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Conserved domains on  [gi|971393678|ref|XP_015131909|]
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nucleoporin p54 isoform X1 [Gallus gallus]

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, ...
 350-487 6.89e-62

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: 200.11  E-value: 6.89e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678  350 PPAGVDPIIWEQAKVDNPDPDKLIPVPMVGFKELLRRLKVQDQMTKQHQTRLDIISEDISELQ-KNQTTTMAKIAQYKRK 428
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQqKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 971393678  429 LMALSHRTLQVLIKQEIQRKSGYAIQADEEQLRVQLDIIQCELNAPTQFRGRLNELMSQ 487
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 503-541 6.72e-16

Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts nucleocytoplasmic transport and contains multiple copies of nucleoporins (nups). This is the C-terminal interacting domain found on Nup54. Nup45 is a splice variant of Nup58 with an identical alpha-helical region. Nup54 along with Nup62 and Nup58 are essential for nuclear transport. The C-terminal part of the alpha-helical region of Nup54 interacts with a C-terminal part of the alpha-helical region of Nup58. Interestingly, this region appears in two distinct conformations: a single helix and a helix-loop-helix, termed 'straight' and 'bent'. Whereas the straight conformer consists of a 34 residues long alpha helix (residues 460-493), the bent conformer is composed of two alpha helices, each 13 residues long, connected by a central loop (N helix, residues 460-472; C helix, residues 477-489).


:

Pssm-ID: 465767  Cd Length: 39  Bit Score: 71.30  E-value: 6.72e-16
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 971393678  503 YYIDSDLLREIKQHLKQQQEGLSHLISIIKDDLEDIKLI 541
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 350-487 6.89e-62

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: 200.11  E-value: 6.89e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678  350 PPAGVDPIIWEQAKVDNPDPDKLIPVPMVGFKELLRRLKVQDQMTKQHQTRLDIISEDISELQ-KNQTTTMAKIAQYKRK 428
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQqKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 971393678  429 LMALSHRTLQVLIKQEIQRKSGYAIQADEEQLRVQLDIIQCELNAPTQFRGRLNELMSQ 487
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 503-541 6.72e-16

Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts nucleocytoplasmic transport and contains multiple copies of nucleoporins (nups). This is the C-terminal interacting domain found on Nup54. Nup45 is a splice variant of Nup58 with an identical alpha-helical region. Nup54 along with Nup62 and Nup58 are essential for nuclear transport. The C-terminal part of the alpha-helical region of Nup54 interacts with a C-terminal part of the alpha-helical region of Nup58. Interestingly, this region appears in two distinct conformations: a single helix and a helix-loop-helix, termed 'straight' and 'bent'. Whereas the straight conformer consists of a 34 residues long alpha helix (residues 460-493), the bent conformer is composed of two alpha helices, each 13 residues long, connected by a central loop (N helix, residues 460-472; C helix, residues 477-489).


Pssm-ID: 465767  Cd Length: 39  Bit Score: 71.30  E-value: 6.72e-16
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 971393678  503 YYIDSDLLREIKQHLKQQQEGLSHLISIIKDDLEDIKLI 541
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
380-547 8.08e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 38.98  E-value: 8.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678 380 FKELLRRLKVQDQMTKQHQT---RLDIISEDISELQKNQTTTMAKIAQYKRKLMALSHRTLQVLIKQEIQRKSGYAIQAD 456
Cdd:COG4717   73 LKELEEELKEAEEKEEEYAElqeELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELE 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678 457 E-----EQLRVQLDIIQCELnapTQFRGRLNELMSQIRMQNHFGAVRAEERYYIDSDLLREIKQHLKQQQEGLSHLISII 531
Cdd:COG4717  153 ErleelRELEEELEELEAEL---AELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEEL 229

                        170
                 ....*....|....*.
gi 971393678 532 kDDLEDIKLIEHELNE 547
Cdd:COG4717  230 -EQLENELEAAALEER 244
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 350-487 6.89e-62

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: 200.11  E-value: 6.89e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678  350 PPAGVDPIIWEQAKVDNPDPDKLIPVPMVGFKELLRRLKVQDQMTKQHQTRLDIISEDISELQ-KNQTTTMAKIAQYKRK 428
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQqKHDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 971393678  429 LMALSHRTLQVLIKQEIQRKSGYAIQADEEQLRVQLDIIQCELNAPTQFRGRLNELMSQ 487
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 503-541 6.72e-16

Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts nucleocytoplasmic transport and contains multiple copies of nucleoporins (nups). This is the C-terminal interacting domain found on Nup54. Nup45 is a splice variant of Nup58 with an identical alpha-helical region. Nup54 along with Nup62 and Nup58 are essential for nuclear transport. The C-terminal part of the alpha-helical region of Nup54 interacts with a C-terminal part of the alpha-helical region of Nup58. Interestingly, this region appears in two distinct conformations: a single helix and a helix-loop-helix, termed 'straight' and 'bent'. Whereas the straight conformer consists of a 34 residues long alpha helix (residues 460-493), the bent conformer is composed of two alpha helices, each 13 residues long, connected by a central loop (N helix, residues 460-472; C helix, residues 477-489).


Pssm-ID: 465767  Cd Length: 39  Bit Score: 71.30  E-value: 6.72e-16
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 971393678  503 YYIDSDLLREIKQHLKQQQEGLSHLISIIKDDLEDIKLI 541
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
380-547 8.08e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 38.98  E-value: 8.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678 380 FKELLRRLKVQDQMTKQHQT---RLDIISEDISELQKNQTTTMAKIAQYKRKLMALSHRTLQVLIKQEIQRKSGYAIQAD 456
Cdd:COG4717   73 LKELEEELKEAEEKEEEYAElqeELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELE 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678 457 E-----EQLRVQLDIIQCELnapTQFRGRLNELMSQIRMQNHFGAVRAEERYYIDSDLLREIKQHLKQQQEGLSHLISII 531
Cdd:COG4717  153 ErleelRELEEELEELEAEL---AELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEEL 229

                        170
                 ....*....|....*.
gi 971393678 532 kDDLEDIKLIEHELNE 547
Cdd:COG4717  230 -EQLENELEAAALEER 244
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
360-549 9.75e-03

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 38.74  E-value: 9.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678  360 EQAKVDNPDPDklipvpmvgFKELLRRLKVQDQMTKQHQTRLDIISEDISELQKNQTTTMAKIAQYKRKLMALSHRTLQV 439
Cdd:COG4913   676 ELERLDASSDD---------LAALEEQLEELEAELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLEAAEDLARLE 746

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971393678  440 LIKQEIQRKSGYAIQADEEQLRVQLDIIQCELNAPT-QFRGRLNELMSQIRMQ-----NHFGAVRAEERYYIdsDLLREI 513
Cdd:COG4913   747 LRALLEERFAAALGDAVERELRENLEERIDALRARLnRAEEELERAMRAFNREwpaetADLDADLESLPEYL--ALLDRL 824

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 971393678  514 KQH-------------LKQQQEGLSHLISIIKDDLEDIKLIEHELNESL 549
Cdd:COG4913   825 EEDglpeyeerfkellNENSIEFVADLLSKLRRAIREIKERIDPLNDSL 873
 
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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