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Conserved domains on  [gi|1304171661|gb|PKC43686|]
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golgi re-assembly stacking protein 1 [Plasmodium falciparum NF54]

Protein Classification

PDZ domain-containing protein( domain architecture ID 650)

PDZ domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PDZ_canonical super family cl49608
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 69-213 5.07e-41

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


The actual alignment was detected with superfamily member pfam04495:

Pssm-ID: 483948 [Multi-domain]  Cd Length: 138  Bit Score: 145.10  E-value: 5.07e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  69 LDIYNCRYDKIKKVKVIPG-KWEGNGLLGIHISYE-FLNALNEGVRILEILENSPAYQSQLIEYEDFIIGYDKGIFRNQD 146
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSnTWGGQGLLGLSLRWCsFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPKGLLKGED 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1304171661 147 EFMSYInmnniikENSHDKKVLfntiLYVYNYKHENIRKVQIQLNDSWGGKGLLGCNVATGYLHKIP 213
Cdd:pfam04495  81 DLYTLV-------EDHEDRPLR----LYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIP 136
PDZ_canonical super family cl49608
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 12-105 4.97e-14

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


The actual alignment was detected with superfamily member pfam04495:

Pssm-ID: 483948 [Multi-domain]  Cd Length: 138  Bit Score: 69.22  E-value: 4.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  12 GYRILRISENSPCSNVGLEIFFDYIIQIDDLKLLDSskrtyDNFIEKIKLHENKELTLDIYNCRYDKIKKVKVIPGK-WE 90
Cdd:pfam04495  44 VWHVLDVHENSPAAKAGLQPYSDYIIGTPKGLLKGE-----DDLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRnWG 118

                          90
                  ....*....|....*
gi 1304171661  91 GNGLLGIHISYEFLN 105
Cdd:pfam04495 119 GEGALGCGLGYGLLH 133
 
Name Accession Description Interval E-value
GRASP55_65 pfam04495
GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 ...
 69-213 5.07e-41

GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain.


Pssm-ID: 427981 [Multi-domain]  Cd Length: 138  Bit Score: 145.10  E-value: 5.07e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  69 LDIYNCRYDKIKKVKVIPG-KWEGNGLLGIHISYE-FLNALNEGVRILEILENSPAYQSQLIEYEDFIIGYDKGIFRNQD 146
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSnTWGGQGLLGLSLRWCsFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPKGLLKGED 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1304171661 147 EFMSYInmnniikENSHDKKVLfntiLYVYNYKHENIRKVQIQLNDSWGGKGLLGCNVATGYLHKIP 213
Cdd:pfam04495  81 DLYTLV-------EDHEDRPLR----LYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIP 136
GRASP55_65 pfam04495
GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 ...
 12-105 4.97e-14

GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain.


Pssm-ID: 427981 [Multi-domain]  Cd Length: 138  Bit Score: 69.22  E-value: 4.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  12 GYRILRISENSPCSNVGLEIFFDYIIQIDDLKLLDSskrtyDNFIEKIKLHENKELTLDIYNCRYDKIKKVKVIPGK-WE 90
Cdd:pfam04495  44 VWHVLDVHENSPAAKAGLQPYSDYIIGTPKGLLKGE-----DDLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRnWG 118

                          90
                  ....*....|....*
gi 1304171661  91 GNGLLGIHISYEFLN 105
Cdd:pfam04495 119 GEGALGCGLGYGLLH 133
GRH1 COG5233
Peripheral Golgi membrane protein [Intracellular trafficking and secretion];
117-247 5.69e-09

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];


Pssm-ID: 227558 [Multi-domain]  Cd Length: 417  Bit Score: 58.22  E-value: 5.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661 117 LENSPAYQSQLIEYEDFIIGydkgifrNQDEFMSYINMNNIikENSHDKKVLFNTILYVYNYKHENIRKVQIQLNDSWGG 196
Cdd:COG5233   195 IQDKPPAYALLSPDEDYIDG-------SSDGQPLEIGELDL--EDVNESPVNLPLSLYYYNPIDDQERAKTERDGVHKGI 265

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1304171661 197 KGLLGCNVATGYLHKIPPCQIKDKEEKENINLKESF--SSSHIKNNESESNNY 247
Cdd:COG5233   266 VGILGCQVGHGFLHRLPLAGVGQKPQLQKLGTTKRTedPESHQVEQRGVEENF 318
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 18-97 3.11e-07

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467638 [Multi-domain]  Cd Length: 83  Bit Score: 48.34  E-value: 3.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  18 ISENSPCSNVGLEIFfDYIIQIDDLKLldsskRTYDNFIEKIKLHENKELTLDIYncRYDKIKKVKVIPGKWE----GNG 93
Cdd:cd23081     6 VVANSPAAEAGLKPG-DRILKIDGQKV-----RTWEDIVRIVRENPGKPLTLKIE--RDGKILTVTVTPELVEvegkGVG 77


                  ....
gi 1304171661  94 LLGI 97
Cdd:cd23081    78 RIGV 81
 
Name Accession Description Interval E-value
GRASP55_65 pfam04495
GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 ...
 69-213 5.07e-41

GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain.


Pssm-ID: 427981 [Multi-domain]  Cd Length: 138  Bit Score: 145.10  E-value: 5.07e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  69 LDIYNCRYDKIKKVKVIPG-KWEGNGLLGIHISYE-FLNALNEGVRILEILENSPAYQSQLIEYEDFIIGYDKGIFRNQD 146
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSnTWGGQGLLGLSLRWCsFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPKGLLKGED 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1304171661 147 EFMSYInmnniikENSHDKKVLfntiLYVYNYKHENIRKVQIQLNDSWGGKGLLGCNVATGYLHKIP 213
Cdd:pfam04495  81 DLYTLV-------EDHEDRPLR----LYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIP 136
GRASP55_65 pfam04495
GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 ...
 12-105 4.97e-14

GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain.


Pssm-ID: 427981 [Multi-domain]  Cd Length: 138  Bit Score: 69.22  E-value: 4.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  12 GYRILRISENSPCSNVGLEIFFDYIIQIDDLKLLDSskrtyDNFIEKIKLHENKELTLDIYNCRYDKIKKVKVIPGK-WE 90
Cdd:pfam04495  44 VWHVLDVHENSPAAKAGLQPYSDYIIGTPKGLLKGE-----DDLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRnWG 118

                          90
                  ....*....|....*
gi 1304171661  91 GNGLLGIHISYEFLN 105
Cdd:pfam04495 119 GEGALGCGLGYGLLH 133
GRH1 COG5233
Peripheral Golgi membrane protein [Intracellular trafficking and secretion];
117-247 5.69e-09

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];


Pssm-ID: 227558 [Multi-domain]  Cd Length: 417  Bit Score: 58.22  E-value: 5.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661 117 LENSPAYQSQLIEYEDFIIGydkgifrNQDEFMSYINMNNIikENSHDKKVLFNTILYVYNYKHENIRKVQIQLNDSWGG 196
Cdd:COG5233   195 IQDKPPAYALLSPDEDYIDG-------SSDGQPLEIGELDL--EDVNESPVNLPLSLYYYNPIDDQERAKTERDGVHKGI 265

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1304171661 197 KGLLGCNVATGYLHKIPPCQIKDKEEKENINLKESF--SSSHIKNNESESNNY 247
Cdd:COG5233   266 VGILGCQVGHGFLHRLPLAGVGQKPQLQKLGTTKRTedPESHQVEQRGVEENF 318
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 18-97 3.11e-07

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467638 [Multi-domain]  Cd Length: 83  Bit Score: 48.34  E-value: 3.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1304171661  18 ISENSPCSNVGLEIFfDYIIQIDDLKLldsskRTYDNFIEKIKLHENKELTLDIYncRYDKIKKVKVIPGKWE----GNG 93
Cdd:cd23081     6 VVANSPAAEAGLKPG-DRILKIDGQKV-----RTWEDIVRIVRENPGKPLTLKIE--RDGKILTVTVTPELVEvegkGVG 77


                  ....
gi 1304171661  94 LLGI 97
Cdd:cd23081    78 RIGV 81
 
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.
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