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Conserved domains on  [gi|19922100|ref|NP_610783|]
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nucleoporin 54kD [Drosophila melanogaster]

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, ...
 409-546 7.15e-60

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: 195.88  E-value: 7.15e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100   409 PPRGVDPRMWRQANSDNPDPTLYIPVPMVGFNDLKWRVKCQEQETDTHALYIKKVESELTELKKRHATAT-AKILEHKRK 487
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETsVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 19922100   488 LAELSHRILRIIVKQECTRKVGTSLTPEEEALRTKLQNMLAVVSAPTQFKGRLSELLSQ 546
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 125-220 8.93e-07

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: 47.23  E-value: 8.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100   125 GLFGAPATSAAppafSGFGQQAAASTAPASGFSGFGTTTTSAPAFGGFGTSQSTGFGGGAFGSTFGKPANTTvtpgfggf 204
Cdd:pfam13634   1 GLFGAATSTSG----GLFGNTSTTAASGGGLFGAASTATATTSGGGLFGNSSSNAPSGGLFGATNTTTQTAT-------- 68

                          90
                  ....*....|....*.
gi 19922100   205 ggTSFMLGQPQQQPAP 220
Cdd:pfam13634  69 --GGGLFGNNAATTTS 82
Nup54_C super family cl39773
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 562-600 1.32e-05

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).


The actual alignment was detected with superfamily member pfam18437:

Pssm-ID: 465767  Cd Length: 39  Bit Score: 42.41  E-value: 1.32e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 19922100   562 YALDKEAEDEMKTFLTMQQRAMEVLSDTVNKDLRALDVI 600
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 2-91 1.77e-03

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: 37.98  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100     2 SFFGSNTS-----LGATSTPAKTTGGLFGSPfGGTAATSQPAPAFGAQATSTPAfgaqpaTSAFGAGSAFGataaapafg 76
Cdd:pfam13634   1 GLFGAATStsgglFGNTSTTAASGGGLFGAA-STATATTSGGGLFGNSSSNAPS------GGLFGATNTTT--------- 64

                          90
                  ....*....|....*
gi 19922100    77 aatgTSAFGGSAFGS 91
Cdd:pfam13634  65 ----QTATGGGLFGN 75
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 409-546 7.15e-60

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: 195.88  E-value: 7.15e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100   409 PPRGVDPRMWRQANSDNPDPTLYIPVPMVGFNDLKWRVKCQEQETDTHALYIKKVESELTELKKRHATAT-AKILEHKRK 487
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETsVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 19922100   488 LAELSHRILRIIVKQECTRKVGTSLTPEEEALRTKLQNMLAVVSAPTQFKGRLSELLSQ 546
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 125-220 8.93e-07

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: 47.23  E-value: 8.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100   125 GLFGAPATSAAppafSGFGQQAAASTAPASGFSGFGTTTTSAPAFGGFGTSQSTGFGGGAFGSTFGKPANTTvtpgfggf 204
Cdd:pfam13634   1 GLFGAATSTSG----GLFGNTSTTAASGGGLFGAASTATATTSGGGLFGNSSSNAPSGGLFGATNTTTQTAT-------- 68

                          90
                  ....*....|....*.
gi 19922100   205 ggTSFMLGQPQQQPAP 220
Cdd:pfam13634  69 --GGGLFGNNAATTTS 82
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 562-600 1.32e-05

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: 42.41  E-value: 1.32e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 19922100   562 YALDKEAEDEMKTFLTMQQRAMEVLSDTVNKDLRALDVI 600
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 2-91 1.77e-03

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: 37.98  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100     2 SFFGSNTS-----LGATSTPAKTTGGLFGSPfGGTAATSQPAPAFGAQATSTPAfgaqpaTSAFGAGSAFGataaapafg 76
Cdd:pfam13634   1 GLFGAATStsgglFGNTSTTAASGGGLFGAA-STATATTSGGGLFGNSSSNAPS------GGLFGATNTTT--------- 64

                          90
                  ....*....|....*
gi 19922100    77 aatgTSAFGGSAFGS 91
Cdd:pfam13634  65 ----QTATGGGLFGN 75
 
Name Accession Description Interval E-value
Nup54 pfam13874
Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, ...
 409-546 7.15e-60

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: 195.88  E-value: 7.15e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100   409 PPRGVDPRMWRQANSDNPDPTLYIPVPMVGFNDLKWRVKCQEQETDTHALYIKKVESELTELKKRHATAT-AKILEHKRK 487
Cdd:pfam13874   1 PPAGIDEELWEQALSDNPDPEKLVPVPVIGFEDLKKRLKLQEEEVAAHRERLHEINEKLTELQQKHDLETsVRIEEAKRR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 19922100   488 LAELSHRILRIIVKQECTRKVGTSLTPEEEALRTKLQNMLAVVSAPTQFKGRLSELLSQ 546
Cdd:pfam13874  81 HTELSHRLLRLARKLEVLRNRGYALSPEEEQLRKRLETLLKQLNDPAQFKGRLNELWAR 139
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 125-220 8.93e-07

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: 47.23  E-value: 8.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100   125 GLFGAPATSAAppafSGFGQQAAASTAPASGFSGFGTTTTSAPAFGGFGTSQSTGFGGGAFGSTFGKPANTTvtpgfggf 204
Cdd:pfam13634   1 GLFGAATSTSG----GLFGNTSTTAASGGGLFGAASTATATTSGGGLFGNSSSNAPSGGLFGATNTTTQTAT-------- 68

                          90
                  ....*....|....*.
gi 19922100   205 ggTSFMLGQPQQQPAP 220
Cdd:pfam13634  69 --GGGLFGNNAATTTS 82
Nup54_C pfam18437
Nup54 C-terminal interacting domain; The mammalian nuclear pore complex (NPC) conducts ...
 562-600 1.32e-05

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: 42.41  E-value: 1.32e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 19922100   562 YALDKEAEDEMKTFLTMQQRAMEVLSDTVNKDLRALDVI 600
Cdd:pfam18437   1 YSMDADLQDEIKQFLKQQQEGLSHLINIIKDDLEDLKLI 39
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 121-196 2.81e-05

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: 42.99  E-value: 2.81e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19922100   121 TSQAGLFGAPATSAAPPAfSGFGQqAAASTAPASGFSGFGTTTTSAPAFGGFG---TSQSTGFGGGAFGSTFGKPANTT 196
Cdd:pfam13634   8 STSGGLFGNTSTTAASGG-GLFGA-ASTATATTSGGGLFGNSSSNAPSGGLFGatnTTTQTATGGGLFGNNAATTTSTT 84
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 2-91 1.77e-03

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: 37.98  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19922100     2 SFFGSNTS-----LGATSTPAKTTGGLFGSPfGGTAATSQPAPAFGAQATSTPAfgaqpaTSAFGAGSAFGataaapafg 76
Cdd:pfam13634   1 GLFGAATStsgglFGNTSTTAASGGGLFGAA-STATATTSGGGLFGNSSSNAPS------GGLFGATNTTT--------- 64

                          90
                  ....*....|....*
gi 19922100    77 aatgTSAFGGSAFGS 91
Cdd:pfam13634  65 ----QTATGGGLFGN 75
 
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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