Citrus Sinensis ID: 033411

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHVDG
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHHccccccccccEEEEEcccccccccccccccHHHHHHHHHHHccccccccccccccccccHHHHHHHHcccEEEEEHHHHHHHHHEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHHHHHHHHcccccccHEEEEEEEEccccccccccccccHHHHHHHHHHHcccccccHHHccHHHHccHHHHHHHccccEEEEEEEEEEEEEEEEEEEEEEcccc
Coil and Loop (DISEMBL)
mapvaplqfsLAERDIQAIVDAykeeptnpkyafkhllfsvtepqfrvkppgvsdIMWAEAMgklegmdstdrerLWPQLVQGFKdlsnrlkvpvVYFRHVAFWLEIHVHSFVCCFHVDG
Flexible Loop (DISEMBL)
mapvaplqfslaeRDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHVDG
Low Complexity Region (SEG)
MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHVDG
Disordered region (IsUnstruct)
**********LAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEAMGKLEGM**TDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHV**
Disordered Region (DISOPRED)
***********AERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEA*************RLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHVDG
Disordered Region (DISEMBL)
MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHVDG
Disordered Region (DISPRO)
*****PLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHVD*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEIHVHSFVCCFHVDG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
225425478	371	PREDICTED: nuclear pore complex protein	0.775	0.250	0.849	2e-42
297738423	265	unnamed protein product [Vitis vinifera]	0.775	0.350	0.849	7e-42
255547750	395	conserved hypothetical protein [Ricinus	0.775	0.235	0.860	8e-42
356566511	391	PREDICTED: uncharacterized protein LOC10	0.775	0.237	0.860	9e-42
224107623	270	predicted protein [Populus trichocarpa]	0.775	0.344	0.870	3e-41
15221725	377	uncharacterized protein [Arabidopsis tha	0.775	0.246	0.827	3e-41
297808793	263	hypothetical protein ARALYDRAFT_910872 [	0.775	0.353	0.827	4e-41
2829886	288	Hypothetical protein [Arabidopsis thalia	0.775	0.322	0.827	9e-41
449435057	389	PREDICTED: uncharacterized protein LOC10	0.775	0.239	0.838	1e-40
297851152	376	hypothetical protein ARALYDRAFT_472914 [	0.775	0.247	0.817	3e-40

>gi|225425478|ref|XP_002279552.1| PREDICTED: nuclear pore complex protein Nup54-like [Vitis vinifera]

 Score =  175 bits (444), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 79/93 (84%), Positives = 88/93 (94%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAPL FSLA+RD+QAIV+AY++EP NPKYAFKHLLFSVT+PQFRVKP G SDIMWAE
Sbjct: 107 MAPVAPLPFSLADRDVQAIVEAYRDEPGNPKYAFKHLLFSVTDPQFRVKPAGASDIMWAE 166

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AMGKLEGM+S+DRERLWPQLVQGFKDLS RLK+
Sbjct: 167 AMGKLEGMESSDRERLWPQLVQGFKDLSQRLKL 199

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738423|emb|CBI27624.3| unnamed protein product [Vitis vinifera]

 Score =  174 bits (441), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 79/93 (84%), Positives = 88/93 (94%)

Query: 1  MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
          MAPVAPL FSLA+RD+QAIV+AY++EP NPKYAFKHLLFSVT+PQFRVKP G SDIMWAE
Sbjct: 1  MAPVAPLPFSLADRDVQAIVEAYRDEPGNPKYAFKHLLFSVTDPQFRVKPAGASDIMWAE 60

Query: 61 AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
          AMGKLEGM+S+DRERLWPQLVQGFKDLS RLK+
Sbjct: 61 AMGKLEGMESSDRERLWPQLVQGFKDLSQRLKL 93

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547750|ref|XP_002514932.1| conserved hypothetical protein [Ricinus communis] gi|223545983|gb|EEF47486.1| conserved hypothetical protein [Ricinus communis]

 Score =  174 bits (440), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 80/93 (86%), Positives = 87/93 (93%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAPL FSL +RDIQAIVDAYKE+P NPKYAFK+LLFSVT+PQ RVKP GVSDIMWAE
Sbjct: 131 MAPVAPLPFSLCDRDIQAIVDAYKEDPGNPKYAFKYLLFSVTDPQHRVKPAGVSDIMWAE 190

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AM KLEGM+S+DRERLWPQLVQGFKDLSNRLK+
Sbjct: 191 AMAKLEGMESSDRERLWPQLVQGFKDLSNRLKL 223

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356566511|ref|XP_003551474.1| PREDICTED: uncharacterized protein LOC100797030 [Glycine max]

 Score =  174 bits (440), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 80/93 (86%), Positives = 86/93 (92%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MA VAP+ FSLA+RD+Q IVDAYKE+P NPKYAFKHLLFSVTEPQFRVKP GVSDIMWAE
Sbjct: 125 MANVAPVPFSLADRDVQTIVDAYKEDPGNPKYAFKHLLFSVTEPQFRVKPAGVSDIMWAE 184

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AMGKLEGM+S DRERLWPQLVQGFKDLS RLK+
Sbjct: 185 AMGKLEGMESADRERLWPQLVQGFKDLSQRLKI 217

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224107623|ref|XP_002314540.1| predicted protein [Populus trichocarpa] gi|222863580|gb|EEF00711.1| predicted protein [Populus trichocarpa]

 Score =  172 bits (435), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 81/93 (87%), Positives = 86/93 (92%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAPL FSLA+RDIQAIVDAYKEEP NPKYAFK+LL SVT+PQ RVKP GVS+IMWAE
Sbjct: 13  MAPVAPLPFSLADRDIQAIVDAYKEEPGNPKYAFKYLLLSVTDPQHRVKPAGVSEIMWAE 72

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AM KLEGMDS DRERLWPQLVQGFKDLSNRLK+
Sbjct: 73  AMAKLEGMDSADRERLWPQLVQGFKDLSNRLKL 105

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221725|ref|NP_173841.1| uncharacterized protein [Arabidopsis thaliana] gi|26450407|dbj|BAC42318.1| unknown protein [Arabidopsis thaliana] gi|28827332|gb|AAO50510.1| unknown protein [Arabidopsis thaliana] gi|332192394|gb|AEE30515.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  172 bits (435), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 77/93 (82%), Positives = 88/93 (94%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAP+ +SLA+RD+QAI++AYKE+PTNPKYAF+HLLFSVTEPQ+RVKP  VSDIMWAE
Sbjct: 114 MAPVAPIPYSLADRDVQAIIEAYKEDPTNPKYAFQHLLFSVTEPQYRVKPAAVSDIMWAE 173

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AM KLEGMDST+RERLWPQLVQGFKDLS RLK+
Sbjct: 174 AMSKLEGMDSTERERLWPQLVQGFKDLSQRLKL 206

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297808793|ref|XP_002872280.1| hypothetical protein ARALYDRAFT_910872 [Arabidopsis lyrata subsp. lyrata] gi|297318117|gb|EFH48539.1| hypothetical protein ARALYDRAFT_910872 [Arabidopsis lyrata subsp. lyrata]

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 77/93 (82%), Positives = 88/93 (94%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAP+ +SLA+RD+QAI++AYKE+PTNPKYAF+HLLFSVTEPQ+RVKP  VSDIMWAE
Sbjct: 109 MAPVAPIPYSLADRDVQAIIEAYKEDPTNPKYAFQHLLFSVTEPQYRVKPAAVSDIMWAE 168

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AM KLEGMDST+RERLWPQLVQGFKDLS RLK+
Sbjct: 169 AMSKLEGMDSTERERLWPQLVQGFKDLSQRLKL 201

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2829886|gb|AAC00594.1| Hypothetical protein [Arabidopsis thaliana]

 Score =  170 bits (431), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 77/93 (82%), Positives = 88/93 (94%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAP+ +SLA+RD+QAI++AYKE+PTNPKYAF+HLLFSVTEPQ+RVKP  VSDIMWAE
Sbjct: 114 MAPVAPIPYSLADRDVQAIIEAYKEDPTNPKYAFQHLLFSVTEPQYRVKPAAVSDIMWAE 173

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AM KLEGMDST+RERLWPQLVQGFKDLS RLK+
Sbjct: 174 AMSKLEGMDSTERERLWPQLVQGFKDLSQRLKL 206

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449435057|ref|XP_004135312.1| PREDICTED: uncharacterized protein LOC101211067 [Cucumis sativus] gi|449494920|ref|XP_004159683.1| PREDICTED: uncharacterized LOC101211067 [Cucumis sativus]

 Score =  170 bits (430), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 78/93 (83%), Positives = 86/93 (92%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAPL FSLA+RDIQAIV+AYK++  NPKYAFKHLLFSVT+PQ+R KPPGVSDIMWAE
Sbjct: 125 MAPVAPLPFSLADRDIQAIVEAYKDDAGNPKYAFKHLLFSVTDPQYRTKPPGVSDIMWAE 184

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AM KLEGM+S DRERLWPQLVQGFKDLS RLK+
Sbjct: 185 AMAKLEGMESADRERLWPQLVQGFKDLSQRLKI 217

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297851152|ref|XP_002893457.1| hypothetical protein ARALYDRAFT_472914 [Arabidopsis lyrata subsp. lyrata] gi|297339299|gb|EFH69716.1| hypothetical protein ARALYDRAFT_472914 [Arabidopsis lyrata subsp. lyrata]

 Score =  168 bits (426), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 76/93 (81%), Positives = 86/93 (92%)

Query: 1   MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
           MAPVAP+ +SLA+RD+Q I++AYKE PTNPKYAF+HLLFSVTEPQ+RVKP  VSDIMWAE
Sbjct: 113 MAPVAPIPYSLADRDVQVIIEAYKEGPTNPKYAFQHLLFSVTEPQYRVKPAAVSDIMWAE 172

Query: 61  AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
           AM KLEGMDST+RERLWPQLVQGFKDLS RLK+
Sbjct: 173 AMSKLEGMDSTERERLWPQLVQGFKDLSQRLKL 205

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
TAIR|locus:2032417	377	AT1G24310 "AT1G24310" [Arabido	0.775	0.246	0.827	1.4e-39

TAIR|locus:2032417 AT1G24310 "AT1G24310" [Arabidopsis thaliana (taxid:3702)]

 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 77/93 (82%), Positives = 88/93 (94%)

Query:     1 MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVTEPQFRVKPPGVSDIMWAE 60
             MAPVAP+ +SLA+RD+QAI++AYKE+PTNPKYAF+HLLFSVTEPQ+RVKP  VSDIMWAE
Sbjct:   114 MAPVAPIPYSLADRDVQAIIEAYKEDPTNPKYAFQHLLFSVTEPQYRVKPAAVSDIMWAE 173

Query:    61 AMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
             AM KLEGMDST+RERLWPQLVQGFKDLS RLK+
Sbjct:   174 AMSKLEGMDSTERERLWPQLVQGFKDLSQRLKL 206


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.325   0.139   0.448    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      120       120   0.00091  102 3  11 22  0.44    30
                                                     29  0.48    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  590 (63 KB)
  Total size of DFA:  141 KB (2086 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  13.15u 0.09s 13.24t   Elapsed:  00:00:01
  Total cpu time:  13.15u 0.09s 13.24t   Elapsed:  00:00:01
  Start:  Sat May 11 02:18:00 2013   End:  Sat May 11 02:18:01 2013

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0005730 "nucleolus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005635 "nuclear envelope" evidence=IDA

GO:0006406 "mRNA export from nucleus" evidence=RCA

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	120
pfam13874	141	pfam13874, Nup54, Nucleoporin complex subunit 54	1e-10

>gnl|CDD|222430 pfam13874, Nup54, Nucleoporin complex subunit 54

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 5/46 (10%)

Query: 48 VKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKV 93
            P G+    W +A+      D+ D  RL P  V GF++L  R+K+
Sbjct: 1  NPPAGIDPEKWEQAL-----EDNPDPNRLIPVPVIGFEELKQRVKL 41

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. Length = 141

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
KOG3091	508	consensus Nuclear pore complex, p54 component (sc	99.9
PF13874	141	Nup54: Nucleoporin complex subunit 54; PDB: 3T97_B	99.7

>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]

Probab=99.90  E-value=2.4e-24  Score=187.84  Aligned_cols=100  Identities=27%  Similarity=0.430  Sum_probs=91.7

Q ss_pred             CCCCCCcccCchHHHHHHHHHhhccCCCCCCCcceeeeccCC---CCCCcCCCCCCCHHHHHHHHhcCCCCCCCCCCCcc
Q 033411            1 MAPVAPLQFSLAERDIQAIVDAYKEEPTNPKYAFKHLLFSVT---EPQFRVKPPGVSDIMWAEAMGKLEGMDSTDRERLW   77 (120)
Q Consensus         1 ~~~~~~~~~~~~~~qi~~Ik~aW~~DP~sp~c~Fk~~fYNvv---dp~~~~kP~gvd~~~W~eAl~k~pg~dnpdp~~li   77 (120)
                      |++++|.|-+|.| +.+++.+.|  +++.|+|++.+|+||.+   |+.+|.||+|||+++|+|||     +||||++++|
T Consensus       258 ~a~~~~~p~~~~~-~~q~~~~~~--~~n~~~t~~~afv~~~~~q~e~~L~~kP~gVd~~~W~QA~-----~dnp~s~kli  329 (508)
T KOG3091|consen  258 VAGRIPAPQSLND-QVQKTLKEW--LLNTPKTRVLAFVYLSVAQTEAYLETKPAGVDQRIWRQAM-----KDNPPSNKLI  329 (508)
T ss_pred             cccCCCcchhHHH-HHHHHHHHH--hhcCCcchhhhhhccCHHHHHHHhcCCCCCcCHHHHHHHh-----hcCCCccccc
Confidence            5677888888988 888889999  99999999999999943   56678999999999999999     6999999999


Q ss_pred             ceecccHHHHHHHhhchHHHHHHHHHHHHhh
Q 033411           78 PQLVQGFKDLSNRLKVPVVYFRHVAFWLEIH  108 (120)
Q Consensus        78 PVl~~GF~dL~~R~k~Q~~~v~~~~~~l~~~  108 (120)
                      ||+|+||+||++|+|+|++++++|+.+|++-
T Consensus       330 PVpvvGF~dL~~R~K~Q~q~~~~~r~ri~~i  360 (508)
T KOG3091|consen  330 PVPVVGFEDLRQRLKVQDQEVKQHRIRINAI  360 (508)
T ss_pred             ceeccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999998863

>PF13874 Nup54: Nucleoporin complex subunit 54; PDB: 3T97_B

Probab=99.70  E-value=2.7e-18  Score=127.12  Aligned_cols=55  Identities=29%  Similarity=0.538  Sum_probs=8.3

Q ss_pred             CCCCCCCHHHHHHHHhcCCCCCCCCCCCccceecccHHHHHHHhhchHHHHHHHHHHHHh
Q 033411           48 VKPPGVSDIMWAEAMGKLEGMDSTDRERLWPQLVQGFKDLSNRLKVPVVYFRHVAFWLEI  107 (120)
Q Consensus        48 ~kP~gvd~~~W~eAl~k~pg~dnpdp~~liPVl~~GF~dL~~R~k~Q~~~v~~~~~~l~~  107 (120)
                      +||+|+|+.+|++|+     .+||||++||||+++||+||.+|+++|++++++++.+|+.
T Consensus         1 ~~P~~~d~~~W~~A~-----~~nPdP~~~~Pv~i~GF~dL~~R~~~Q~~~~~~~~~~l~~   55 (141)
T PF13874_consen    1 QPPPGIDEELWEQAL-----RDNPDPSRLIPVPIIGFEDLKKRVEAQEEEIAQHRERLKE   55 (141)
T ss_dssp             --------------------------------------------------HHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHH-----HHCcCCcCeeeehhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999999999     5899999999999999999999999999999999888763

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

No hit with probability above 80.00