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Conserved domains on  [gi|939186768|pdb|5CWS|K]
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Chain K, Nucleoporin NUP57

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 44-180 3.31e-53

Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them.


:

Pssm-ID: 464011 [Multi-domain]  Cd Length: 139  Bit Score: 168.53  E-value: 3.31e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K         44 PGPNEDPKEWEEALQRKPAP-NFIPVLCSGFPSIVARLMLQRRVITEFNNKLHQINASLDAILSRHDLDHTVRAFNARRR 122
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPeKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
5CWS_K        123 HAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIDKTLNDPAQ-GSRLEELWSR 180
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQfKGRLNELWAR 139
Nup54_57_C pfam18570
NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for ...
 211-239 1.48e-11

NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. NPCs are formed by multiple copies of 34 distinct proteins, termed nucleoporins (nups). In yeast, the channel nups Nsp1, Nup49, and Nup57 constitute part of the central transport channel and form the diffusion barrier with their disordered phenylalanine-glycine (FG) repeats. Structural studies of yeast Nup57 indicate that it contains left-handed coiled-coil domains (CCD1-3). This entry represents the third CCD located at the C-terminal region of Nup57 which is composed of five heptad repeats. Nup57 in yeast is the equivalent to human Nup54 pfam13874.


:

Pssm-ID: 408354  Cd Length: 29  Bit Score: 57.34  E-value: 1.48e-11
                          10        20
                  ....*....|....*....|....*....
5CWS_K        211 EAKAKKILEDYDKQLQHLKKQVEEAKKDF 239
Cdd:pfam18570   1 EAKAKKILEDYEKQLQHLKKELESIKKDY 29
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 44-180 3.31e-53

Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them.


Pssm-ID: 464011 [Multi-domain]  Cd Length: 139  Bit Score: 168.53  E-value: 3.31e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K         44 PGPNEDPKEWEEALQRKPAP-NFIPVLCSGFPSIVARLMLQRRVITEFNNKLHQINASLDAILSRHDLDHTVRAFNARRR 122
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPeKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
5CWS_K        123 HAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIDKTLNDPAQ-GSRLEELWSR 180
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQfKGRLNELWAR 139
Nup54_57_C pfam18570
NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for ...
 211-239 1.48e-11

NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. NPCs are formed by multiple copies of 34 distinct proteins, termed nucleoporins (nups). In yeast, the channel nups Nsp1, Nup49, and Nup57 constitute part of the central transport channel and form the diffusion barrier with their disordered phenylalanine-glycine (FG) repeats. Structural studies of yeast Nup57 indicate that it contains left-handed coiled-coil domains (CCD1-3). This entry represents the third CCD located at the C-terminal region of Nup57 which is composed of five heptad repeats. Nup57 in yeast is the equivalent to human Nup54 pfam13874.


Pssm-ID: 408354  Cd Length: 29  Bit Score: 57.34  E-value: 1.48e-11
                          10        20
                  ....*....|....*....|....*....
5CWS_K        211 EAKAKKILEDYDKQLQHLKKQVEEAKKDF 239
Cdd:pfam18570   1 EAKAKKILEDYEKQLQHLKKELESIKKDY 29
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
109-241 3.97e-04

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 41.44  E-value: 3.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K       109 DLDHTVRAFNARRRHAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIDKTLNDpAQGSRLEElwsrlivlrgya 188
Cdd:COG4913  276 YLRAALRLWFAQRRLELLEAELEELRAELARLEAELERLEARLDALREELDELEAQIRG-NGGDRLEQ------------ 342

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
5CWS_K       189 edLKDQINQAgitesdglgEEIEAKAKKILEDYDKQLQHLKKQVEEAKKDFEE 241
Cdd:COG4913  343 --LEREIERL---------ERELEERERRRARLEALLAALGLPLPASAEEFAA 384
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 119-245 2.26e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 38.90  E-value: 2.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K         119 ARRRHAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIDKTLNDPAqgSRLEELWSRLIVLRGYAEDLKDQINQA 198
Cdd:TIGR02169  714 ASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELE--ARIEELEEDLHKLEEALNDLEARLSHS 791

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
5CWS_K         199 GITESDGLGEEIEAKAKKI----------LEDYDKQLQHLKKQVEEAKKDFEEWEKQ 245
Cdd:TIGR02169  792 RIPEIQAELSKLEEEVSRIearlreieqkLNRLTLEKEYLEKEIQELQEQRIDLKEQ 848
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 44-180 3.31e-53

Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them.


Pssm-ID: 464011 [Multi-domain]  Cd Length: 139  Bit Score: 168.53  E-value: 3.31e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K         44 PGPNEDPKEWEEALQRKPAP-NFIPVLCSGFPSIVARLMLQRRVITEFNNKLHQINASLDAILSRHDLDHTVRAFNARRR 122
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPeKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
5CWS_K        123 HAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIDKTLNDPAQ-GSRLEELWSR 180
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQfKGRLNELWAR 139
Nup54_57_C pfam18570
NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for ...
 211-239 1.48e-11

NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. NPCs are formed by multiple copies of 34 distinct proteins, termed nucleoporins (nups). In yeast, the channel nups Nsp1, Nup49, and Nup57 constitute part of the central transport channel and form the diffusion barrier with their disordered phenylalanine-glycine (FG) repeats. Structural studies of yeast Nup57 indicate that it contains left-handed coiled-coil domains (CCD1-3). This entry represents the third CCD located at the C-terminal region of Nup57 which is composed of five heptad repeats. Nup57 in yeast is the equivalent to human Nup54 pfam13874.


Pssm-ID: 408354  Cd Length: 29  Bit Score: 57.34  E-value: 1.48e-11
                          10        20
                  ....*....|....*....|....*....
5CWS_K        211 EAKAKKILEDYDKQLQHLKKQVEEAKKDF 239
Cdd:pfam18570   1 EAKAKKILEDYEKQLQHLKKELESIKKDY 29
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
109-241 3.97e-04

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 41.44  E-value: 3.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K       109 DLDHTVRAFNARRRHAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIDKTLNDpAQGSRLEElwsrlivlrgya 188
Cdd:COG4913  276 YLRAALRLWFAQRRLELLEAELEELRAELARLEAELERLEARLDALREELDELEAQIRG-NGGDRLEQ------------ 342

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
5CWS_K       189 edLKDQINQAgitesdglgEEIEAKAKKILEDYDKQLQHLKKQVEEAKKDFEE 241
Cdd:COG4913  343 --LEREIERL---------ERELEERERRRARLEALLAALGLPLPASAEEFAA 384
Adhesin_P1_N pfam18652
Adhesin P1 N-terminal domain; The cariogenic bacterium Streptococcus mutans uses adhesin P1 to ...
 192-247 5.88e-04

Adhesin P1 N-terminal domain; The cariogenic bacterium Streptococcus mutans uses adhesin P1 to adhere to tooth surfaces, extracellular matrix components, and other bacteria. The N terminus forms a stabilizing scaffold by wrapping behind the base of P1's elongated stalk and physically 'locking' it into place. It is suggested that the N-terminal has such a pronounced impact on P1 immunogenicity, antigenicity, folding, stability, and adherent function.


Pssm-ID: 465829 [Multi-domain]  Cd Length: 106  Bit Score: 38.50  E-value: 5.88e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
5CWS_K        192 KDQINQAGITESDglgEEIEAKAKKILEDYDKQLQHLKKQVEEAKKDFEEWEKQHN 247
Cdd:pfam18652  34 QDPTVDKGTATTA---EEAAAKKAEIKADYAKQVKEIKEATAKYKAKKAAYDKKYD 86
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 119-245 2.26e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 38.90  E-value: 2.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K         119 ARRRHAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIDKTLNDPAqgSRLEELWSRLIVLRGYAEDLKDQINQA 198
Cdd:TIGR02169  714 ASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELE--ARIEELEEDLHKLEEALNDLEARLSHS 791

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
5CWS_K         199 GITESDGLGEEIEAKAKKI----------LEDYDKQLQHLKKQVEEAKKDFEEWEKQ 245
Cdd:TIGR02169  792 RIPEIQAELSKLEEEVSRIearlreieqkLNRLTLEKEYLEKEIQELQEQRIDLKEQ 848
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
107-247 3.89e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 38.36  E-value: 3.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5CWS_K       107 RHDLDHTVRA-----FNARRRHAELSRRCLHLAARVQVLRNRGYALSGDEDELKQKLQQIdktlndpaqgSRLEELWSRL 181
Cdd:COG4913  591 EKDDRRRIRSryvlgFDNRAKLAALEAELAELEEELAEAEERLEALEAELDALQERREAL----------QRLAEYSWDE 660

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
5CWS_K       182 IVLRGYAEDLkdqinqagitesDGLGEEIEAkakkiLEDYDKQLQHLKKQVEEAKKDFEEWEKQHN 247
Cdd:COG4913  661 IDVASAEREI------------AELEAELER-----LDASSDDLAALEEQLEELEAELEELEEELD 709
 
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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