Citrus Sinensis ID: 032351

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140--
Protein Sequence
MAQQAAADHQQLDSPLQSPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV
Secondary Structure (PSIPRED)
cHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
maqqaaadhqqldsplqspqpsrddmnmISCVTALEAAllpclparelqaidrsphpshqidvERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV
Flexible Loop (DISEMBL)
maqqaaadhqqldsplqspqpsrDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFIslqredqpteVEMLRKDIAIMEEELKAKKELIKKQERLVQRWrndlkgqldkhitelerv
Low Complexity Region (SEG)
MaqqaaadhqqldsplqspqpsrddMNMISCVTaleaallpclparelQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMeeelkakkelikkqeRLVQRWRNDLKGQLDKHITELERV
Disordered region (IsUnstruct)
***************************MISCVTALEAALLPCLPARELQ******************RDFMEAAKKLQLYFISLQ*************DIAI*****************LVQRW******************
Disordered Region (DISOPRED)
****************************ISCVTALEAALLPCLPARE***********HQIDVERHARDFMEAAKKLQLYFI*****************IAIMEEELKA**ELIKKQERLVQRWRNDLKGQLDKH*******
Disordered Region (DISEMBL)
**********************RDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV
Disordered Region (DISPRO)
**********************RDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELER*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAQQAAADHQQLDSPLQSPQPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxHITELERV
Positional Conservation
no confident homologs detected

---

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	142	2.2.26 [Sep-21-2011]
Q9LFA5	156	Mediator of RNA polymeras	yes	no	0.894	0.814	0.676	4e-42

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

 Score =  169 bits (429), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 90/133 (67%), Positives = 108/133 (81%), Gaps = 6/133 (4%)

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

Query: 71  MEAAKKLQLYFISLQREDQ-PTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLK 129
           MEAAKKLQLYF+ L+RED+ P+  E L+KDIA+MEEELK K ELIKK  RL Q  +  +K
Sbjct: 84  MEAAKKLQLYFMGLKREDRAPSRAESLKKDIAVMEEELKTKDELIKKHMRLFQESQKLVK 143

Query: 130 GQLDKHITELERV 142
            Q++KH  ELE+V
Sbjct: 144 EQIEKHRDELEKV 156

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	142
356512776	141	PREDICTED: uncharacterized protein LOC10	0.985	0.992	0.727	2e-50
356525553	141	PREDICTED: uncharacterized protein LOC10	0.985	0.992	0.713	2e-49
225437408	139	PREDICTED: uncharacterized protein LOC10	0.816	0.834	0.836	3e-49
449469116	141	PREDICTED: mediator of RNA polymerase II	0.985	0.992	0.720	8e-49
255564204	140	conserved hypothetical protein [Ricinus	0.816	0.828	0.827	4e-48
224131100	115	predicted protein [Populus trichocarpa]	0.809	1.0	0.826	8e-47
297743905	110	unnamed protein product [Vitis vinifera]	0.767	0.990	0.853	5e-46
357519693	115	hypothetical protein MTR_8g092180 [Medic	0.809	1.0	0.791	1e-45
115462173	146	Os05g0154900 [Oryza sativa Japonica Grou	0.852	0.828	0.739	5e-44
242089591	145	hypothetical protein SORBIDRAFT_09g00428	0.816	0.8	0.767	6e-44

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

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 104/143 (72%), Positives = 118/143 (82%), Gaps = 3/143 (2%)

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

Query: 60  QIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQER 119
           QIDV+R+ARDFMEAAKKLQLYFISLQRED+PT+VEMLRK+IA+MEEEL  K ELIKKQE 
Sbjct: 59  QIDVDRYARDFMEAAKKLQLYFISLQREDKPTKVEMLRKEIALMEEELNIKNELIKKQEN 118

Query: 120 LVQRWRNDLKGQLDKHITELERV 142
           L+Q W+ +LK QLDKH  EL+RV
Sbjct: 119 LIQEWKKELKDQLDKHKIELDRV 141

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 =  200 bits (508), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 102/143 (71%), Positives = 118/143 (82%), Gaps = 3/143 (2%)

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

Query: 60  QIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQER 119
           QIDV+R+ARDFMEAAKKLQLYFISLQRED+PT++EMLRK++A+MEEEL  K ELIKKQE 
Sbjct: 59  QIDVDRYARDFMEAAKKLQLYFISLQREDKPTKLEMLRKEVALMEEELNKKNELIKKQEN 118

Query: 120 LVQRWRNDLKGQLDKHITELERV 142
           L+Q W+ +LK QLDKH  EL+RV
Sbjct: 119 LIQEWKKELKDQLDKHKIELDRV 141

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 97/116 (83%), Positives = 106/116 (91%)

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

Query: 87  EDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV 142
           EDQPT+ E LRK+IA+MEEEL+ K ELI KQERL+Q WR +LK QLDKH TELERV
Sbjct: 84  EDQPTKAETLRKEIAVMEEELRLKTELINKQERLIQGWRKELKDQLDKHNTELERV 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  198 bits (503), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 103/143 (72%), Positives = 118/143 (82%), Gaps = 3/143 (2%)

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

Query: 60  QIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQER 119
           Q+DVERHARDFMEAAKKLQLYFI LQREDQPT+VE LRK+I+ +EEELK K E+IKKQE+
Sbjct: 59  QVDVERHARDFMEAAKKLQLYFIGLQREDQPTKVETLRKEISAIEEELKVKNEIIKKQEK 118

Query: 120 LVQRWRNDLKGQLDKHITELERV 142
           L++ W+ DLK QLDKH  ELE+V
Sbjct: 119 LIEGWKKDLKDQLDKHNNELEKV 141

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 96/116 (82%), Positives = 102/116 (87%)

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

Query: 87  EDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV 142
           EDQPT  E LRK+IA+MEEELK K E+IKKQERL+Q WR +L  QL KH TELERV
Sbjct: 85  EDQPTAAETLRKEIAVMEEELKIKDEIIKKQERLIQEWRKELTDQLQKHKTELERV 140

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 =  191 bits (485), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 95/115 (82%), Positives = 100/115 (86%)

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

Query: 88  DQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV 142
           DQPT  E LRKDI +MEEELK K ELIK+QERL+Q W  +LK Q +KH TELERV
Sbjct: 61  DQPTMSETLRKDIGMMEEELKVKDELIKRQERLIQGWWKELKDQAEKHNTELERV 115

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743905|emb|CBI36875.3| unnamed protein product [Vitis vinifera]

 Score =  188 bits (478), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 93/109 (85%), Positives = 100/109 (91%)

Query: 34  ALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEV 93
           ALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQ+YFISLQREDQPT+ 
Sbjct: 2   ALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQVYFISLQREDQPTKA 61

Query: 94  EMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV 142
           E LRK+IA+MEEEL+ K ELI KQERL+Q WR +LK QLDKH TELERV
Sbjct: 62  ETLRKEIAVMEEELRLKTELINKQERLIQGWRKELKDQLDKHNTELERV 110

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 91/115 (79%), Positives = 101/115 (87%)

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

Query: 88  DQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV 142
           D+PT+ EMLRK+I +ME+EL  K ELIKKQE L+Q W+ +L  QL+KH  EL RV
Sbjct: 61  DKPTKAEMLRKEITLMEDELNEKNELIKKQEHLIQEWKKELSDQLEKHNIELNRV 115

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115462173|ref|NP_001054686.1| Os05g0154900 [Oryza sativa Japonica Group] gi|54291848|gb|AAV32216.1| unknown protein [Oryza sativa Japonica Group] gi|113578237|dbj|BAF16600.1| Os05g0154900 [Oryza sativa Japonica Group] gi|215678528|dbj|BAG92183.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  182 bits (461), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 91/123 (73%), Positives = 105/123 (85%), Gaps = 2/123 (1%)

Query: 20  QPSRDDMNMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQL 79
           + +RDDM  ++CV ALEAALLPCLPARELQA+DRS   SHQIDVERHARDFMEAAKKLQ 
Sbjct: 26  ESARDDM--MACVAALEAALLPCLPARELQAVDRSLQSSHQIDVERHARDFMEAAKKLQS 83

Query: 80  YFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITEL 139
           YFISLQRED+P+  EMLRKDIAIMEEELK K ELI K ++L++ W+ +LK QL KH+TEL
Sbjct: 84  YFISLQREDRPSTEEMLRKDIAIMEEELKTKSELIDKHKKLIEGWQKELKDQLGKHVTEL 143

Query: 140 ERV 142
           ERV
Sbjct: 144 ERV 146

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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 =  181 bits (460), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 89/116 (76%), Positives = 99/116 (85%)

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

Query: 87  EDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELERV 142
           EDQPT  EMLRK+I  MEEELK K ELI K ++L++ WR +LK QL KHITELERV
Sbjct: 90  EDQPTAEEMLRKEITTMEEELKTKSELIAKHKKLIEGWRKELKEQLGKHITELERV 145

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	142
TAIR|locus:2085156	156	AT3G52860 "AT3G52860" [Arabido	0.816	0.743	0.504	4.2e-24

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

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 59/117 (50%), Positives = 74/117 (63%)

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

Query:    87 EDQ-PTEVEMLRKDIAIMXXXXXXXXXXXXXXXRLVQRWRNDLKGQLDKHITELERV 142
             ED+ P+  E L+KDIA+M               RL Q  +  +K Q++KH  ELE+V
Sbjct:   100 EDRAPSRAESLKKDIAVMEEELKTKDELIKKHMRLFQESQKLVKEQIEKHRDELEKV 156


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        0.324   0.134   0.388    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      142        88   0.00091  102 3  11 22  0.40    29
                                                     29  0.49    30


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:  517 (55 KB)
  Total size of DFA:  104 KB (2073 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:  9.30u 0.14s 9.44t   Elapsed:  00:00:00
  Total cpu time:  9.30u 0.14s 9.44t   Elapsed:  00:00:00
  Start:  Sat May 11 02:23:54 2013   End:  Sat May 11 02:23:54 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0016592 "mediator complex" evidence=IDA

---

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	0.6766	0.8943	0.8141	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!

---

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.

---

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

ID	Length	Definition	Probability
Query	142
PF11594	106	Med28: Mediator complex subunit 28; InterPro: IPR0	99.76
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	88.31
PF07544	83	Med9: RNA polymerase II transcription mediator com	82.49

>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]

Probab=99.76  E-value=2.9e-18  Score=127.99  Aligned_cols=76  Identities=24%  Similarity=0.496  Sum_probs=71.4

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHHHhhhhccC--CChHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032351           59 HQIDVERHARDFMEAAKKLQLYFISLQREDQ--PTEVE-MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKH  135 (142)
Q Consensus        59 hqiDVErhardFmeaAkqLq~yFi~lQr~~~--p~k~E-~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh  135 (142)
                      .+.+||+++.+|+|+||++++||+  |||+.  ..++| +||+||++|++||.||++||.||+.+|..|+++|.|.-+.|
T Consensus         2 irt~vEq~~~~FlD~aRq~e~~Fl--qKr~~LS~~kpe~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d~~~~~   79 (106)
T PF11594_consen    2 IRTYVEQLIQSFLDVARQMEAFFL--QKRFELSAYKPEQVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLSDAQNQH   79 (106)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            467899999999999999999998  99998  66888 99999999999999999999999999999999999998887


Q ss_pred             h
Q 032351          136 I  136 (142)
Q Consensus       136 ~  136 (142)
                      .
T Consensus        80 k   80 (106)
T PF11594_consen   80 K   80 (106)
T ss_pred             c
Confidence            4

It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].

>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division []

Probab=88.31  E-value=2.9  Score=29.27  Aligned_cols=46  Identities=33%  Similarity=0.637  Sum_probs=30.2

Q ss_pred             HHHHHHHh--hhhccCCChHHH------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351           76 KLQLYFIS--LQREDQPTEVEM------LRKDIAIMEEELKAKKELIKKQERLV  121 (142)
Q Consensus        76 qLq~yFi~--lQr~~~p~k~E~------lkkeI~~le~EL~~KdELIkkh~~lI  121 (142)
                      ||..||+.  |++.......++      ||-++..|..||..+..+|....+-|
T Consensus        20 KLrI~fLee~l~~~~~~~~~~~~keNieLKve~~~L~~el~~~~~~l~~a~~~~   73 (75)
T PF07989_consen   20 KLRIYFLEERLQKLGPESIEELLKENIELKVEVESLKRELQEKKKLLKEAEKAI   73 (75)
T ss_pred             HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            78899982  332222222323      45578888888988888888777655

>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=82.49  E-value=4.1  Score=28.44  Aligned_cols=28  Identities=29%  Similarity=0.494  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351           94 EMLRKDIAIMEEELKAKKELIKKQERLV  121 (142)
Q Consensus        94 E~lkkeI~~le~EL~~KdELIkkh~~lI  121 (142)
                      |--..+|..||+++.+|.+++.+..+.+
T Consensus        55 eeq~~~i~~Le~~i~~k~~~L~~~~~~~   82 (83)
T PF07544_consen   55 EEQEEEIEELEEQIRKKREVLQKFKERV   82 (83)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3445789999999999999999988764

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. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex

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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

ID	Length	Definition	Probability
Query	142
4fla_A	152	Regulation of nuclear PRE-mRNA domain-containing 1	86.38

>4fla_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, transcription; 2.20A {Homo sapiens}

Probab=86.38  E-value=8.7  Score=28.82  Aligned_cols=113  Identities=20%  Similarity=0.247  Sum_probs=80.0

Q ss_pred             CCchhHhHHHHHHHHhhc---------CCCccc--hhhcccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHhhhhccC--
Q 032351           23 RDDMNMISCVTALEAALL---------PCLPAR--ELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQ--   89 (142)
Q Consensus        23 ~~~~d~~~~V~~lEaAll---------pCLpar--eLqaiDrs~hpshqiDVErhardFmeaAkqLq~yFi~lQr~~~--   89 (142)
                      ..-+|++.+++.||.+.-         .-||.-  +...+++-.   .+-..++-...|-+++..|..|-=+|..+-.  
T Consensus        22 ~~~~elik~L~~le~sassDa~vrq~Ia~LP~eVsd~s~l~klk---Dk~~~e~l~~~veeA~~~L~eYn~rL~~E~~dR   98 (152)
T 4fla_A           22 LLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKIT---DKEAAERLSKTVDEACLLLAEYNGRLAAELEDR   98 (152)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHTSCGGGTCGGGGGGCC---SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhhccccchHHHHHHHHcCCccccCHHHHHHcc---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344679999999997642         234433  444566655   6677999999999999999999877766543  


Q ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032351           90 PTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITEL  139 (142)
Q Consensus        90 p~k~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~el  139 (142)
                      ..-.++|+.=++-.++.++......+-++++...=. .++..++.|+.-|
T Consensus        99 ~~L~~~L~~~~~~~~~~l~e~e~~leeyK~Kl~rv~-~vkkeL~~hi~sL  147 (152)
T 4fla_A           99 RQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVT-QVRKELKSHIQSL  147 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhcC
Confidence            555668888888888888888887777777766543 3455666777544

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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