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Conserved domains on  [gi|15221725|ref|NP_173841|]
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nuclear pore complex protein [Arabidopsis thaliana]

Protein Classification

Nucleoporin_FG and Nup54 domain-containing protein( domain architecture ID 10614400)

Nucleoporin_FG and Nup54 domain-containing protein

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, ...
162-305 7.71e-37

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: 130.39  E-value: 7.71e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221725   162 KPAAVSDIMWAEAMsklegMDSTERERLWPQLVQGFKDLSQRLKLQDEVLVSDRDRIKTTQSNVKMLQRHLQASTFPSIE 241
Cdd:pfam13874   1 PPAGIDEELWEQAL-----SDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIE 75
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15221725   242 RLRQKEQSLQRRMLRVMRIIEGLEGKGFrlPLTKGEAELSEKLTAITRQVKGPgAELSRRVQSL 305
Cdd:pfam13874  76 EAKRRHTELSHRLLRLARKLEVLRNRGY--ALSPEEEQLRKRLETLLKQLNDP-AQFKGRLNEL 136
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
1-42 4.75e-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: 38.75  E-value: 4.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15221725     1 MFG--TPSSSPSFGTPSSTPA-----FGTSSPAFGTPSATPAFGTPSNP 42
Cdd:pfam13634   2 LFGaaTSTSGGLFGNTSTTAAsggglFGAASTATATTSGGGLFGNSSSN 50
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
162-305 7.71e-37

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: 130.39  E-value: 7.71e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221725   162 KPAAVSDIMWAEAMsklegMDSTERERLWPQLVQGFKDLSQRLKLQDEVLVSDRDRIKTTQSNVKMLQRHLQASTFPSIE 241
Cdd:pfam13874   1 PPAGIDEELWEQAL-----SDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIE 75
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15221725   242 RLRQKEQSLQRRMLRVMRIIEGLEGKGFrlPLTKGEAELSEKLTAITRQVKGPgAELSRRVQSL 305
Cdd:pfam13874  76 EAKRRHTELSHRLLRLARKLEVLRNRGY--ALSPEEEQLRKRLETLLKQLNDP-AQFKGRLNEL 136
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
1-42 4.75e-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: 38.75  E-value: 4.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15221725     1 MFG--TPSSSPSFGTPSSTPA-----FGTSSPAFGTPSATPAFGTPSNP 42
Cdd:pfam13634   2 LFGaaTSTSGGLFGNTSTTAAsggglFGAASTATATTSGGGLFGNSSSN 50
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
162-305 7.71e-37

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: 130.39  E-value: 7.71e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221725   162 KPAAVSDIMWAEAMsklegMDSTERERLWPQLVQGFKDLSQRLKLQDEVLVSDRDRIKTTQSNVKMLQRHLQASTFPSIE 241
Cdd:pfam13874   1 PPAGIDEELWEQAL-----SDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETSVRIE 75
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15221725   242 RLRQKEQSLQRRMLRVMRIIEGLEGKGFrlPLTKGEAELSEKLTAITRQVKGPgAELSRRVQSL 305
Cdd:pfam13874  76 EAKRRHTELSHRLLRLARKLEVLRNRGY--ALSPEEEQLRKRLETLLKQLNDP-AQFKGRLNEL 136
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
1-42 4.75e-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: 38.75  E-value: 4.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15221725     1 MFG--TPSSSPSFGTPSSTPA-----FGTSSPAFGTPSATPAFGTPSNP 42
Cdd:pfam13634   2 LFGaaTSTSGGLFGNTSTTAAsggglFGAASTATATTSGGGLFGNSSSN 50
 
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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