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Conserved domains on  [gi|1207158515|ref|XP_021324439|]
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nucleoporin p54 isoform X6 [Danio rerio]

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, ...
340-477 4.06e-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: 200.50  E-value: 4.06e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515 340 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 418
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158515 419 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 477
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
493-531 1.51e-13

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: 64.75  E-value: 1.51e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158515 493 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 531
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG2 super family cl37900
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
3-121 8.47e-04

Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of chordate nucleoporins. The proteins carry many repeats of the FG sequence motif.


The actual alignment was detected with superfamily member pfam15967:

Pssm-ID: 435043 [Multi-domain]  Cd Length: 586  Bit Score: 41.96  E-value: 8.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515   3 FNFGGA--SGSASAPGFSFKSSSSTP------FGFGASTTTTASSATGFGLTGTGFGA--------------PTTTSASt 60
Cdd:pfam15967   4 FSFGGGpgSTATAGGGFSFGAAAASNpgstggFSFGTLGAAPAATATTTTATLGLGGGlfgqkpatgftfgtPASSTAA- 82
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207158515  61 gfgfgTGGTGAFGGFGSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS--------SAPAPASGFT 121
Cdd:pfam15967  83 -----TGPTGLTLGTPAATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvltstAAQQGATGFT 148
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
340-477 4.06e-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: 200.50  E-value: 4.06e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515 340 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 418
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158515 419 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 477
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
493-531 1.51e-13

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: 64.75  E-value: 1.51e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158515 493 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 531
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
371-517 7.53e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 42.45  E-value: 7.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515 371 RELLRRLKIQEQMTKQHQTRVDIISTDISELQRNQATTAAKITQYKRKLMDLSHRVLQVLIRQEVQRKSGYAVQLDE--- 447
Cdd:COG4717    77 EEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELEErle 156
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207158515 448 --EHLRVQLETIQSELnapTQFKGRLNELMSQIRMQNHFGAVRAEERYRVDADLLREIRQHLKHQQEGLSHL 517
Cdd:COG4717   157 elRELEEELEELEAEL---AELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEEL 225
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
3-121 8.47e-04

Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of chordate nucleoporins. The proteins carry many repeats of the FG sequence motif.


Pssm-ID: 435043 [Multi-domain]  Cd Length: 586  Bit Score: 41.96  E-value: 8.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515   3 FNFGGA--SGSASAPGFSFKSSSSTP------FGFGASTTTTASSATGFGLTGTGFGA--------------PTTTSASt 60
Cdd:pfam15967   4 FSFGGGpgSTATAGGGFSFGAAAASNpgstggFSFGTLGAAPAATATTTTATLGLGGGlfgqkpatgftfgtPASSTAA- 82
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207158515  61 gfgfgTGGTGAFGGFGSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS--------SAPAPASGFT 121
Cdd:pfam15967  83 -----TGPTGLTLGTPAATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvltstAAQQGATGFT 148
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
340-477 4.06e-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: 200.50  E-value: 4.06e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515 340 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 418
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158515 419 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 477
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
493-531 1.51e-13

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: 64.75  E-value: 1.51e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158515 493 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 531
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
371-517 7.53e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 42.45  E-value: 7.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515 371 RELLRRLKIQEQMTKQHQTRVDIISTDISELQRNQATTAAKITQYKRKLMDLSHRVLQVLIRQEVQRKSGYAVQLDE--- 447
Cdd:COG4717    77 EEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELEErle 156
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207158515 448 --EHLRVQLETIQSELnapTQFKGRLNELMSQIRMQNHFGAVRAEERYRVDADLLREIRQHLKHQQEGLSHL 517
Cdd:COG4717   157 elRELEEELEELEAEL---AELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEEL 225
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
3-121 8.47e-04

Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of chordate nucleoporins. The proteins carry many repeats of the FG sequence motif.


Pssm-ID: 435043 [Multi-domain]  Cd Length: 586  Bit Score: 41.96  E-value: 8.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158515   3 FNFGGA--SGSASAPGFSFKSSSSTP------FGFGASTTTTASSATGFGLTGTGFGA--------------PTTTSASt 60
Cdd:pfam15967   4 FSFGGGpgSTATAGGGFSFGAAAASNpgstggFSFGTLGAAPAATATTTTATLGLGGGlfgqkpatgftfgtPASSTAA- 82
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207158515  61 gfgfgTGGTGAFGGFGSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS--------SAPAPASGFT 121
Cdd:pfam15967  83 -----TGPTGLTLGTPAATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvltstAAQQGATGFT 148
 
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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