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Conserved domains on  [gi|1207158507|ref|XP_021324437|]
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nucleoporin p54 isoform X5 [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, ...
 350-487 6.21e-63

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: 202.81  E-value: 6.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507 350 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 428
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158507 429 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 487
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 503-541 4.63e-14

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: 66.29  E-value: 4.63e-14
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158507 503 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 541
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG2 super family cl37900
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 3-131 1.78e-06

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: 50.82  E-value: 1.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507   3 FNFGGASGSASLTGTGFGAPTTTSASTGFGFGTGFGPLVCSAGPGPAPSAAAVSFGG--FGLGPAAPvFS-----FGSGL 75
Cdd:pfam15967   4 FSFGGGPGSTATAGGGFSFGAAAASNPGSTGGFSFGTLGAAPAATATTTTATLGLGGglFGQKPATG-FTfgtpaSSTAA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1207158507  76 GGAAGAFGGFGSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS--------SAPAPASGFT 131
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, ...
 350-487 6.21e-63

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: 202.81  E-value: 6.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507 350 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 428
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158507 429 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 487
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 503-541 4.63e-14

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: 66.29  E-value: 4.63e-14
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158507 503 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 541
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 3-131 1.78e-06

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: 50.82  E-value: 1.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507   3 FNFGGASGSASLTGTGFGAPTTTSASTGFGFGTGFGPLVCSAGPGPAPSAAAVSFGG--FGLGPAAPvFS-----FGSGL 75
Cdd:pfam15967   4 FSFGGGPGSTATAGGGFSFGAAAASNPGSTGGFSFGTLGAAPAATATTTTATLGLGGglFGQKPATG-FTfgtpaSSTAA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1207158507  76 GGAAGAFGGFGSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS--------SAPAPASGFT 131
Cdd:pfam15967  83 TGPTGLTLGTPAATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvltstAAQQGATGFT 148
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
381-527 4.30e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 43.22  E-value: 4.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507 381 RELLRRLKIQEQMTKQHQTRVDIISTDISELQRNQATTAAKITQYKRKLMDLSHRVLQVLIRQEVQRKSGYAVQLDE--- 457
Cdd:COG4717    77 EEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELEErle 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207158507 458 --EHLRVQLETIQSELnapTQFKGRLNELMSQIRMQNHFGAVRAEERYRVDADLLREIRQHLKHQQEGLSHL 527
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, ...
 350-487 6.21e-63

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: 202.81  E-value: 6.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507 350 PPAGVDPIIWEQAKVDNPDPEKLIPVPMVGFRELLRRLKIQEQMTKQHQTRVDIISTDISELQRN-QATTAAKITQYKRK 428
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKhDLETSVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207158507 429 LMDLSHRVLQVLIRQEVQRKSGYAVQLDEEHLRVQLETIQSELNAPTQFKGRLNELMSQ 487
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 503-541 4.63e-14

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: 66.29  E-value: 4.63e-14
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207158507 503 YRVDADLLREIRQHLKHQQEGLSHLISVIKDDLDDIKTI 541
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 3-131 1.78e-06

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: 50.82  E-value: 1.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507   3 FNFGGASGSASLTGTGFGAPTTTSASTGFGFGTGFGPLVCSAGPGPAPSAAAVSFGG--FGLGPAAPvFS-----FGSGL 75
Cdd:pfam15967   4 FSFGGGPGSTATAGGGFSFGAAAASNPGSTGGFSFGTLGAAPAATATTTTATLGLGGglFGQKPATG-FTfgtpaSSTAA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1207158507  76 GGAAGAFGGFGSTTTSAGTGSSFSFSTPANTGS--SLFNTQSKGFGFS--------SAPAPASGFT 131
Cdd:pfam15967  83 TGPTGLTLGTPAATTAASTGFSLGFNKPAASATpfSLPASSTSGGGLSlgsvltstAAQQGATGFT 148
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
381-527 4.30e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 43.22  E-value: 4.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507 381 RELLRRLKIQEQMTKQHQTRVDIISTDISELQRNQATTAAKITQYKRKLMDLSHRVLQVLIRQEVQRKSGYAVQLDE--- 457
Cdd:COG4717    77 EEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLEELEErle 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207158507 458 --EHLRVQLETIQSELnapTQFKGRLNELMSQIRMQNHFGAVRAEERYRVDADLLREIRQHLKHQQEGLSHL 527
Cdd:COG4717   157 elRELEEELEELEAEL---AELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEEL 225
HOOK pfam05622
HOOK protein coiled-coil region; This family consists of several HOOK1, 2 and 3 proteins from ...
 400-521 3.30e-03

HOOK protein coiled-coil region; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organizms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas this central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head. This entry includes the central coiled-coiled domain and the divergent C-terminal domain.


Pssm-ID: 461694 [Multi-domain]  Cd Length: 528  Bit Score: 40.06  E-value: 3.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507 400 RVDIISTDISELQ-RNQATTA--------------------------AKITQYKRKLMDLSHRVLQVLIRQEvqRKSGYA 452
Cdd:pfam05622  88 KCEELEKEVLELQhRNEELTSlaeeaqalkdemdilressdkvkkleATVETYKKKLEDLGDLRRQVKLLEE--RNAEYM 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507 453 ---VQLDEE-----HLRVQLETIQSELnapTQFKGRLNELMSQI--------RMQNHFGAV-RAEERYRVDADLLREIRQ 515
Cdd:pfam05622 166 qrtLQLEEElkkanALRGQLETYKRQV---QELHGKLSEESKKAdklefeykKLEEKLEALqKEKERLIIERDTLRETNE 242


                  ....*.
gi 1207158507 516 HLKHQQ 521
Cdd:pfam05622 243 ELRCAQ 248
Nucleoporin_FG2 pfam15967
Nucleoporin FG repeated region; Nucleoporin_FG2, or nucleoporin p58/p45, is a family of ...
 3-119 9.28e-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: 38.88  E-value: 9.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207158507   3 FNFGGASGSASLTGTG---FGAPTTTSASTGFGFGTGFGPlVCSAGPGPAPSAAAVSfGGFGLGPAAPVFSFGSGLGGAA 79
Cdd:pfam15967  71 FTFGTPASSTAATGPTgltLGTPAATTAASTGFSLGFNKP-AASATPFSLPASSTSG-GGLSLGSVLTSTAAQQGATGFT 148

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1207158507  80 GAFGGFGSTTTSAGTGSSFSfSTPANTGSSLF-NTQSKGFG 119
Cdd:pfam15967 149 LNLGGTPATTTAVSTGLSLG-STLTSLGGSLFqNTNSTGLG 188
 
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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