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Conserved domains on  [gi|512192669|gb|EPE08428|]
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nuclear pore protein [Ophiostoma piceae UAMH 11346]

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, ...
 202-338 1.95e-45

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: 153.51  E-value: 1.95e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669  202 PQAFENPREWEEALQNKPAP-GYLPVLCTGFAGLATRLQLQRRTVSTFNTGLHEINEKLDKILSQHDLQTSVRALAARRR 280
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPeKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 512192669  281 HAELSKRCLALAAKTQVLRNRGYALSGDEDDLKQKLQAIEKTMQDPA-LSARMEELWSR 338
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAqFKGRLNELWAR 139
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 11-116 6.71e-15

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


:

Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 69.57  E-value: 6.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669   11 GLFGQPAAAaqpaTGGLFGQSTQQPAASGGIFGQPQQQQQQQqqqqqTSGGIFGQPQQQQPaTGGMFGQSTQQQQPAATG 90
Cdd:pfam13634   1 GLFGAATST----SGGLFGNTSTTAASGGGLFGAASTATATT-----SGGGLFGNSSSNAP-SGGLFGATNTTTQTATGG 70

                          90       100
                  ....*....|....*....|....*.
gi 512192669   91 GIFGQPAQQQQQQQqqqsqfGSSLFG 116
Cdd:pfam13634  71 GLFGNNAATTTSTT------GGGLFG 90
Nup54_57_C pfam18570
NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for ...
 369-397 5.21e-13

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: 62.73  E-value: 5.21e-13
                          10        20
                  ....*....|....*....|....*....
gi 512192669  369 EAKAKKIVEDYEKQLQHLKKEVDQISSDF 397
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, ...
 202-338 1.95e-45

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: 153.51  E-value: 1.95e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669  202 PQAFENPREWEEALQNKPAP-GYLPVLCTGFAGLATRLQLQRRTVSTFNTGLHEINEKLDKILSQHDLQTSVRALAARRR 280
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPeKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 512192669  281 HAELSKRCLALAAKTQVLRNRGYALSGDEDDLKQKLQAIEKTMQDPA-LSARMEELWSR 338
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAqFKGRLNELWAR 139
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 11-116 6.71e-15

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 69.57  E-value: 6.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669   11 GLFGQPAAAaqpaTGGLFGQSTQQPAASGGIFGQPQQQQQQQqqqqqTSGGIFGQPQQQQPaTGGMFGQSTQQQQPAATG 90
Cdd:pfam13634   1 GLFGAATST----SGGLFGNTSTTAASGGGLFGAASTATATT-----SGGGLFGNSSSNAP-SGGLFGATNTTTQTATGG 70

                          90       100
                  ....*....|....*....|....*.
gi 512192669   91 GIFGQPAQQQQQQQqqqsqfGSSLFG 116
Cdd:pfam13634  71 GLFGNNAATTTSTT------GGGLFG 90
Nup54_57_C pfam18570
NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for ...
 369-397 5.21e-13

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: 62.73  E-value: 5.21e-13
                          10        20
                  ....*....|....*....|....*....
gi 512192669  369 EAKAKKIVEDYEKQLQHLKKEVDQISSDF 397
Cdd:pfam18570   1 EAKAKKILEDYEKQLQHLKKELESIKKDY 29
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 283-403 7.84e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 37.60  E-value: 7.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669 283 ELSKRCLALAAKTQVLRNRGYALSGDEDDLKQKLQAIEKTMQDpaLSARMEELWSRLIVLRNY--ADALRVEVNKrgVKE 360
Cdd:COG1579   28 ELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEE--VEARIKKYEEQLGNVRNNkeYEALQKEIES--LKR 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 512192669 361 EEGLGEDIEAKAKKIVEDYEKQLQHLKKEVDQISSDFDTWQKE 403
Cdd:COG1579  104 RISDLEDEILELMERIEELEEELAELEAELAELEAELEEKKAE 146
BAR_SNX cd07596
The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins; BAR domains are dimerization, lipid ...
 235-403 9.99e-03

The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.


Pssm-ID: 153280 [Multi-domain]  Cd Length: 218  Bit Score: 37.34  E-value: 9.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669 235 ATRLQLQRRTVSTfntGLHEINEKLDKiLSQHDLQtsvralaarrRHAELSKRCLALAAKTQVLRNRGYALSGDEDD--- 311
Cdd:cd07596   27 AQRLVKRRRELGS---ALGEFGKALIK-LAKCEEE----------VGGELGEALSKLGKAAEELSSLSEAQANQELVkll 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669 312 --LKQKLQAIEKTMQdpALSARMEeLWSRLIVLRNYADALRVEVNKrgVKEEEGLGEDIEAKAKKIVEDYEKQLQHLKKE 389
Cdd:cd07596   93 epLKEYLRYCQAVKE--TLDDRAD-ALLTLQSLKKDLASKKAQLEK--LKAAPGIKPAKVEELEEELEEAESALEEARKR 167

                        170
                 ....*....|....*...
gi 512192669 390 VDQIS----SDFDTWQKE 403
Cdd:cd07596  168 YEEISerlkEELKRFHEE 185
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 202-338 1.95e-45

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: 153.51  E-value: 1.95e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669  202 PQAFENPREWEEALQNKPAP-GYLPVLCTGFAGLATRLQLQRRTVSTFNTGLHEINEKLDKILSQHDLQTSVRALAARRR 280
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPeKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 512192669  281 HAELSKRCLALAAKTQVLRNRGYALSGDEDDLKQKLQAIEKTMQDPA-LSARMEELWSR 338
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAqFKGRLNELWAR 139
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 11-116 6.71e-15

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 69.57  E-value: 6.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669   11 GLFGQPAAAaqpaTGGLFGQSTQQPAASGGIFGQPQQQQQQQqqqqqTSGGIFGQPQQQQPaTGGMFGQSTQQQQPAATG 90
Cdd:pfam13634   1 GLFGAATST----SGGLFGNTSTTAASGGGLFGAASTATATT-----SGGGLFGNSSSNAP-SGGLFGATNTTTQTATGG 70

                          90       100
                  ....*....|....*....|....*.
gi 512192669   91 GIFGQPAQQQQQQQqqqsqfGSSLFG 116
Cdd:pfam13634  71 GLFGNNAATTTSTT------GGGLFG 90
Nup54_57_C pfam18570
NUP57/Nup54 C-terminal domain; The nuclear pore complex (NPC) constitutes the sole gateway for ...
 369-397 5.21e-13

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: 62.73  E-value: 5.21e-13
                          10        20
                  ....*....|....*....|....*....
gi 512192669  369 EAKAKKIVEDYEKQLQHLKKEVDQISSDF 397
Cdd:pfam18570   1 EAKAKKILEDYEKQLQHLKKELESIKKDY 29
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 2-94 2.00e-10

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 56.86  E-value: 2.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669    2 SLFG-----RPATGGLFGQPAAAAQPATGG-LFGQsTQQPAASGGIFGQpqqqqqqqqqqqqtsggifGQPQQQQPATGG 75
Cdd:pfam13634  12 GLFGntsttAASGGGLFGAASTATATTSGGgLFGN-SSSNAPSGGLFGA-------------------TNTTTQTATGGG 71

                          90
                  ....*....|....*....
gi 512192669   76 MFGQSTQQQQPAATGGIFG 94
Cdd:pfam13634  72 LFGNNAATTTSTTGGGLFG 90
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 58-122 7.63e-10

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 55.31  E-value: 7.63e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 512192669   58 TSGGIFGQPQQQQPATGGMFGQSTQQQQPAATGGIFGQPAQQQQqqqqqqsqfGSSLFGASTQPN 122
Cdd:pfam13634   9 TSGGLFGNTSTTAASGGGLFGAASTATATTSGGGLFGNSSSNAP---------SGGLFGATNTTT 64
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 283-403 7.84e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 37.60  E-value: 7.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669 283 ELSKRCLALAAKTQVLRNRGYALSGDEDDLKQKLQAIEKTMQDpaLSARMEELWSRLIVLRNY--ADALRVEVNKrgVKE 360
Cdd:COG1579   28 ELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEE--VEARIKKYEEQLGNVRNNkeYEALQKEIES--LKR 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 512192669 361 EEGLGEDIEAKAKKIVEDYEKQLQHLKKEVDQISSDFDTWQKE 403
Cdd:COG1579  104 RISDLEDEILELMERIEELEEELAELEAELAELEAELEEKKAE 146
BAR_SNX cd07596
The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins; BAR domains are dimerization, lipid ...
 235-403 9.99e-03

The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.


Pssm-ID: 153280 [Multi-domain]  Cd Length: 218  Bit Score: 37.34  E-value: 9.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669 235 ATRLQLQRRTVSTfntGLHEINEKLDKiLSQHDLQtsvralaarrRHAELSKRCLALAAKTQVLRNRGYALSGDEDD--- 311
Cdd:cd07596   27 AQRLVKRRRELGS---ALGEFGKALIK-LAKCEEE----------VGGELGEALSKLGKAAEELSSLSEAQANQELVkll 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 512192669 312 --LKQKLQAIEKTMQdpALSARMEeLWSRLIVLRNYADALRVEVNKrgVKEEEGLGEDIEAKAKKIVEDYEKQLQHLKKE 389
Cdd:cd07596   93 epLKEYLRYCQAVKE--TLDDRAD-ALLTLQSLKKDLASKKAQLEK--LKAAPGIKPAKVEELEEELEEAESALEEARKR 167

                        170
                 ....*....|....*...
gi 512192669 390 VDQIS----SDFDTWQKE 403
Cdd:cd07596  168 YEEISerlkEELKRFHEE 185
 
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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