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Conserved domains on  [gi|1207158539|ref|XP_021324445|]
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nucleoporin p54 isoform X12 [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, ...
 306-443 7.61e-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: 198.96  E-value: 7.61e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539 306 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 384
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158539 385 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 443
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 459-497 2.38e-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: 63.98  E-value: 2.38e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158539 459 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 497
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG2 super family cl37900
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 6-87 3.74e-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: 43.12  E-value: 3.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539   6 GGASGSASLTGTGFGAPTTTSASTGFGFGTGAFGgfgSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS------ 77
Cdd:pfam15967  60 GGLFGQKPATGFTFGTPASSTAATGPTGLTLGTP---AATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvlt 136

                          90
                  ....*....|..
gi 1207158539  78 --SAPAPASGFT 87
Cdd:pfam15967 137 stAAQQGATGFT 148
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 306-443 7.61e-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: 198.96  E-value: 7.61e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539 306 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 384
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158539 385 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 443
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 459-497 2.38e-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: 63.98  E-value: 2.38e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158539 459 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 497
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 6-87 3.74e-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: 43.12  E-value: 3.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539   6 GGASGSASLTGTGFGAPTTTSASTGFGFGTGAFGgfgSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS------ 77
Cdd:pfam15967  60 GGLFGQKPATGFTFGTPASSTAATGPTGLTLGTP---AATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvlt 136

                          90
                  ....*....|..
gi 1207158539  78 --SAPAPASGFT 87
Cdd:pfam15967 137 stAAQQGATGFT 148
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
337-483 1.09e-03

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 41.68  E-value: 1.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539 337 RELLRRLKIQEQMTKQHQTRVDIISTDISELQRNQATTAAKITQYKRKLMDLSHRVLQVLIRQEVQRKSGYAVQLDE--- 413
Cdd:COG4717    77 EEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELEErle 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207158539 414 --EHLRVQLETIQSELnapTQFKGRLNELMSQIRMQNHFGAVRAEERYRVDADLLREIRQHLKHQQEGLSHL 483
Cdd:COG4717   157 elRELEEELEELEAEL---AELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEEL 225
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 306-443 7.61e-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: 198.96  E-value: 7.61e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539 306 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 384
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158539 385 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 443
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 459-497 2.38e-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: 63.98  E-value: 2.38e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158539 459 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 497
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 6-87 3.74e-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: 43.12  E-value: 3.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539   6 GGASGSASLTGTGFGAPTTTSASTGFGFGTGAFGgfgSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS------ 77
Cdd:pfam15967  60 GGLFGQKPATGFTFGTPASSTAATGPTGLTLGTP---AATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvlt 136

                          90
                  ....*....|..
gi 1207158539  78 --SAPAPASGFT 87
Cdd:pfam15967 137 stAAQQGATGFT 148
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 5-113 4.37e-04

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: 39.14  E-value: 4.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539   5 FGGASGSASLTGTGFGAPTTTsastgfgfgtgafggfgstTTSAGTGSSFSFSTPANTGSSLF-------NTQSKGFGFS 77
Cdd:pfam13634  14 FGNTSTTAASGGGLFGAASTA-------------------TATTSGGGLFGNSSSNAPSGGLFgatntttQTATGGGLFG 74

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1207158539  78 SAPAPAsgftgalgggalgfggfgalQNTQQGGVFG 113
Cdd:pfam13634  75 NNAATT--------------------TSTTGGGLFG 90
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
337-483 1.09e-03

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 41.68  E-value: 1.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539 337 RELLRRLKIQEQMTKQHQTRVDIISTDISELQRNQATTAAKITQYKRKLMDLSHRVLQVLIRQEVQRKSGYAVQLDE--- 413
Cdd:COG4717    77 EEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELEErle 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207158539 414 --EHLRVQLETIQSELnapTQFKGRLNELMSQIRMQNHFGAVRAEERYRVDADLLREIRQHLKHQQEGLSHL 483
Cdd:COG4717   157 elRELEEELEELEAEL---AELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEEL 225
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 3-87 5.88e-03

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: 39.27  E-value: 5.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158539   3 FNFGGASGSASLTGTGF--GA-----PTTTSASTGFGFGTGAFGGFGSTTTSAGTGSS---------FSFSTPANTGSSL 66
Cdd:pfam15967   4 FSFGGGPGSTATAGGGFsfGAaaasnPGSTGGFSFGTLGAAPAATATTTTATLGLGGGlfgqkpatgFTFGTPASSTAAT 83

                          90       100
                  ....*....|....*....|.
gi 1207158539  67 FNTQSKGFGFSSAPAPASGFT 87
Cdd:pfam15967  84 GPTGLTLGTPAATTAASTGFS 104
 
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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