Citrus Sinensis ID: 034026

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100------
Protein Sequence
MAQQAAADHQQLDSPLQSPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVIYSPRGI
Secondary Structure (PSIPRED)
cHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
maqqaaadhqqldsplqspqpsrddmnmISCVTALEAAllpclparelqaidrsphpshqidvERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKviysprgi
Flexible Loop (DISEMBL)
maqqaaadhqqldsplqspqpsrDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISlqredqptevemlrkviysprgi
Low Complexity Region (SEG)
MaqqaaadhqqldsplqspqpsrddMNMISCVTaleaallpclparelQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVIYSPRGI
Disordered region (IsUnstruct)
***************************MISCVTALEAALLPCLPARELQ*******************DFMEAAKKLQLYFISLQ*********************
Disordered Region (DISOPRED)
****************************ISCVTALEAALLPCLPARE**************DVERHARDFMEAAKKLQLYFIS****************IYSP***
Disordered Region (DISEMBL)
**********************RDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVIYSPRGI
Disordered Region (DISPRO)
**********************RDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVIYSPRG*
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAQQAAADHQQLDSPLQSPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVIYSPRGI
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	106	2.2.26 [Sep-21-2011]
Q9LFA5	156	Mediator of RNA polymeras	yes	no	0.801	0.544	0.714	5e-29

>sp|Q9LFA5|MED28_ARATH Mediator of RNA polymerase II transcription subunit 28 OS=Arabidopsis thaliana GN=MED28 PE=1 SV=1

 Score =  126 bits (316), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 65/91 (71%), Positives = 77/91 (84%), Gaps = 6/91 (6%)

Query: 16  LQSPQ-PSRDDMN----MISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDF 70
           ++SP+ PS +  N    +++CVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDF
Sbjct: 24  IRSPETPSNNQNNDIEDIMACVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDF 83

Query: 71  MEAAKKLQLYFISLQREDQ-PTEVEMLRKVI 100
           MEAAKKLQLYF+ L+RED+ P+  E L+K I
Sbjct: 84  MEAAKKLQLYFMGLKREDRAPSRAESLKKDI 114

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.
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	106
356512776	141	PREDICTED: uncharacterized protein LOC10	0.924	0.695	0.752	9e-34
356525553	141	PREDICTED: uncharacterized protein LOC10	0.924	0.695	0.732	6e-33
449469116	141	PREDICTED: mediator of RNA polymerase II	0.924	0.695	0.762	8e-33
357519693	115	hypothetical protein MTR_8g092180 [Medic	0.688	0.634	0.917	1e-31
225437408	139	PREDICTED: uncharacterized protein LOC10	0.698	0.532	0.891	3e-31
255564204	140	conserved hypothetical protein [Ricinus	0.698	0.528	0.891	7e-31
224131100	115	predicted protein [Populus trichocarpa]	0.688	0.634	0.904	2e-30
326529489	146	predicted protein [Hordeum vulgare subsp	0.735	0.534	0.8	2e-28
297820014	156	hypothetical protein ARALYDRAFT_906664 [	0.783	0.532	0.761	3e-28
242089591	145	hypothetical protein SORBIDRAFT_09g00428	0.716	0.524	0.815	4e-28

>gi|356512776|ref|XP_003525092.1| PREDICTED: uncharacterized protein LOC100815419 [Glycine max]

 Score =  147 bits (371), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 76/101 (75%), Positives = 84/101 (83%), Gaps = 3/101 (2%)

Query: 1   MAQQAAADHQQLDSP-LQSPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSH 59
           M  +   D Q +  P L S  PS+DDM  +SCV ALEAALLPCLPARELQAIDRSPHPSH
Sbjct: 1   MGDRQVVDQQHMGDPQLPSSPPSKDDM--VSCVMALEAALLPCLPARELQAIDRSPHPSH 58

Query: 60  QIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVI 100
           QIDV+R+ARDFMEAAKKLQLYFISLQRED+PT+VEMLRK I
Sbjct: 59  QIDVDRYARDFMEAAKKLQLYFISLQREDKPTKVEMLRKEI 99

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525553|ref|XP_003531389.1| PREDICTED: uncharacterized protein LOC100789247 [Glycine max]

 Score =  144 bits (363), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 74/101 (73%), Positives = 84/101 (83%), Gaps = 3/101 (2%)

Query: 1   MAQQAAADHQQL-DSPLQSPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSH 59
           M  +   D Q   D+ L S  PS+DDM  +SCV ALEAALLPCLPARELQAIDRSPHPSH
Sbjct: 1   MGDRLVVDQQHTGDAQLPSSPPSKDDM--VSCVMALEAALLPCLPARELQAIDRSPHPSH 58

Query: 60  QIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVI 100
           QIDV+R+ARDFMEAAKKLQLYFISLQRED+PT++EMLRK +
Sbjct: 59  QIDVDRYARDFMEAAKKLQLYFISLQREDKPTKLEMLRKEV 99

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449469116|ref|XP_004152267.1| PREDICTED: mediator of RNA polymerase II transcription subunit 28-like [Cucumis sativus] gi|449484322|ref|XP_004156851.1| PREDICTED: mediator of RNA polymerase II transcription subunit 28-like [Cucumis sativus]

 Score =  144 bits (362), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 77/101 (76%), Positives = 83/101 (82%), Gaps = 3/101 (2%)

Query: 1   MAQQAAADHQQ-LDSPLQSPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSH 59
           MA++   D Q  LD  LQS Q  R+DM  I+ V ALEAALLPCLPARELQAIDRSPHPSH
Sbjct: 1   MAERQPIDQQHSLDPQLQSSQSPREDM--IAYVMALEAALLPCLPARELQAIDRSPHPSH 58

Query: 60  QIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKVI 100
           Q+DVERHARDFMEAAKKLQLYFI LQREDQPT+VE LRK I
Sbjct: 59  QVDVERHARDFMEAAKKLQLYFIGLQREDQPTKVETLRKEI 99

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357519693|ref|XP_003630135.1| hypothetical protein MTR_8g092180 [Medicago truncatula] gi|355524157|gb|AET04611.1| hypothetical protein MTR_8g092180 [Medicago truncatula]

 Score =  140 bits (352), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 67/73 (91%), Positives = 70/73 (95%)

Query: 28  MISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQRE 87
           MISCV ALEAALLPCLPARELQAIDRSPHPSHQIDV+RHARDFMEAAKKLQLYFISLQRE
Sbjct: 1   MISCVMALEAALLPCLPARELQAIDRSPHPSHQIDVDRHARDFMEAAKKLQLYFISLQRE 60

Query: 88  DQPTEVEMLRKVI 100
           D+PT+ EMLRK I
Sbjct: 61  DKPTKAEMLRKEI 73

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225437408|ref|XP_002268380.1| PREDICTED: uncharacterized protein LOC100246950 [Vitis vinifera]

 Score =  138 bits (348), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 66/74 (89%), Positives = 70/74 (94%)

Query: 27  NMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQR 86
           +MI+CV ALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQ+YFISLQR
Sbjct: 24  DMIACVMALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQVYFISLQR 83

Query: 87  EDQPTEVEMLRKVI 100
           EDQPT+ E LRK I
Sbjct: 84  EDQPTKAETLRKEI 97

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564204|ref|XP_002523099.1| conserved hypothetical protein [Ricinus communis] gi|223537661|gb|EEF39284.1| conserved hypothetical protein [Ricinus communis]

 Score =  137 bits (346), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 66/74 (89%), Positives = 67/74 (90%)

Query: 27  NMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQR 86
           +MI CV ALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFI LQR
Sbjct: 25  DMIECVMALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFIGLQR 84

Query: 87  EDQPTEVEMLRKVI 100
           EDQPT  E LRK I
Sbjct: 85  EDQPTAAETLRKEI 98

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224131100|ref|XP_002321001.1| predicted protein [Populus trichocarpa] gi|222861774|gb|EEE99316.1| predicted protein [Populus trichocarpa]

 Score =  135 bits (341), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 66/73 (90%), Positives = 66/73 (90%)

Query: 28  MISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQRE 87
           MI CV ALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFI LQRE
Sbjct: 1   MIGCVMALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFIGLQRE 60

Query: 88  DQPTEVEMLRKVI 100
           DQPT  E LRK I
Sbjct: 61  DQPTMSETLRKDI 73

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326529489|dbj|BAK04691.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 64/80 (80%), Positives = 69/80 (86%), Gaps = 2/80 (2%)

Query: 23  RDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFI 82
           RDDM  ++CV ALEAALLPCLPARELQA+DRS   SHQIDVERHARDFMEAAKKLQ YFI
Sbjct: 29  RDDM--MACVAALEAALLPCLPARELQAVDRSLQSSHQIDVERHARDFMEAAKKLQSYFI 86

Query: 83  SLQREDQPTEVEMLRKVIYS 102
           SLQREDQPT  E+LRK I +
Sbjct: 87  SLQREDQPTNEELLRKEITT 106

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297820014|ref|XP_002877890.1| hypothetical protein ARALYDRAFT_906664 [Arabidopsis lyrata subsp. lyrata] gi|297323728|gb|EFH54149.1| hypothetical protein ARALYDRAFT_906664 [Arabidopsis lyrata subsp. lyrata]

 Score =  128 bits (322), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 64/84 (76%), Positives = 72/84 (85%), Gaps = 1/84 (1%)

Query: 18  SPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKL 77
           S   + D  ++++CVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKL
Sbjct: 31  SNNQNHDIEDIMACVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKL 90

Query: 78  QLYFISLQREDQ-PTEVEMLRKVI 100
           QLYF+ L+RED+ PT  E LRK I
Sbjct: 91  QLYFMGLKREDRSPTRAESLRKEI 114

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242089591|ref|XP_002440628.1| hypothetical protein SORBIDRAFT_09g004280 [Sorghum bicolor] gi|241945913|gb|EES19058.1| hypothetical protein SORBIDRAFT_09g004280 [Sorghum bicolor]

 Score =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 67/76 (88%)

Query: 27  NMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQR 86
           +M++CV ALEAALLPCLPARELQA+DRS   SHQIDVERHARDFMEAAKKLQ YFISLQR
Sbjct: 30  DMLACVAALEAALLPCLPARELQAVDRSLQSSHQIDVERHARDFMEAAKKLQSYFISLQR 89

Query: 87  EDQPTEVEMLRKVIYS 102
           EDQPT  EMLRK I +
Sbjct: 90  EDQPTAEEMLRKEITT 105

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	106
TAIR|locus:2085156	156	AT3G52860 "AT3G52860" [Arabido	0.698	0.474	0.6	3.6e-18

TAIR|locus:2085156 AT3G52860 "AT3G52860" [Arabidopsis thaliana (taxid:3702)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 45/75 (60%), Positives = 54/75 (72%)

Query:    27 NMISCVTXXXXXXXXXXXXXXXQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQR 86
             ++++CVT               QAIDRSPHPSHQIDVERHARDFMEAAKKLQLYF+ L+R
Sbjct:    40 DIMACVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFMGLKR 99

Query:    87 EDQ-PTEVEMLRKVI 100
             ED+ P+  E L+K I
Sbjct:   100 EDRAPSRAESLKKDI 114


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        0.323   0.134   0.385    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      106        67   0.00091  102 3  11 22  0.38    28
                                                     29  0.49    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:  462 (49 KB)
  Total size of DFA:  82 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:  8.45u 0.15s 8.60t   Elapsed:  00:00:00
  Total cpu time:  8.45u 0.15s 8.60t   Elapsed:  00:00:00
  Start:  Fri May 10 12:16:43 2013   End:  Fri May 10 12:16:43 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0016592 "mediator complex" evidence=IDA

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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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LFA5	MED28_ARATH	No assigned EC number	0.7142	0.8018	0.5448	yes	no

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: GSVIVG00028023001 SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (139 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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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