Citrus Sinensis ID: 032021

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------15
Protein Sequence
MDPFSGSGSWNMMPSIPSHNSSPAASNQDNLFLSPQHQQQFYQQPTQFPQQQFQQQGRTPQQQQQPQQQQQQNQHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEERN
Secondary Structure (PSIPRED)
ccccccccccEEcccccccccccccccccccccccccccccccccccccccHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccHEEEcccccccccccHHHHccccHHHccccccHccHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccEHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mdpfsgsgswnmmpsipshnsspaasnqdnlflspqhqqqfyqqptqfpqqqfqqqgrtpqqqqqpqqqQQQNQHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEERN
Flexible Loop (DISEMBL)
MDPFSGSGSWNMMPSIPSHNSSPAASNQDNLFLSPQHQQQFYQQPTQFPQQQFQQQGRTPQQQQQPQQQQQQNQHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSisesldtkamtvegqrrkleern
Low Complexity Region (SEG)
MDPFSGSGSWNMMPSIPSHNSSPAASNQDNLFLSpqhqqqfyqqptqfpqqqfqqqgrtpqqqqqpqqqqqqnqhhqSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEERN
Disordered region (IsUnstruct)
**********************************************************************************FHLLHLMENLAD******************************************************
Disordered Region (DISOPRED)
*********WN**********************************************************************NFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSI**********************
Disordered Region (DISEMBL)
********SWNMMPSIPS********NQDNLFLSPQHQ***************************************SLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTK***************
Disordered Region (DISPRO)
****************************DNLFLS*******************************************SLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTV***********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDPFSGSGSWNMMPSIPSHNSSPAASNQDNLFLSPQHQQQFYQQPTQFPQQQFQQQGRTPQQQQQPQQQQQQNQHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEERN
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	148	2.2.26 [Sep-21-2011]
Q8RWA2	244	Mediator of RNA polymeras	yes	no	0.493	0.299	0.726	1e-24

>sp|Q8RWA2|MED9_ARATH Mediator of RNA polymerase II transcription subunit 9 OS=Arabidopsis thaliana GN=MED9 PE=1 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 53/73 (72%), Positives = 63/73 (86%)

Query: 74  QHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTK 133
           Q HQSLAS+FHL  ++E LAD IENGTRDQ SDALVNELN+HF+KCQQLL+SIS SL +K
Sbjct: 145 QQHQSLASHFHLYPMVEKLADVIENGTRDQNSDALVNELNSHFDKCQQLLNSISGSLGSK 204

Query: 134 AMTVEGQRRKLEE 146
            MTV+GQ+R +EE
Sbjct: 205 TMTVDGQKRNVEE 217

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	148
224135025	190	predicted protein [Populus trichocarpa]	0.966	0.752	0.622	1e-34
225442291	166	PREDICTED: uncharacterized protein LOC10	0.932	0.831	0.646	1e-28
449458229	133	PREDICTED: mediator of RNA polymerase II	0.466	0.518	0.826	4e-25
356522394	195	PREDICTED: uncharacterized protein LOC10	0.466	0.353	0.782	5e-24
12321581	234	hypothetical protein [Arabidopsis thalia	0.493	0.311	0.726	7e-23
22330255	244	uncharacterized protein [Arabidopsis tha	0.493	0.299	0.726	8e-23
351723835	177	uncharacterized protein LOC100305737 [Gl	0.959	0.802	0.574	1e-22
357513635	196	hypothetical protein MTR_8g017180 [Medic	0.466	0.352	0.739	1e-21
242074772	174	hypothetical protein SORBIDRAFT_06g03295	0.554	0.471	0.609	8e-20
115436772	152	Os01g0501000 [Oryza sativa Japonica Grou	0.486	0.473	0.666	1e-19

>gi|224135025|ref|XP_002327548.1| predicted protein [Populus trichocarpa] gi|222836102|gb|EEE74523.1| predicted protein [Populus trichocarpa]

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 99/159 (62%), Positives = 112/159 (70%), Gaps = 16/159 (10%)

Query: 4   FSGSGSWNMMPSIPSHNSSPAASNQDNLFLSPQHQQQFYQQPTQFPQQQFQQQGRTPQQQ 63
           FSG GSW ++PS+P+H+ SPA SNQD  +LSPQ QQ  + Q  Q  Q   QQQ    QQQ
Sbjct: 5   FSGGGSWTVIPSVPTHSGSPAHSNQDQFYLSPQQQQPQFTQFQQQQQFNQQQQQFQQQQQ 64

Query: 64  QQPQQQQQQ----------------NQHHQSLASNFHLLHLMENLADAIENGTRDQQSDA 107
            Q QQ QQQ                N HHQSLAS+FHLL L ENLADAIENGTRDQ SDA
Sbjct: 65  YQQQQSQQQRFIQQQQQQQPQVQQQNHHHQSLASHFHLLQLAENLADAIENGTRDQHSDA 124

Query: 108 LVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEE 146
           LVNELN HF+KCQQLL+SIS S++ KAMTVEGQ+RKLEE
Sbjct: 125 LVNELNTHFDKCQQLLNSISSSINAKAMTVEGQKRKLEE 163

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442291|ref|XP_002280177.1| PREDICTED: uncharacterized protein LOC100260024 [Vitis vinifera] gi|147856497|emb|CAN78638.1| hypothetical protein VITISV_031737 [Vitis vinifera] gi|297743090|emb|CBI35957.3| unnamed protein product [Vitis vinifera]

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 95/147 (64%), Positives = 113/147 (76%), Gaps = 9/147 (6%)

Query: 1   MD-PFSGSGSWNMMPSIPSHNSSPAASNQDNLFLSPQHQQQFYQQPTQFPQQQFQQQGRT 59
           MD P+SG GSW+M+PS+  H+++   S+QD+            QQP Q    Q QQQ   
Sbjct: 1   MDHPYSG-GSWSMIPSMSPHSNAATPSDQDH-------LFLQQQQPQQHHLYQHQQQRLH 52

Query: 60  PQQQQQPQQQQQQNQHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKC 119
            QQQQQ QQQQQQ+ HHQSLAS+FHLLHL+ENL+DAIENGTRDQ SDALV ELN+HFEKC
Sbjct: 53  HQQQQQQQQQQQQHHHHQSLASHFHLLHLVENLSDAIENGTRDQHSDALVRELNSHFEKC 112

Query: 120 QQLLSSISESLDTKAMTVEGQRRKLEE 146
           QQLL+SIS S++TKAMTVEGQ+RKLEE
Sbjct: 113 QQLLNSISVSINTKAMTVEGQKRKLEE 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458229|ref|XP_004146850.1| PREDICTED: mediator of RNA polymerase II transcription subunit 9-like [Cucumis sativus]

 Score =  119 bits (298), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 65/69 (94%)

Query: 78  SLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTV 137
           SLAS+FHLLHL+E LADAIENGTRDQQSDALVN+LNNHFEKC+QLL+SIS SL +KAMT 
Sbjct: 38  SLASHFHLLHLVEKLADAIENGTRDQQSDALVNDLNNHFEKCRQLLNSISGSLSSKAMTK 97

Query: 138 EGQRRKLEE 146
           EGQ++KLEE
Sbjct: 98  EGQKKKLEE 106

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522394|ref|XP_003529831.1| PREDICTED: uncharacterized protein LOC100803884 [Glycine max]

 Score =  115 bits (289), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 54/69 (78%), Positives = 66/69 (95%)

Query: 78  SLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTV 137
           SLAS++HLLHL+ENLA+ IE+GT DQQSDAL+NEL+NHFEKCQQLL+SIS+S+ TKAMTV
Sbjct: 100 SLASHYHLLHLVENLAEVIEHGTPDQQSDALINELSNHFEKCQQLLNSISDSISTKAMTV 159

Query: 138 EGQRRKLEE 146
           EGQ++KLEE
Sbjct: 160 EGQKKKLEE 168

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12321581|gb|AAG50844.1|AC073944_11 hypothetical protein [Arabidopsis thaliana]

 Score =  112 bits (279), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 53/73 (72%), Positives = 63/73 (86%)

Query: 74  QHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTK 133
           Q HQSLAS+FHL  ++E LAD IENGTRDQ SDALVNELN+HF+KCQQLL+SIS SL +K
Sbjct: 145 QQHQSLASHFHLYPMVEKLADVIENGTRDQNSDALVNELNSHFDKCQQLLNSISGSLGSK 204

Query: 134 AMTVEGQRRKLEE 146
            MTV+GQ+R +EE
Sbjct: 205 TMTVDGQKRNVEE 217

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330255|ref|NP_175905.2| uncharacterized protein [Arabidopsis thaliana] gi|75158655|sp|Q8RWA2.1|MED9_ARATH RecName: Full=Mediator of RNA polymerase II transcription subunit 9 gi|20260684|gb|AAM13240.1| unknown protein [Arabidopsis thaliana] gi|30023712|gb|AAP13389.1| At1g55080 [Arabidopsis thaliana] gi|110742509|dbj|BAE99172.1| hypothetical protein [Arabidopsis thaliana] gi|332195062|gb|AEE33183.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  111 bits (278), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 53/73 (72%), Positives = 63/73 (86%)

Query: 74  QHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTK 133
           Q HQSLAS+FHL  ++E LAD IENGTRDQ SDALVNELN+HF+KCQQLL+SIS SL +K
Sbjct: 145 QQHQSLASHFHLYPMVEKLADVIENGTRDQNSDALVNELNSHFDKCQQLLNSISGSLGSK 204

Query: 134 AMTVEGQRRKLEE 146
            MTV+GQ+R +EE
Sbjct: 205 TMTVDGQKRNVEE 217

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723835|ref|NP_001236013.1| uncharacterized protein LOC100305737 [Glycine max] gi|255626477|gb|ACU13583.1| unknown [Glycine max]

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/148 (57%), Positives = 101/148 (68%), Gaps = 6/148 (4%)

Query: 1   MDPFSGSG-SWNMMPSIPSHNSSPAASNQD-NLFLSPQHQQQFYQQPTQFPQQQFQQQGR 58
           MD +  SG SW M   IP+HNS  + SNQD NLFL  Q   Q          Q   QQ +
Sbjct: 1   MDHYGSSGGSWTM---IPTHNSQ-SQSNQDPNLFLQQQQFLQSQPFQQALAPQSPFQQQQ 56

Query: 59  TPQQQQQPQQQQQQNQHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEK 118
             +  QQ QQQQQ    HQSLAS++HLLHL+ENLA+ IE+GT DQ SDAL+NE +NHFEK
Sbjct: 57  QQRLLQQQQQQQQPQNLHQSLASHYHLLHLVENLAEVIEHGTPDQPSDALINESSNHFEK 116

Query: 119 CQQLLSSISESLDTKAMTVEGQRRKLEE 146
           C QLL+SIS S+ TKAMTVEGQ++KLEE
Sbjct: 117 CLQLLNSISGSISTKAMTVEGQKKKLEE 144

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357513635|ref|XP_003627106.1| hypothetical protein MTR_8g017180 [Medicago truncatula] gi|355521128|gb|AET01582.1| hypothetical protein MTR_8g017180 [Medicago truncatula] gi|388506434|gb|AFK41283.1| unknown [Medicago truncatula]

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 63/69 (91%)

Query: 78  SLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTV 137
           SLAS+FHLL+L+ENLA+ +E+G  DQQSDAL+ EL+NHFEKCQQLL+SIS S+ TKAMTV
Sbjct: 101 SLASHFHLLNLVENLAEVVEHGNPDQQSDALITELSNHFEKCQQLLNSISASISTKAMTV 160

Query: 138 EGQRRKLEE 146
           EGQ++KLEE
Sbjct: 161 EGQKKKLEE 169

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242074772|ref|XP_002447322.1| hypothetical protein SORBIDRAFT_06g032950 [Sorghum bicolor] gi|241938505|gb|EES11650.1| hypothetical protein SORBIDRAFT_06g032950 [Sorghum bicolor]

 Score =  101 bits (252), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 53/87 (60%), Positives = 64/87 (73%), Gaps = 5/87 (5%)

Query: 65  QPQQQ-----QQQNQHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKC 119
           QPQQ      Q Q  HH SLAS+FHLLHL+  LADAI  GTRDQ SDALV EL + F +C
Sbjct: 60  QPQQALMSPPQPQQHHHASLASHFHLLHLVTRLADAIGTGTRDQNSDALVEELTSQFARC 119

Query: 120 QQLLSSISESLDTKAMTVEGQRRKLEE 146
           QQLL+SIS ++ +K+ TVEGQR+ L+E
Sbjct: 120 QQLLNSISGTISSKSTTVEGQRQSLDE 146

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115436772|ref|NP_001043132.1| Os01g0501000 [Oryza sativa Japonica Group] gi|56201801|dbj|BAD73251.1| unknown protein [Oryza sativa Japonica Group] gi|113532663|dbj|BAF05046.1| Os01g0501000 [Oryza sativa Japonica Group]

 Score =  100 bits (250), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/72 (66%), Positives = 58/72 (80%)

Query: 75  HHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKA 134
           HH SLAS+FHLLHL   LADAI  GTRDQ SDALV +L + F +CQQLL+SIS +L +K+
Sbjct: 52  HHASLASHFHLLHLTTRLADAIGKGTRDQNSDALVEDLTSQFARCQQLLNSISGTLSSKS 111

Query: 135 MTVEGQRRKLEE 146
           +TVEGQR+ LEE
Sbjct: 112 ITVEGQRKSLEE 123

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

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	148
TAIR|locus:2205662	244	MED9 "AT1G55080" [Arabidopsis	0.466	0.282	0.724	1.4e-27
TAIR|locus:2013768	89	AT1G29580 "AT1G29580" [Arabido	0.398	0.662	0.419	8.1e-05

TAIR|locus:2205662 MED9 "AT1G55080" [Arabidopsis thaliana (taxid:3702)]

 Score = 257 (95.5 bits), Expect = 1.4e-27, Sum P(2) = 1.4e-27
 Identities = 50/69 (72%), Positives = 60/69 (86%)

Query:    78 SLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTV 137
             SLAS+FHL  ++E LAD IENGTRDQ SDALVNELN+HF+KCQQLL+SIS SL +K MTV
Sbjct:   149 SLASHFHLYPMVEKLADVIENGTRDQNSDALVNELNSHFDKCQQLLNSISGSLGSKTMTV 208

Query:   138 EGQRRKLEE 146
             +GQ+R +EE
Sbjct:   209 DGQKRNVEE 217

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0016592 "mediator complex" evidence=IDA

TAIR|locus:2013768 AT1G29580 "AT1G29580" [Arabidopsis thaliana (taxid:3702)]

 Score = 94 (38.1 bits), Expect = 8.1e-05, P = 8.1e-05
 Identities = 26/62 (41%), Positives = 36/62 (58%)

Query:    78 SLASNFHLLHLMENLADAIENGTRDQQSDAL-VNELNNHFEKCQQLLSSISESLDTKAMT 136
             +LAS  HL  L+ENL D  E+  RDQ SDAL V+    + E+ +QLL    E ++    +
Sbjct:    23 TLAS--HLYPLVENLKDVTESRARDQNSDALYVDVQKQNLEESEQLLQQRMELIEEYKKS 80

Query:   137 VE 138
             VE
Sbjct:    81 VE 82


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        0.310   0.123   0.343    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      148       105   0.00091  102 3  11 23  0.48    30
                                                     29  0.39    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  548 (58 KB)
  Total size of DFA:  116 KB (2077 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:  12.92u 0.12s 13.04t   Elapsed:  00:00:00
  Total cpu time:  12.92u 0.12s 13.04t   Elapsed:  00:00:00
  Start:  Fri May 10 11:39:10 2013   End:  Fri May 10 11:39:10 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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)
Q8RWA2	MED9_ARATH	No assigned EC number	0.7260	0.4932	0.2991	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

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	148
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	9e-05
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	2e-04
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	9e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	0.001
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	0.002

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 18/45 (40%), Positives = 21/45 (46%)

Query: 36  QHQQQFYQQPTQFPQQQFQQQGRTPQQQQQPQQQQQQNQHHQSLA 80
           + +QQ  Q      Q Q  QQG+  Q QQQ QQ Q       SLA
Sbjct: 619 RGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLA 663

Length = 820

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 18/48 (37%), Positives = 19/48 (39%), Gaps = 2/48 (4%)

Query: 36  QHQQQFYQQ--PTQFPQQQFQQQGRTPQQQQQPQQQQQQNQHHQSLAS 81
             Q+QF  Q    Q  Q Q  Q    P QQ Q  Q QQQ Q  Q    
Sbjct: 610 DLQEQFNAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQG 657

Length = 820

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 12/43 (27%), Positives = 16/43 (37%)

Query: 36  QHQQQFYQQPTQFPQQQFQQQGRTPQQQQQPQQQQQQNQHHQS 78
           + QQ    +  +  Q+QF  Q    Q QQ    Q Q     Q 
Sbjct: 598 REQQGLSDETFRDLQEQFNAQRGEQQGQQGQGGQGQGQPGQQG 640

Length = 820

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 24/64 (37%), Positives = 26/64 (40%), Gaps = 11/64 (17%)

Query: 23  PAASNQDNLFLSPQHQQQFYQQPTQ--FPQQQFQQ---------QGRTPQQQQQPQQQQQ 71
            A   Q      P   Q  YQQP Q   PQ Q+QQ         Q + PQQ   PQ Q Q
Sbjct: 759 VAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQ 818

Query: 72  QNQH 75
           Q Q 
Sbjct: 819 QPQQ 822

Length = 1355

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 14/43 (32%), Positives = 15/43 (34%)

Query: 32  FLSPQHQQQFYQQPTQFPQQQFQQQGRTPQQQQQPQQQQQQNQ 74
            L  Q   Q  +Q  Q  Q    Q     Q QQ   QQQ Q  
Sbjct: 610 DLQEQFNAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQG 652

Length = 820

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	148
PF07544	83	Med9: RNA polymerase II transcription mediator com	92.56
PF07197	51	DUF1409: Protein of unknown function (DUF1409); In	89.44

>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=92.56  E-value=0.24  Score=34.75  Aligned_cols=59  Identities=19%  Similarity=0.305  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHhc-CCCC-cchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhhc
Q 032021           85 LLHLMENLADAIEN-GTRD-QQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEER  147 (148)
Q Consensus        85 L~~lve~Ladaie~-GtRD-Q~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE~  147 (148)
                      ++|.+-++-..+++ |..| ...+.-+.+|.-+|.+|..++.++.+    -..||+-|..++++.
T Consensus         4 ~lP~i~~~l~~~~~d~~~~~kd~~~~~~~lk~Klq~ar~~i~~lpg----i~~s~eeq~~~i~~L   64 (83)
T PF07544_consen    4 FLPLIFDILHQISKDPPLSSKDLDTATGSLKHKLQKARAAIRELPG----IDRSVEEQEEEIEEL   64 (83)
T ss_pred             ccchHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCC----ccCCHHHHHHHHHHH
Confidence            56777777777776 6665 34567788899999999999999776    355677777776654

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

>PF07197 DUF1409: Protein of unknown function (DUF1409); InterPro: IPR010811 This represents a short conserved region (approximately 50 residues long), sometimes repeated, within a number of hypothetical Oryza sativa proteins of unknown function

Probab=89.44  E-value=0.33  Score=32.97  Aligned_cols=40  Identities=30%  Similarity=0.358  Sum_probs=35.2

Q ss_pred             HHHHHH---HHHhHHHHHHHHHHhhhhcccccceehhhhhhhh
Q 032021          106 DALVNE---LNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLE  145 (148)
Q Consensus       106 DaLv~E---L~s~FekcQQLLnSis~sl~tk~~TVegQk~kLE  145 (148)
                      |.||..   +.++|++|+-.|-.=...+.+-++.||-||-|||
T Consensus         8 d~lv~~cg~IrarleE~qa~i~~e~~~l~~~~~~lEq~~~KL~   50 (51)
T PF07197_consen    8 DLLVVDCGSIRARLEEIQAQIPDELAKLATPAVYLEQHQFKLE   50 (51)
T ss_pred             HHHHhccchHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHhc
Confidence            566665   4799999999999988999999999999999997

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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	148
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	92.89

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=92.89  E-value=0.031  Score=48.63  Aligned_cols=12  Identities=25%  Similarity=0.504  Sum_probs=0.0

Q ss_pred             CcceeccCCCCC
Q 032021            8 GSWNMMPSIPSH   19 (148)
Q Consensus         8 GSwtMiPs~~s~   19 (148)
                      .+..|+|..+.+
T Consensus         9 ~~~~~~~~~~~~   20 (727)
T 4b8c_D            9 NSIGMVPTVGTP   20 (727)
T ss_dssp             ------------
T ss_pred             cccCCCcccCCc
Confidence            455677744433

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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