NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|3879948|emb|CAA99917|]
View 

Secretory carrier membrane protein [Caenorhabditis elegans]

Protein Classification

PAT1 family protein( domain architecture ID 1001013)

PAT1 family protein similar to Saccharomyces cerevisiae DNA topoisomerase 2-associated protein PAT1, an activator of decapping that functions as a general and active mechanism of translational repression and required for P-body formation

Gene Ontology:  GO:0003723

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PAT1 super family cl37801
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 10-242 7.20e-06

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


The actual alignment was detected with superfamily member pfam09770:

Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 48.49  E-value: 7.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     10 QNVDTHDEYNDEAAGAPEMTGTLSKQfqpKKYKD----GT--KMWNAeQQEETYSYtpfkaatlNRTPKPTRDSVHSGTl 83
Cdd:pfam09770  51 QLDETGDAFNDDTFGGGGGGDDVSAG---PVGKDfdffGQtaKVSDA-IEEEQVRF--------NRQQPAARAAQSSAQ- 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     84 rpPKMSPFVYATDEFSPPSAPATPKigRT------RPE---------SAAGTMTREQKLTWGRPPPAShfRSASSMSHGR 148
Cdd:pfam09770 118 --PPASSLPQYQYASQQSQQPSKPV--RTgyekykEPEpipdlqvdaSLWGVAPKKAAAPAPAPQPAA--QPASLPAPSR 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948    149 --------------QPHHGSEFVPLSMVAPPMHPMAQQYQSFNTIPRGDQQMQQREAMHSHSGPFYPLGTP-QIHSRPPS 213
Cdd:pfam09770 192 kmmsleeveaamraQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPvTILQRPQS 271

                         250       260
                  ....*....|....*....|....*....
gi 3879948    214 AVPSMGHPVPLSQMGAFVPPMLEQKPSPR 242
Cdd:pfam09770 272 PQPDPAQPSIQPQAQQFHQQPPPVPVQPT 300
 
Name Accession Description Interval E-value
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 10-242 7.20e-06

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 48.49  E-value: 7.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     10 QNVDTHDEYNDEAAGAPEMTGTLSKQfqpKKYKD----GT--KMWNAeQQEETYSYtpfkaatlNRTPKPTRDSVHSGTl 83
Cdd:pfam09770  51 QLDETGDAFNDDTFGGGGGGDDVSAG---PVGKDfdffGQtaKVSDA-IEEEQVRF--------NRQQPAARAAQSSAQ- 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     84 rpPKMSPFVYATDEFSPPSAPATPKigRT------RPE---------SAAGTMTREQKLTWGRPPPAShfRSASSMSHGR 148
Cdd:pfam09770 118 --PPASSLPQYQYASQQSQQPSKPV--RTgyekykEPEpipdlqvdaSLWGVAPKKAAAPAPAPQPAA--QPASLPAPSR 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948    149 --------------QPHHGSEFVPLSMVAPPMHPMAQQYQSFNTIPRGDQQMQQREAMHSHSGPFYPLGTP-QIHSRPPS 213
Cdd:pfam09770 192 kmmsleeveaamraQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPvTILQRPQS 271

                         250       260
                  ....*....|....*....|....*....
gi 3879948    214 AVPSMGHPVPLSQMGAFVPPMLEQKPSPR 242
Cdd:pfam09770 272 PQPDPAQPSIQPQAQQFHQQPPPVPVQPT 300
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 145-241 7.83e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 37.08  E-value: 7.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     145 SHGRQPHHGSEFVPLSMVAPPMHPMAQQYQSFNTIPrgdQQMQQREAMHSHSGPFYPLGTPQIHSRPPSAVPSMGHPVPL 224
Cdd:smart00818  49 THTLQPHHHIPVLPAQQPVVPQQPLMPVPGQHSMTP---TQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPVHPIPP 125

                           90
                   ....*....|....*..
gi 3879948     225 SQMGAFVPPMLEQKPSP 241
Cdd:smart00818 126 LPPQPPLPPMFPMQPLP 142
 
Name Accession Description Interval E-value
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 10-242 7.20e-06

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 48.49  E-value: 7.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     10 QNVDTHDEYNDEAAGAPEMTGTLSKQfqpKKYKD----GT--KMWNAeQQEETYSYtpfkaatlNRTPKPTRDSVHSGTl 83
Cdd:pfam09770  51 QLDETGDAFNDDTFGGGGGGDDVSAG---PVGKDfdffGQtaKVSDA-IEEEQVRF--------NRQQPAARAAQSSAQ- 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     84 rpPKMSPFVYATDEFSPPSAPATPKigRT------RPE---------SAAGTMTREQKLTWGRPPPAShfRSASSMSHGR 148
Cdd:pfam09770 118 --PPASSLPQYQYASQQSQQPSKPV--RTgyekykEPEpipdlqvdaSLWGVAPKKAAAPAPAPQPAA--QPASLPAPSR 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948    149 --------------QPHHGSEFVPLSMVAPPMHPMAQQYQSFNTIPRGDQQMQQREAMHSHSGPFYPLGTP-QIHSRPPS 213
Cdd:pfam09770 192 kmmsleeveaamraQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPvTILQRPQS 271

                         250       260
                  ....*....|....*....|....*....
gi 3879948    214 AVPSMGHPVPLSQMGAFVPPMLEQKPSPR 242
Cdd:pfam09770 272 PQPDPAQPSIQPQAQQFHQQPPPVPVQPT 300
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 113-227 5.35e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 39.25  E-value: 5.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948    113 RPESAAGTMTREQKLTWGRPPPASHFRSASSMSHGRQPHHGSEFVPLSMVAPP--MHPMaQQYQSFNTIPRGDQQMQQRE 190
Cdd:pfam09770 242 QQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQPQAQQFHQQPPPvpVQPT-QILQNPNRLSAARVGYPQNP 320

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 3879948    191 AMHSHSGPfyPLGTPQIHSRPPSAVPSMGHPVPLSQM 227
Cdd:pfam09770 321 QPGVQPAP--AHQAHRQQGSFGRQAPIITHPQQLAQL 355
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 145-241 7.83e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 37.08  E-value: 7.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3879948     145 SHGRQPHHGSEFVPLSMVAPPMHPMAQQYQSFNTIPrgdQQMQQREAMHSHSGPFYPLGTPQIHSRPPSAVPSMGHPVPL 224
Cdd:smart00818  49 THTLQPHHHIPVLPAQQPVVPQQPLMPVPGQHSMTP---TQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPVHPIPP 125

                           90
                   ....*....|....*..
gi 3879948     225 SQMGAFVPPMLEQKPSP 241
Cdd:smart00818 126 LPPQPPLPPMFPMQPLP 142
 
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