY-WWPgmRKDVKKYVKSCETCQRR 55
 
Name Accession Description Interval E-value
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 94-255 6.45e-04

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 42.59  E-value: 6.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569003995  94 NSQQDEDESSiESDEFDMSDSTRMSAVNSDLSSNLEERMQSPQTVHGQQDDDSAAESSNGNETLGHSSAASGGAHGREPE 173
Cdd:NF033609 715 DSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 793

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569003995 174 -DSSSDGKTGLEQEEQPLNLSDSPSSAQLTSEfriDDQGSDGKNKYKNLLISDLKMEREArENGSKSPAHSYSSYDSGKN 252
Cdd:NF033609 794 sDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSESDSNSDSESGSN 869


                 ...
gi 569003995 253 ESV 255
Cdd:NF033609 870 NNV 872
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 15-50 8.66e-04

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 37.61  E-value: 8.66e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 569003995   15 HAGQKRTYKAISESYaFLP--REAVTRFLMSCSECQKR 50
Cdd:pfam17921  19 HLGIEKTLARLRRRY-WWPgmRKDVKKYVKSCETCQRR 55
 
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