NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1720393198|ref|XP_030106359|]
View 

nucleolar protein 4 isoform X2 [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
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 37-91 9.50e-05

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: 40.31  E-value: 9.50e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720393198  37 DIIYSMHVETGpngeqirkHAGQKRTYKAISESYaFLP--REAVTRFLMSCSECQKR 91
Cdd:pfam17921   8 EILKEAHDSGG--------HLGIEKTLARLRRRY-WWPgmRKDVKKYVKSCETCQRR 55
MSCRAMM_ClfA super family cl41352
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 135-296 2.67e-03

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: 40.66  E-value: 2.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720393198 135 NSQQDEDESSiESDEFDMSDSTRMSAVNSDLSSNLEERMQSPQTVHGQQDDDSAAESSNGNETLGHSSAASGGAHGREPE 214
Cdd:NF033609  715 DSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 793

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720393198 215 -DSSSDGKTGLEQEEQPLNLSDSPSSAQLTSEfriDDQGSDGKNKYKNLLISDLKMEREArENGSKSPAHSYSSYDSGKN 293
Cdd:NF033609  794 sDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSESDSNSDSESGSN 869


                  ...
gi 1720393198 294 ESV 296
Cdd:NF033609  870 NNV 872
 
Name Accession Description Interval E-value
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 37-91 9.50e-05

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: 40.31  E-value: 9.50e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720393198  37 DIIYSMHVETGpngeqirkHAGQKRTYKAISESYaFLP--REAVTRFLMSCSECQKR 91
Cdd:pfam17921   8 EILKEAHDSGG--------HLGIEKTLARLRRRY-WWPgmRKDVKKYVKSCETCQRR 55
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 135-296 2.67e-03

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: 40.66  E-value: 2.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720393198 135 NSQQDEDESSiESDEFDMSDSTRMSAVNSDLSSNLEERMQSPQTVHGQQDDDSAAESSNGNETLGHSSAASGGAHGREPE 214
Cdd:NF033609  715 DSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 793

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720393198 215 -DSSSDGKTGLEQEEQPLNLSDSPSSAQLTSEfriDDQGSDGKNKYKNLLISDLKMEREArENGSKSPAHSYSSYDSGKN 293
Cdd:NF033609  794 sDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSESDSNSDSESGSN 869


                  ...
gi 1720393198 294 ESV 296
Cdd:NF033609  870 NNV 872
 
Name Accession Description Interval E-value
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 37-91 9.50e-05

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: 40.31  E-value: 9.50e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720393198  37 DIIYSMHVETGpngeqirkHAGQKRTYKAISESYaFLP--REAVTRFLMSCSECQKR 91
Cdd:pfam17921   8 EILKEAHDSGG--------HLGIEKTLARLRRRY-WWPgmRKDVKKYVKSCETCQRR 55
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 135-296 2.67e-03

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: 40.66  E-value: 2.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720393198 135 NSQQDEDESSiESDEFDMSDSTRMSAVNSDLSSNLEERMQSPQTVHGQQDDDSAAESSNGNETLGHSSAASGGAHGREPE 214
Cdd:NF033609  715 DSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 793

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720393198 215 -DSSSDGKTGLEQEEQPLNLSDSPSSAQLTSEfriDDQGSDGKNKYKNLLISDLKMEREArENGSKSPAHSYSSYDSGKN 293
Cdd:NF033609  794 sDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSESDSNSDSESGSN 869


                  ...
gi 1720393198 294 ESV 296
Cdd:NF033609  870 NNV 872
 
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