Citrus Sinensis ID: 033626

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-----
Protein Sequence
MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECNDTC
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHccHHHHHHHHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MDSQSQTTSLQRLQNVEKRVVRVLELAGGvmdelanpmgprkeIINNHCREFMQLIKDIQVTLRDEIKSaceyrpfekcdystRILNEICCKKLEYVLSQLDAMKQTIDECNDTC
Flexible Loop (DISEMBL)
mdsqsqttslqrlqnveKRVVRVLELAggvmdelanpmgPRKEIINNHCREFMQLIKDIQVTLRDEIKSACeyrpfekcdystRILNEICCKKLEYVLSQLDAMKQTIDECNDTC
Low Complexity Region (SEG)
MDsqsqttslqrlqNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECNDTC
Disordered region (IsUnstruct)
****************EKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAM***********
Disordered Region (DISOPRED)
*************QNVEKRVVRVLELAGGVMD***************HCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQ*********
Disordered Region (DISEMBL)
************LQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECNDTC
Disordered Region (DISPRO)
*******TSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECN**C
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECNDTC
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	115	2.2.26 [Sep-21-2011]
Q6ID77	115	Mediator of RNA polymeras	yes	no	0.947	0.947	0.770	8e-46

>sp|Q6ID77|MED11_ARATH Mediator of RNA polymerase II transcription subunit 11 OS=Arabidopsis thaliana GN=MED11 PE=1 SV=1

 Score =  181 bits (460), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 98/109 (89%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MD Q+Q TSLQRLQNVE RVV+VLELAGGVM+ELA+P GP+KE +N+HCREFMQ +KDIQ
Sbjct: 1   MDPQTQNTSLQRLQNVENRVVKVLELAGGVMEELASPSGPKKEFVNSHCREFMQSMKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTID 109
           VTLR+EIKSACEYRPFEKCDY+ RI NEIC +KLEYVL+QL+ +KQT D
Sbjct: 61  VTLREEIKSACEYRPFEKCDYNARIANEICFQKLEYVLTQLEDLKQTAD 109

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	115
351727381	115	uncharacterized protein LOC100306257 [Gl	0.956	0.956	0.827	2e-49
356505076	115	PREDICTED: uncharacterized protein LOC10	0.956	0.956	0.809	1e-48
449453808	118	PREDICTED: mediator of RNA polymerase II	0.956	0.932	0.818	1e-48
388490816	115	unknown [Lotus japonicus]	0.956	0.956	0.818	2e-48
225455764	115	PREDICTED: uncharacterized protein LOC10	0.991	0.991	0.798	2e-47
255554731	117	conserved hypothetical protein [Ricinus	0.973	0.957	0.796	1e-44
224118176	129	predicted protein [Populus trichocarpa]	0.939	0.837	0.787	3e-44
42572221	115	uncharacterized protein [Arabidopsis tha	0.947	0.947	0.770	3e-44
297828600	115	hypothetical protein ARALYDRAFT_317046 [	0.930	0.930	0.785	4e-44
224034395	115	unknown [Zea mays] gi|413935989|gb|AFW70	0.982	0.982	0.681	2e-40

>gi|351727381|ref|NP_001236135.1| uncharacterized protein LOC100306257 [Glycine max] gi|255628025|gb|ACU14357.1| unknown [Glycine max]

 Score =  199 bits (505), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 91/110 (82%), Positives = 103/110 (93%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MDSQ QTTSLQRLQNVEKR+V+VLELAGGVMDELA+P+GPRK+++ NHC EFMQLIKDIQ
Sbjct: 1   MDSQGQTTSLQRLQNVEKRIVKVLELAGGVMDELASPVGPRKDVVQNHCLEFMQLIKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110
           V LRDEIKSACEYRPFEKCDY +RI NEIC KK+E+++SQLDAMKQTIDE
Sbjct: 61  VALRDEIKSACEYRPFEKCDYGSRIANEICHKKVEFIMSQLDAMKQTIDE 110

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505076|ref|XP_003521318.1| PREDICTED: uncharacterized protein LOC100792126 [Glycine max]

 Score =  196 bits (499), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 89/110 (80%), Positives = 103/110 (93%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MDSQ QTTSLQRLQNVEKR+V+VLELAGGVMDELA+P+GPRK+++ NHC EFMQLIKDIQ
Sbjct: 1   MDSQGQTTSLQRLQNVEKRIVKVLELAGGVMDELASPVGPRKDVVQNHCLEFMQLIKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110
           V LRDEIKSACEYRPFEKCDY +RI NEIC KK+E+++SQLDA+KQT+DE
Sbjct: 61  VALRDEIKSACEYRPFEKCDYGSRIANEICHKKVEFIMSQLDAIKQTVDE 110

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453808|ref|XP_004144648.1| PREDICTED: mediator of RNA polymerase II transcription subunit 11-like [Cucumis sativus] gi|449504225|ref|XP_004162288.1| PREDICTED: mediator of RNA polymerase II transcription subunit 11-like [Cucumis sativus]

 Score =  196 bits (498), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 90/110 (81%), Positives = 100/110 (90%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MD  +  TSLQRLQNVEKR+VRVLELAGGVM+ELANP GPRKE +NNHC EFMQ IKDIQ
Sbjct: 1   MDPPAHNTSLQRLQNVEKRIVRVLELAGGVMEELANPAGPRKEFVNNHCSEFMQFIKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110
           VTLRDEIKSACEYRPFEKCDYS+RI NE+CCKKLEY++S+LD MKQTID+
Sbjct: 61  VTLRDEIKSACEYRPFEKCDYSSRITNELCCKKLEYMVSKLDGMKQTIDD 110

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388490816|gb|AFK33474.1| unknown [Lotus japonicus]

 Score =  196 bits (498), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 90/110 (81%), Positives = 102/110 (92%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MD Q QTTSLQRLQNVEKR+V+VLELAGGVMDELA+P+GPRK+++ NHC EFMQLIKDIQ
Sbjct: 1   MDPQGQTTSLQRLQNVEKRIVKVLELAGGVMDELASPLGPRKDVVQNHCLEFMQLIKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110
           V LRDEIKSACEYRPFEKCDY +RI NEIC +K+E+V+SQLDAMKQTIDE
Sbjct: 61  VALRDEIKSACEYRPFEKCDYGSRIANEICYQKVEFVMSQLDAMKQTIDE 110

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455764|ref|XP_002269953.1| PREDICTED: uncharacterized protein LOC100255926 [Vitis vinifera] gi|297734129|emb|CBI15376.3| unnamed protein product [Vitis vinifera]

 Score =  192 bits (489), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 91/114 (79%), Positives = 103/114 (90%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MDSQ+  TSLQRLQNVEKR+++VLELAGGVMDEL NP GPRKE+++ HC EFMQLIKDIQ
Sbjct: 1   MDSQTPNTSLQRLQNVEKRIIKVLELAGGVMDELCNPSGPRKELLSIHCGEFMQLIKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECNDT 114
           +TLRDEIKSACEYRPFEKCDY +RI NEICCKKLEYV+SQLD MK+TIDE +D 
Sbjct: 61  MTLRDEIKSACEYRPFEKCDYISRISNEICCKKLEYVISQLDGMKETIDEYHDA 114

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255554731|ref|XP_002518403.1| conserved hypothetical protein [Ricinus communis] gi|223542248|gb|EEF43790.1| conserved hypothetical protein [Ricinus communis]

 Score =  183 bits (464), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 90/113 (79%), Positives = 99/113 (87%), Gaps = 1/113 (0%)

Query: 3   SQSQTTSLQRLQNVEK-RVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQV 61
           SQ+Q TSLQRLQNVEK  +VRVLELA GVMDELA P GPRKE INN+CREFMQ+IKDIQ 
Sbjct: 4   SQTQNTSLQRLQNVEKVTIVRVLELASGVMDELAAPTGPRKEFINNNCREFMQMIKDIQF 63

Query: 62  TLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECNDT 114
           TLR+EIKSACEYRPFEKCDYS RI NEICCKKLEYV+SQLDA+K +ID+  D 
Sbjct: 64  TLRNEIKSACEYRPFEKCDYSCRISNEICCKKLEYVISQLDAIKLSIDQYEDA 116

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118176|ref|XP_002331576.1| predicted protein [Populus trichocarpa] gi|222873800|gb|EEF10931.1| predicted protein [Populus trichocarpa]

 Score =  182 bits (462), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 85/108 (78%), Positives = 95/108 (87%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MDSQ+Q TSLQRLQNVEK VVRVLE+AG VMDEL+NP GPRKE INNHCR+FMQ+IKDIQ
Sbjct: 1   MDSQTQNTSLQRLQNVEKTVVRVLEVAGAVMDELSNPTGPRKEFINNHCRDFMQMIKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTI 108
            TLR+EIKSACEYRPFEK DY+ RI NEIC  KLE++LSQLD + QTI
Sbjct: 61  FTLRNEIKSACEYRPFEKSDYTCRISNEICLSKLEHILSQLDLITQTI 108

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42572221|ref|NP_974205.1| uncharacterized protein [Arabidopsis thaliana] gi|75123851|sp|Q6ID77.1|MED11_ARATH RecName: Full=Mediator of RNA polymerase II transcription subunit 11 gi|48310228|gb|AAT41779.1| At3g01435 [Arabidopsis thaliana] gi|52218796|gb|AAU29468.1| At3g01435 [Arabidopsis thaliana] gi|110738543|dbj|BAF01197.1| hypothetical protein [Arabidopsis thaliana] gi|332640145|gb|AEE73666.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  181 bits (460), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 98/109 (89%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MD Q+Q TSLQRLQNVE RVV+VLELAGGVM+ELA+P GP+KE +N+HCREFMQ +KDIQ
Sbjct: 1   MDPQTQNTSLQRLQNVENRVVKVLELAGGVMEELASPSGPKKEFVNSHCREFMQSMKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTID 109
           VTLR+EIKSACEYRPFEKCDY+ RI NEIC +KLEYVL+QL+ +KQT D
Sbjct: 61  VTLREEIKSACEYRPFEKCDYNARIANEICFQKLEYVLTQLEDLKQTAD 109

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297828600|ref|XP_002882182.1| hypothetical protein ARALYDRAFT_317046 [Arabidopsis lyrata subsp. lyrata] gi|297328022|gb|EFH58441.1| hypothetical protein ARALYDRAFT_317046 [Arabidopsis lyrata subsp. lyrata]

 Score =  181 bits (460), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 84/107 (78%), Positives = 97/107 (90%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           MD Q+Q TSLQRLQNVE RVV+VLELAGGVM+ELA+P GP+KE +N+HCREFMQ +KDIQ
Sbjct: 1   MDPQTQNTSLQRLQNVENRVVKVLELAGGVMEELASPSGPKKEFVNSHCREFMQSMKDIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQT 107
           VTLR+EIKSACEYRPFEKCDY+ RI NEIC +KLEYVL+QLD +KQT
Sbjct: 61  VTLREEIKSACEYRPFEKCDYNARIANEICFQKLEYVLTQLDDLKQT 107

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224034395|gb|ACN36273.1| unknown [Zea mays] gi|413935989|gb|AFW70540.1| hypothetical protein ZEAMMB73_750956 [Zea mays] gi|413935990|gb|AFW70541.1| hypothetical protein ZEAMMB73_750956 [Zea mays]

 Score =  169 bits (427), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 77/113 (68%), Positives = 94/113 (83%)

Query: 1   MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
           M  QSQ++SLQRLQ+VEKR+VRVLELAG VM+EL N  GPR + ++ HCREFM  +K+IQ
Sbjct: 1   MIPQSQSSSLQRLQHVEKRIVRVLELAGAVMEELGNSHGPRTDAVSAHCREFMIAMKEIQ 60

Query: 61  VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDECND 113
            TLR+EIKSACEYRPFEKCDYS RI NEICCKKLEYV+ +LD M+Q+++   D
Sbjct: 61  TTLREEIKSACEYRPFEKCDYSARIANEICCKKLEYVIEKLDTMQQSLEHITD 113

Source: Zea mays

Species: Zea mays

Genus: Zea

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	115
TAIR|locus:1006230250	115	AT3G01435 [Arabidopsis thalian	0.947	0.947	0.688	4.9e-37

TAIR|locus:1006230250 AT3G01435 [Arabidopsis thaliana (taxid:3702)]

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 75/109 (68%), Positives = 88/109 (80%)

Query:     1 MDXXXXXXXXXXXXNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQ 60
             MD            NVE RVV+VLELAGGVM+ELA+P GP+KE +N+HCREFMQ +KDIQ
Sbjct:     1 MDPQTQNTSLQRLQNVENRVVKVLELAGGVMEELASPSGPKKEFVNSHCREFMQSMKDIQ 60

Query:    61 VTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTID 109
             VTLR+EIKSACEYRPFEKCDY+ RI NEIC +KLEYVL+QL+ +KQT D
Sbjct:    61 VTLREEIKSACEYRPFEKCDYNARIANEICFQKLEYVLTQLEDLKQTAD 109


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        0.322   0.137   0.411    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      115       103   0.00091  102 3  11 22  0.38    30
                                                     29  0.49    31


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:  525 (56 KB)
  Total size of DFA:  113 KB (2076 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:  11.23u 0.12s 11.35t   Elapsed:  00:00:00
  Total cpu time:  11.23u 0.12s 11.35t   Elapsed:  00:00:00
  Start:  Thu May  9 21:36:20 2013   End:  Thu May  9 21:36:20 2013

GO:0001104 "RNA polymerase II transcription cofactor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016592 "mediator complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

---

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)
Q6ID77	MED11_ARATH	No assigned EC number	0.7706	0.9478	0.9478	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

Fail to connect to STRING server

---

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	115
pfam10280	113	pfam10280, Med11, Mediator complex protein	2e-23

>gnl|CDD|220673 pfam10280, Med11, Mediator complex protein

 Score = 86.6 bits (215), Expect = 2e-23
 Identities = 28/111 (25%), Positives = 52/111 (46%), Gaps = 5/111 (4%)

Query: 6   QTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPR--KEIINNHCREFMQLIKDIQVTL 63
               LQ L  ++K++V +L+ AG V++EL+        KE   +H +EF + +  ++  L
Sbjct: 1   VQERLQSLNEIDKKIVSLLQSAGQVIEELSKEKSGESSKEQFESHTKEFYKTLSSVETEL 60

Query: 64  RDEIKSACEYRPF---EKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDEC 111
           R +IK   E       E   Y    +N++  K L     +L+ +  T+ + 
Sbjct: 61  RKQIKYLDEVIGGQPHEGSGYGALPINQLNQKALTVGRDKLNELWATLKKL 111

Mediator is a large, modular protein complex that is conserved from yeast to human and conveys regulatory signals from DNA-binding transcription factors to RNA polymerase II. Not only are the polypeptides conserved but the structural organisation is also largely conserved. One or two subunits are either fungal or vertebral specific but Med11 is one of the subunits that is conserved from fungi to humans. Med11 appears to be necessary for the full and successful assembly of the core head sub-region. Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	115
PF10280	117	Med11: Mediator complex protein ; InterPro: IPR019	99.93
KOG4057	180	consensus Uncharacterized conserved protein [Funct	99.75

>PF10280 Med11: Mediator complex protein ; InterPro: IPR019404 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=99.93  E-value=7.5e-27  Score=167.89  Aligned_cols=105  Identities=30%  Similarity=0.471  Sum_probs=78.5

Q ss_pred             hhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc---CCCC
Q 033626            7 TTSLQRLQNVEKRVVRVLELAGGVMDELANPMGP------RKEIINNHCREFMQLIKDIQVTLRDEIKSACEY---RPFE   77 (115)
Q Consensus         7 ~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gp------r~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~ey---rPfe   77 (115)
                      .++|++|++||++||.+|++||+||.+|+++.+|      ++++|..||++|+..+++|+++|+.||+++++|   +||+
T Consensus         2 ~eRL~~L~~Idk~I~~lL~~A~~ai~~Ls~~~~~~~~~~~~k~~f~~~~~~f~~~L~~V~~~Lr~qI~~L~e~~~~~~~~   81 (117)
T PF10280_consen    2 AERLQQLNEIDKKIVSLLQHAGQAIQELSNPKSPDQDPESSKEAFESATSEFFSTLSSVEVELRRQIKYLEEVSIIQPHE   81 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---TGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTT----
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence            4799999999999999999999999999999777      899999999999999999999999999999999   9999


Q ss_pred             CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626           78 KCDYSTRILNEICCKKLEYVLSQLDAMKQTIDEC  111 (115)
Q Consensus        78 ~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~~  111 (115)
                      +|+|++.+.++++.+++.+.+++|+++-..++++
T Consensus        82 ~s~~~~l~v~~ln~~~~~~~~~~l~el~~~~~~~  115 (117)
T PF10280_consen   82 GSSYGALDVGWLNSKKTEVGRDKLAELWATLREF  115 (117)
T ss_dssp             ----TBS---------------GGGTTTHHHHHH
T ss_pred             cccccccchHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999998876

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 Med11 of the Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3R84_S 3RJ1_O.

>KOG4057 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.75  E-value=1.7e-17  Score=127.95  Aligned_cols=106  Identities=21%  Similarity=0.359  Sum_probs=98.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hhccCCCCCcchh
Q 033626            6 QTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKS---ACEYRPFEKCDYS   82 (115)
Q Consensus         6 q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s---~~eyrPfe~s~Y~   82 (115)
                      =+.++++|..+||.|..+|+.||.++-||++. +......+.++..|..+|..|+.+|+++|.|   ||.+.|+|+|+|+
T Consensus         7 ~~dri~Al~~iEkeI~~~mq~Ag~iiqeLgKE-K~~~kn~e~qa~~F~ksit~VE~eLSaQi~YLtqV~tGqpHeGS~y~   85 (180)
T KOG4057|consen    7 LTDRIQALVTIEKEIDEMMQCAGEIIQELGKE-KQIGKNMEDQANNFKKSITQVENELSAQIQYLTQVCTGQPHEGSTYG   85 (180)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH-hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchH
Confidence            36899999999999999999999999999999 6666669999999999999999999999999   6999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033626           83 TRILNEICCKKLEYVLSQLDAMKQTIDECN  112 (115)
Q Consensus        83 ~r~~~Ei~~~k~e~v~~qL~~l~~~i~~~~  112 (115)
                      .++++.++.+++.+.++.|-.+-++++--.
T Consensus        86 s~k~~qmA~~r~~~ars~l~~i~rt~~~~s  115 (180)
T KOG4057|consen   86 SLKNSQMAQSRLSSARSELFQIVRTLDPTS  115 (180)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            999999999999999999999988876433

---

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	115
3r84_A	86	Mediator of RNA polymerase II transcription subun;	98.71
4gwp_A	115	Mediator of RNA polymerase II transcription subun;	98.18
3rj1_A	131	Mediator of RNA polymerase II transcription subun;	97.38
4h63_K	112	Mediator of RNA polymerase II transcription subun;	95.95

>3r84_A Mediator of RNA polymerase II transcription subun; four-helix bundle, nucleus; HET: MSE; 2.05A {Saccharomyces cerevisiae}

Probab=98.71  E-value=4.2e-08  Score=67.92  Aligned_cols=64  Identities=22%  Similarity=0.319  Sum_probs=58.4

Q ss_pred             hhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626            7 TTSLQRLQNVEKRVVRVLELAGGVMDELANPMG---PRKEIINNHCREFMQLIKDIQVTLRDEIKSA   70 (115)
Q Consensus         7 ~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~g---pr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~   70 (115)
                      ..+|+.|+.|.++||.+|+.|++++..|+++-.   ..+++|..|+++|+..+.+|...||.||+.+
T Consensus         4 qERL~sL~~ID~~i~sLL~~as~~i~tls~~k~~~~~~K~~F~~~t~~fy~tL~~v~v~LrkEIk~L   70 (86)
T 3r84_A            4 QERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESVKPQFENHVKQFYERLDKSTTQLRKEIQLL   70 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999997632   3459999999999999999999999999997

>4gwp_A Mediator of RNA polymerase II transcription subun; binding sites, mediator complex, models, molecular, phosphor protein structure; 4.20A {Saccharomyces cerevisiae} PDB: 4gwq_A

Probab=98.18  E-value=6.4e-06  Score=59.79  Aligned_cols=99  Identities=22%  Similarity=0.257  Sum_probs=73.2

Q ss_pred             CCchhhhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc-----
Q 033626            1 MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPM---GPRKEIINNHCREFMQLIKDIQVTLRDEIKSACE-----   72 (115)
Q Consensus         1 m~~~~q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~---gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~e-----   72 (115)
                      |-|+.=..+|..|+.|..+||..|+.|..+++-++..-   ...+..|..|+++|+..+.++-+.||.|||.+-|     
T Consensus         1 mqp~~VqERLdSL~~ID~kl~slL~~~S~~~~t~~elK~g~~~~K~qF~~~~~~fY~~Ls~~a~~LRkEIK~lDeNiG~~   80 (115)
T 4gwp_A            1 MQPPYIQERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESVKPQFENHVKQFYERLDKSTTQLRKEIQLLDENVGTR   80 (115)
T ss_dssp             ---CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCce
Confidence            77888889999999999999999999999998887532   2567999999999999999999999999999743     


Q ss_pred             cCCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Q 033626           73 YRPFEKCDYSTRILNEICCKKLEYVLSQLDA  103 (115)
Q Consensus        73 yrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~  103 (115)
                      ..|-.-    -.++.-.--+|+..-+.+|+.
T Consensus        81 lLPInV----dkKa~~~~~~Kl~eqi~~L~~  107 (115)
T 4gwp_A           81 LLPINV----NKKALGQDTEKMEEQLDLLSA  107 (115)
T ss_dssp             SSCCSS----CCCCCTHHHHHHHHHHHHHHH
T ss_pred             Eecccc----ccccccccHHHHHHHHHHHHH
Confidence            334321    123334445666544444443

>3rj1_A Mediator of RNA polymerase II transcription subun; RNA polymeras II, POL II, head module, head, regulator, helical bundle; 4.30A {Saccharomyces cerevisiae}

Probab=97.38  E-value=2.7e-06  Score=62.91  Aligned_cols=69  Identities=20%  Similarity=0.283  Sum_probs=59.7

Q ss_pred             CchhhhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626            2 DSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMG---PRKEIINNHCREFMQLIKDIQVTLRDEIKSA   70 (115)
Q Consensus         2 ~~~~q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~g---pr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~   70 (115)
                      -|++=..+|+.|+.|..+||..|+.|+.++.-|+++..   .-+++|..|+++|+..+.+|-..||.||+-+
T Consensus        18 q~~~IqERL~sL~~ID~~ivsLL~~aS~~~~tls~~k~g~~~~K~qF~~~t~~fy~~L~~v~v~LRkEIk~L   89 (131)
T 3rj1_A           18 QPPYIQERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESVKPQFENHVKQFYERLDKSTTQLRKEIQLL   89 (131)
T ss_dssp             ---CHHHHTTTTTTTTTTTHHHHSTTTHHHHHHHHSCCSTTTTHHHHHHHHHHHHGGGTTTTTTTTTTTSST
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555789999999999999999999999999987533   3459999999999999999999999999986

>4h63_K Mediator of RNA polymerase II transcription subun; mediator complex, nucleus; 3.40A {Schizosaccharomyces pombe}

Probab=95.95  E-value=0.037  Score=39.44  Aligned_cols=62  Identities=19%  Similarity=0.329  Sum_probs=53.5

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033626            6 QTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKS   69 (115)
Q Consensus         6 q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s   69 (115)
                      -.+-|+-.-++|+||-.+|-.||.-++-.--  ..+-+.|..|+++|..-|.=|-|+|+.+.--
T Consensus        17 ~T~~~~~I~EiE~rIPDILsSA~~CIEAI~~--~~SiE~F~~~sr~F~~TVEFiSTGL~RQ~L~   78 (112)
T 4h63_K           17 DTQQVQNILELEAKIPDILSSAGKCIEAIQL--NNSLEDFRKYSKEFLETVEFISTGLRRQALE   78 (112)
T ss_dssp             HHHHHHHHHHHHHHSTHHHHHHHHHHHHHHT--TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHhHHHHHHHHHH--hccHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            3456788889999999999999999987643  4678999999999999999999999988654

---

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