Citrus Sinensis ID: 039315

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-------
Protein Sequence
MVEATDMGALIGMAEKTDYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS
Secondary Structure (PSIPRED)
ccccccHHHHHHcccccHHHHHHcccccccccccccccHHHHHccccccccccccccccccccccccccHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHcccccHHHccccccccccccccccccHcccccccccccccccccccccccccccHHHHcccc
Coil and Loop (DISEMBL)
MVEATDMGALIGMAektdyqrkrhreddrhahetskrsadfesrrnsdhdsrpeknprfresgdsdddedddrkqrs
Flexible Loop (DISEMBL)
mveatdmgaligmaektdyqrkrhreddrhahetskrsadfesrrnsdhdsrpeknprfresgdsdddedddrkqrs
Low Complexity Region (SEG)
MVEATDMGALIGMAEKTDYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFResgdsdddedddRKQRS
Disordered region (IsUnstruct)
*****************************************************************************
Disordered Region (DISOPRED)
*****DMGALIGMAE**************************************************************
Disordered Region (DISEMBL)
MVEATDMGALIGMAEKT************************************************************
Disordered Region (DISPRO)
***************K*************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVEATDMGALIGMAEKTDYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	77	2.2.26 [Sep-21-2011]
Q9XFD1	257	Nuclear cap-binding prote	yes	no	0.779	0.233	0.683	2e-08

>sp|Q9XFD1|NCBP2_ARATH Nuclear cap-binding protein subunit 2 OS=Arabidopsis thaliana GN=CBP20 PE=1 SV=1

 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 41/60 (68%), Positives = 50/60 (83%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS 77
           DY RKR R+DDR+  + S+R+ D ESRR++D D RPEKNPRFRESGDSDDD +DDRK+RS
Sbjct: 198 DYHRKRQRDDDRYGRDNSRRNTDHESRRDTDSDMRPEKNPRFRESGDSDDDGEDDRKRRS 257

Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing and RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs). The CBC complex is involved in miRNA-mediated RNA interference and is required for primary miRNA processing. In the CBC complex, CBP20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires ABH1/CBP80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. CBP20 also plays a role in stabilization of ABH1/CBP80 and ABH1/CBP80 localization to the nucleus. Involved in flowering regulation via its interaction with FRIGIDA.
Arabidopsis thaliana (taxid: 3702)

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	77
255553647	255	20 kD nuclear cap binding protein, putat	0.779	0.235	0.716	1e-14
224133438	263	predicted protein [Populus trichocarpa]	0.844	0.247	0.651	1e-13
224092924	255	predicted protein [Populus trichocarpa]	0.740	0.223	0.719	3e-13
356549892	258	PREDICTED: nuclear cap-binding protein s	0.779	0.232	0.766	7e-12
449438721	251	PREDICTED: nuclear cap-binding protein s	0.727	0.223	0.785	1e-11
225446445	253	PREDICTED: nuclear cap-binding protein s	0.766	0.233	0.796	3e-11
388501070	253	unknown [Lotus japonicus]	0.779	0.237	0.783	4e-11
302143336	132	unnamed protein product [Vitis vinifera]	0.766	0.446	0.796	8e-11
219944397	255	nuclear cap-binding protein CBP20 [Solan	0.779	0.235	0.75	8e-10
224460055	254	nuclear cap-binding protein [Nicotiana t	0.779	0.236	0.733	9e-09

>gi|255553647|ref|XP_002517864.1| 20 kD nuclear cap binding protein, putative [Ricinus communis] gi|223542846|gb|EEF44382.1| 20 kD nuclear cap binding protein, putative [Ricinus communis]

 Score = 83.6 bits (205), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 43/60 (71%), Positives = 53/60 (88%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS 77
           DY RKR R+DDR A E S+R++D ESRRN+D DSRPEKNPRFRESG+SD++E+DDRK+RS
Sbjct: 196 DYHRKRFRDDDRQAREPSRRTSDHESRRNNDPDSRPEKNPRFRESGNSDEEEEDDRKRRS 255

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133438|ref|XP_002328042.1| predicted protein [Populus trichocarpa] gi|222837451|gb|EEE75830.1| predicted protein [Populus trichocarpa]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/66 (65%), Positives = 54/66 (81%), Gaps = 1/66 (1%)

Query: 13  MAEKTDYQ-RKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDD 71
           + +  DY  RKRHREDDR   E+SKR++D ESRRN D DSRPEKNPRFRES +SDD+E+D
Sbjct: 198 LRQSGDYHHRKRHREDDRPPRESSKRTSDHESRRNFDPDSRPEKNPRFRESANSDDEEED 257

Query: 72  DRKQRS 77
           D++QR+
Sbjct: 258 DKQQRT 263

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224092924|ref|XP_002309756.1| predicted protein [Populus trichocarpa] gi|118488601|gb|ABK96113.1| unknown [Populus trichocarpa] gi|222852659|gb|EEE90206.1| predicted protein [Populus trichocarpa]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 50/57 (87%)

Query: 20  QRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQR 76
           QRKR+REDD+   E+SKR++D ESRRN D DSRPEKNPRFRES +SDD+E+DDR+QR
Sbjct: 198 QRKRNREDDQQPRESSKRTSDHESRRNFDPDSRPEKNPRFRESTNSDDEEEDDRQQR 254

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356549892|ref|XP_003543324.1| PREDICTED: nuclear cap-binding protein subunit 2-like [Glycine max]

 Score = 74.7 bits (182), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 46/60 (76%), Positives = 57/60 (95%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS 77
           DY RKRHR+D+RH HE+SKR++D ESRRN+DH+SRPEKNPRFRESGDSD+DE+DDRK+R+
Sbjct: 199 DYYRKRHRDDERHTHESSKRTSDHESRRNTDHESRPEKNPRFRESGDSDEDEEDDRKRRA 258

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438721|ref|XP_004137136.1| PREDICTED: nuclear cap-binding protein subunit 2-like [Cucumis sativus] gi|449476391|ref|XP_004154724.1| PREDICTED: nuclear cap-binding protein subunit 2-like [Cucumis sativus]

 Score = 73.6 bits (179), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/56 (78%), Positives = 56/56 (100%)

Query: 21  RKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQR 76
           RKR+R+DDRHAHE+SKR++D+ESRRNS+++SRPEKNPRFRESGDSD+++DDDRKQR
Sbjct: 195 RKRYRDDDRHAHESSKRTSDYESRRNSNYESRPEKNPRFRESGDSDEEDDDDRKQR 250

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446445|ref|XP_002276868.1| PREDICTED: nuclear cap-binding protein subunit 2-like isoform 1 [Vitis vinifera] gi|359485224|ref|XP_003633238.1| PREDICTED: nuclear cap-binding protein subunit 2-like isoform 2 [Vitis vinifera] gi|359485226|ref|XP_003633239.1| PREDICTED: nuclear cap-binding protein subunit 2-like isoform 3 [Vitis vinifera]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 56/59 (94%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQR 76
           DY RKRHR+DDRH+H+ SKR++D +SRRNSDHDSRPEKNPRFRESGDSDD+E+DDRK+R
Sbjct: 194 DYPRKRHRDDDRHSHDFSKRTSDHDSRRNSDHDSRPEKNPRFRESGDSDDEEEDDRKRR 252

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388501070|gb|AFK38601.1| unknown [Lotus japonicus]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 47/60 (78%), Positives = 56/60 (93%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS 77
           DY RKRHR+DD H +E+SKR++D ESRRNSDH+SRPEKNPRFRESGDSDD+E+DDRK+RS
Sbjct: 194 DYHRKRHRDDDHHTNESSKRTSDHESRRNSDHESRPEKNPRFRESGDSDDEEEDDRKRRS 253

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143336|emb|CBI21897.3| unnamed protein product [Vitis vinifera]

 Score = 71.2 bits (173), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 56/59 (94%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQR 76
           DY RKRHR+DDRH+H+ SKR++D +SRRNSDHDSRPEKNPRFRESGDSDD+E+DDRK+R
Sbjct: 73  DYPRKRHRDDDRHSHDFSKRTSDHDSRRNSDHDSRPEKNPRFRESGDSDDEEEDDRKRR 131

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|219944397|gb|ACL54980.1| nuclear cap-binding protein CBP20 [Solanum tuberosum] gi|219944399|gb|ACL54981.1| nuclear cap-binding protein CBP20 [Solanum tuberosum] gi|224460063|gb|ACN43582.1| nuclear cap-binding protein [Solanum tuberosum] gi|262065509|gb|ACY07775.1| CBP20 protein [Solanum tuberosum]

 Score = 67.8 bits (164), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 45/60 (75%), Positives = 53/60 (88%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS 77
           DYQRKRHREDD H  +  KR+ D ESRRNSDH+SRPEKNPRFRESGDSD+++DDDRK+R+
Sbjct: 196 DYQRKRHREDDHHRPDYPKRTYDRESRRNSDHESRPEKNPRFRESGDSDEEDDDDRKRRT 255

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224460055|gb|ACN43578.1| nuclear cap-binding protein [Nicotiana tabacum] gi|261866539|gb|ACY02034.1| cap binding protein 20 [Nicotiana tabacum]

 Score = 64.3 bits (155), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 44/60 (73%), Positives = 51/60 (85%)

Query: 18  DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRESGDSDDDEDDDRKQRS 77
           DY RKRHREDD H  +  KRS D ESRR SDH+SRPEKNPRFRESGDSD+++DDDRK+R+
Sbjct: 195 DYHRKRHREDDHHRSDYPKRSYDRESRRTSDHESRPEKNPRFRESGDSDEEDDDDRKRRT 254

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

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	77
TAIR|locus:2167649	257	CBP20 "CAP-binding protein 20"	0.779	0.233	0.516	2.4e-12

TAIR|locus:2167649 CBP20 "CAP-binding protein 20" [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 31/60 (51%), Positives = 39/60 (65%)

Query:    18 DYQRKRHREDDRHAHETSKRSADFESRRNSDHDSRPEKNPRFRXXXXXXXXXXXXRKQRS 77
             DY RKR R+DDR+  + S+R+ D ESRR++D D RPEKNPRFR            RK+RS
Sbjct:   198 DYHRKRQRDDDRYGRDNSRRNTDHESRRDTDSDMRPEKNPRFRESGDSDDDGEDDRKRRS 257


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        0.314   0.125   0.353    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       77        65   0.00091  102 3  11 23  0.43    28
                                                     29  0.46    28


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:  379 (40 KB)
  Total size of DFA:  75 KB (2065 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:  10.33u 0.13s 10.46t   Elapsed:  00:00:00
  Total cpu time:  10.33u 0.13s 10.46t   Elapsed:  00:00:00
  Start:  Fri May 10 20:24:41 2013   End:  Fri May 10 20:24:41 2013

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0000339 "RNA cap binding" evidence=IDA

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0005845 "mRNA cap binding complex" evidence=TAS

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA;IMP

GO:0031053 "primary miRNA processing" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

GO:0009086 "methionine biosynthetic process" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" 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

Your Input:
	estExt_fgenesh4_pm.C_640064	hypothetical protein (264 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.00180400	SubName- Full=Putative uncharacterized protein; (221 aa)						•			0.800
	eugene3.00061817	SubName- Full=Putative uncharacterized protein; (221 aa)						•			0.800
	estExt_Genewise1_v1.C_LG_VI2910	SubName- Full=Putative uncharacterized protein; (221 aa)						•			0.800
	estExt_Genewise1_v1.C_LG_IX3662	hypothetical protein (787 aa)					•	•	•		0.519
	estExt_fgenesh4_pg.C_LG_I2483	hypothetical protein (199 aa)			•			•			0.430
	eugene3.00440042	hypothetical protein (2357 aa)					•	•			0.418

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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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

No hit with probability above 80.00

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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