Citrus Sinensis ID: 040074

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------15
Protein Sequence
MDDQEQQDQQHQVDQQMQSVQQQAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASDDFPPPLDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELERV
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccccccccccccccccccHHHHHHccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccHcccccccHHcccccccccHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHcHHccccccccccHHHHHHHHHHccHHHHHHHHHHcccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MDDQEQQDQQHQVDQQMQSVQQQAEIEDMIACVNVmddallpclteldlnkaimpdfeapltdfdepavqpavetelqasddfpppldhqklyFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELERV
Flexible Loop (DISEMBL)
MDDQEQQDQQHQVDQQMQSVQQQAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETElqasddfppplDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELrdrldkhnaelerv
Low Complexity Region (SEG)
MddqeqqdqqhqvdqqmqsvqqqAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASDDFPPPLDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELERV
Disordered region (IsUnstruct)
*************************IEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDF************************HQKLYFRLTIVKE***********************************************
Disordered Region (DISOPRED)
******************************ACVNVMDDALLPCLTELDLNKAIMPDF***L*DFDEPAVQPAVETEL**SDDFPPPLDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD*LDK********
Disordered Region (DISEMBL)
**********************QAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASDDFPPPLDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELERV
Disordered Region (DISPRO)
**********************QAEIEDMIACVNVMDDALLPCLTELDLNKAIMPD**APLTDFDEPAVQPAVETELQASDDFPPPLDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAEL***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDDQEQQDQQHQVDQQMQSVQQQAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASDDFPPPLDHQKLYFRLTIVKEPRHExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLERV
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	148	2.2.26 [Sep-21-2011]
Q9LFA5	156	Mediator of RNA polymeras	yes	no	0.790	0.75	0.338	7e-09

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

 Score = 59.7 bits (143), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 47/139 (33%), Positives = 74/139 (53%), Gaps = 22/139 (15%)

Query: 19  SVQQQAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQ 78
           S  Q  +IED++ACV  ++ ALLPCL   +L           +     P+ Q  VE   +
Sbjct: 31  SNNQNNDIEDIMACVTALEAALLPCLPARELQ---------AIDRSPHPSHQIDVE---R 78

Query: 79  ASDDFPPPLDHQKLYFRLTIVKEPR---------HEIDAMEEELKIKDELVQKQEKVIQE 129
            + DF       +LYF + + +E R          +I  MEEELK KDEL++K  ++ QE
Sbjct: 79  HARDFMEAAKKLQLYF-MGLKREDRAPSRAESLKKDIAVMEEELKTKDELIKKHMRLFQE 137

Query: 130 LKKELRDRLDKHNAELERV 148
            +K ++++++KH  ELE+V
Sbjct: 138 SQKLVKEQIEKHRDELEKV 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	148
449469116	141	PREDICTED: mediator of RNA polymerase II	0.858	0.900	0.418	9e-15
356512776	141	PREDICTED: uncharacterized protein LOC10	0.905	0.950	0.393	5e-13
255564204	140	conserved hypothetical protein [Ricinus	0.763	0.807	0.416	2e-12
225437408	139	PREDICTED: uncharacterized protein LOC10	0.743	0.791	0.418	6e-12
356525553	141	PREDICTED: uncharacterized protein LOC10	0.905	0.950	0.374	2e-11
224131100	115	predicted protein [Populus trichocarpa]	0.729	0.939	0.385	1e-10
326529489	146	predicted protein [Hordeum vulgare subsp	0.729	0.739	0.387	3e-09
226492024	145	uncharacterized protein LOC100276705 [Ze	0.702	0.717	0.354	5e-09
357134587	146	PREDICTED: uncharacterized protein LOC10	0.729	0.739	0.372	6e-09
242089591	145	hypothetical protein SORBIDRAFT_09g00428	0.675	0.689	0.352	1e-08

>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 = 85.1 bits (209), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 62/148 (41%), Positives = 87/148 (58%), Gaps = 21/148 (14%)

Query: 8   DQQHQVDQQMQSVQQQAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEP 67
           DQQH +D Q+QS   Q+  EDMIA V  ++ ALLPCL   +L           +     P
Sbjct: 8   DQQHSLDPQLQS--SQSPREDMIAYVMALEAALLPCLPARELQ---------AIDRSPHP 56

Query: 68  AVQPAVETELQASDDFPPPLDHQKLYF-------RLTIVKEPRHEIDAMEEELKIKDELV 120
           + Q  VE   + + DF       +LYF       + T V+  R EI A+EEELK+K+E++
Sbjct: 57  SHQVDVE---RHARDFMEAAKKLQLYFIGLQREDQPTKVETLRKEISAIEEELKVKNEII 113

Query: 121 QKQEKVIQELKKELRDRLDKHNAELERV 148
           +KQEK+I+  KK+L+D+LDKHN ELE+V
Sbjct: 114 KKQEKLIEGWKKDLKDQLDKHNNELEKV 141

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 79.3 bits (194), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 81/155 (52%), Gaps = 21/155 (13%)

Query: 1   MDDQEQQDQQHQVDQQMQSVQQQAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAP 60
           M D++  DQQH  D Q+ S     +  DM++CV  ++ ALLPCL   +L         + 
Sbjct: 1   MGDRQVVDQQHMGDPQLPSSPPSKD--DMVSCVMALEAALLPCLPARELQAIDRSPHPSH 58

Query: 61  LTDFDEPAVQPAVETELQASDDFPPPLDHQKLYF-------RLTIVKEPRHEIDAMEEEL 113
             D D  A             DF       +LYF       + T V+  R EI  MEEEL
Sbjct: 59  QIDVDRYA------------RDFMEAAKKLQLYFISLQREDKPTKVEMLRKEIALMEEEL 106

Query: 114 KIKDELVQKQEKVIQELKKELRDRLDKHNAELERV 148
            IK+EL++KQE +IQE KKEL+D+LDKH  EL+RV
Sbjct: 107 NIKNELIKKQENLIQEWKKELKDQLDKHKIELDRV 141

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/132 (41%), Positives = 72/132 (54%), Gaps = 19/132 (14%)

Query: 24  AEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASDDF 83
           A  EDMI CV  ++ ALLPCL   +L           +     P+ Q  VE   + + DF
Sbjct: 21  AATEDMIECVMALEAALLPCLPARELQ---------AIDRSPHPSHQIDVE---RHARDF 68

Query: 84  PPPLDHQKLYF-------RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136
                  +LYF       + T  +  R EI  MEEELKIKDE+++KQE++IQE +KEL D
Sbjct: 69  MEAAKKLQLYFIGLQREDQPTAAETLRKEIAVMEEELKIKDEIIKKQERLIQEWRKELTD 128

Query: 137 RLDKHNAELERV 148
           +L KH  ELERV
Sbjct: 129 QLQKHKTELERV 140

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 75.9 bits (185), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 54/129 (41%), Positives = 72/129 (55%), Gaps = 19/129 (14%)

Query: 27  EDMIACVNVMDDALLPCLTELDL---NKAIMP----DFEAPLTDFDEPAVQPAVETELQA 79
           +DMIACV  ++ ALLPCL   +L   +++  P    D E    DF E A +  V      
Sbjct: 23  QDMIACVMALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQVYFISLQ 82

Query: 80  SDDFPPPLDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLD 139
            +D P            T  +  R EI  MEEEL++K EL+ KQE++IQ  +KEL+D+LD
Sbjct: 83  REDQP------------TKAETLRKEIAVMEEELRLKTELINKQERLIQGWRKELKDQLD 130

Query: 140 KHNAELERV 148
           KHN ELERV
Sbjct: 131 KHNTELERV 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/155 (37%), Positives = 79/155 (50%), Gaps = 21/155 (13%)

Query: 1   MDDQEQQDQQHQVDQQMQSVQQQAEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAP 60
           M D+   DQQH  D Q+ S       +DM++CV  ++ ALLPCL   +L         + 
Sbjct: 1   MGDRLVVDQQHTGDAQLPS--SPPSKDDMVSCVMALEAALLPCLPARELQAIDRSPHPSH 58

Query: 61  LTDFDEPAVQPAVETELQASDDFPPPLDHQKLYF-------RLTIVKEPRHEIDAMEEEL 113
             D D  A             DF       +LYF       + T ++  R E+  MEEEL
Sbjct: 59  QIDVDRYA------------RDFMEAAKKLQLYFISLQREDKPTKLEMLRKEVALMEEEL 106

Query: 114 KIKDELVQKQEKVIQELKKELRDRLDKHNAELERV 148
             K+EL++KQE +IQE KKEL+D+LDKH  EL+RV
Sbjct: 107 NKKNELIKKQENLIQEWKKELKDQLDKHKIELDRV 141

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 71.2 bits (173), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 70/127 (55%), Gaps = 19/127 (14%)

Query: 29  MIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASDDFPPPLD 88
           MI CV  ++ ALLPCL   +L           +     P+ Q  VE   + + DF     
Sbjct: 1   MIGCVMALEAALLPCLPARELQ---------AIDRSPHPSHQIDVE---RHARDFMEAAK 48

Query: 89  HQKLYF-------RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKH 141
             +LYF       + T+ +  R +I  MEEELK+KDEL+++QE++IQ   KEL+D+ +KH
Sbjct: 49  KLQLYFIGLQREDQPTMSETLRKDIGMMEEELKVKDELIKRQERLIQGWWKELKDQAEKH 108

Query: 142 NAELERV 148
           N ELERV
Sbjct: 109 NTELERV 115

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 = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 50/129 (38%), Positives = 66/129 (51%), Gaps = 21/129 (16%)

Query: 28  DMIACVNVMDDALLPCL-------TELDLNKAIMPDFEAPLTDFDEPAVQ-PAVETELQA 79
           DM+ACV  ++ ALLPCL        +  L  +   D E    DF E A +  +    LQ 
Sbjct: 31  DMMACVAALEAALLPCLPARELQAVDRSLQSSHQIDVERHARDFMEAAKKLQSYFISLQR 90

Query: 80  SDDFPPPLDHQKLYFRLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLD 139
            D    P + + L          R EI  MEEELK K EL+ K + +I+  +KEL+D+L 
Sbjct: 91  EDQ---PTNEELL----------RKEITTMEEELKTKSELIAKHKSLIEGWQKELKDQLG 137

Query: 140 KHNAELERV 148
           KHN ELERV
Sbjct: 138 KHNTELERV 146

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226492024|ref|NP_001143902.1| uncharacterized protein LOC100276705 [Zea mays] gi|195629348|gb|ACG36315.1| hypothetical protein [Zea mays] gi|413948788|gb|AFW81437.1| hypothetical protein ZEAMMB73_104324 [Zea mays]

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 50/141 (35%), Positives = 67/141 (47%), Gaps = 37/141 (26%)

Query: 24  AEIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASD-- 81
             +EDM+ACV  ++ ALLPCL   +L                      AV+  LQ+S   
Sbjct: 26  GGLEDMLACVAALEAALLPCLPARELQ---------------------AVDRSLQSSHQI 64

Query: 82  -------DFPPPLDHQKLYFRLTIVKEP-------RHEIDAMEEELKIKDELVQKQEKVI 127
                  DF       + YF     +EP       R EI  MEEELK K EL+ K +K+I
Sbjct: 65  DVERHARDFMEAAKKLQSYFISLQREEPPSAEEMLRKEITTMEEELKSKSELIAKHKKLI 124

Query: 128 QELKKELRDRLDKHNAELERV 148
           +  +KEL+++L KH  ELERV
Sbjct: 125 EGWQKELKEQLSKHITELERV 145

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357134587|ref|XP_003568898.1| PREDICTED: uncharacterized protein LOC100840919 [Brachypodium distachyon]

 Score = 65.9 bits (159), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 48/129 (37%), Positives = 66/129 (51%), Gaps = 21/129 (16%)

Query: 28  DMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPA--VETELQASDDFPP 85
           DM+ACV  ++ ALLPCL          P  E    D    ++Q +  ++ E  A D    
Sbjct: 31  DMMACVAALEAALLPCL----------PARELQAVD---RSLQSSHQIDVERHARDFMEA 77

Query: 86  PLDHQKLYFRLTIVKEP------RHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLD 139
               Q  +  L    +P      + EI  MEEELK K EL+ K +K+I+  +KEL+D+L 
Sbjct: 78  AKKLQSYFISLQREDQPTTEEMLQKEIATMEEELKTKSELIAKHKKLIEGWQKELKDQLG 137

Query: 140 KHNAELERV 148
           KHN ELERV
Sbjct: 138 KHNTELERV 146

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

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 = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 49/139 (35%), Positives = 68/139 (48%), Gaps = 39/139 (28%)

Query: 27  EDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASD----- 81
           EDM+ACV  ++ ALLPCL   +L                      AV+  LQ+S      
Sbjct: 29  EDMLACVAALEAALLPCLPARELQ---------------------AVDRSLQSSHQIDVE 67

Query: 82  ----DFPPPLDHQKLYFRLTIVKEP--------RHEIDAMEEELKIKDELVQKQEKVIQE 129
               DF       + YF +++ +E         R EI  MEEELK K EL+ K +K+I+ 
Sbjct: 68  RHARDFMEAAKKLQSYF-ISLQREDQPTAEEMLRKEITTMEEELKTKSELIAKHKKLIEG 126

Query: 130 LKKELRDRLDKHNAELERV 148
            +KEL+++L KH  ELERV
Sbjct: 127 WRKELKEQLGKHITELERV 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	148
TAIR|locus:2085156	156	AT3G52860 "AT3G52860" [Arabido	0.75	0.711	0.368	6.4e-12

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

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 49/133 (36%), Positives = 77/133 (57%)

Query:    25 EIEDMIACVNVMDDALLPCLTELDLNKAIMPDFEAPLTDFDEPAVQPAVETELQASDDFP 84
             +IED++ACV  ++ ALLPCL   +L +AI  D  +P      P+ Q  ++ E  A D F 
Sbjct:    37 DIEDIMACVTALEAALLPCLPAREL-QAI--D-RSP-----HPSHQ--IDVERHARD-FM 84

Query:    85 PPLDHQKLYFRLTIVKEPR---------HEIDAMEEELKIKDELVQKQEKVIQELKKELR 135
                   +LYF + + +E R          +I  MEEELK KDEL++K  ++ QE +K ++
Sbjct:    85 EAAKKLQLYF-MGLKREDRAPSRAESLKKDIAVMEEELKTKDELIKKHMRLFQESQKLVK 143

Query:   136 DRLDKHNAELERV 148
             ++++KH  ELE+V
Sbjct:   144 EQIEKHRDELEKV 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        0.316   0.135   0.378    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       126   0.00091  102 3  11 22  0.41    31
                                                     29  0.40    33


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:  499 (53 KB)
  Total size of DFA:  112 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:  23.06u 0.11s 23.17t   Elapsed:  00:00:01
  Total cpu time:  23.06u 0.11s 23.17t   Elapsed:  00:00:01
  Start:  Mon May 20 18:03:20 2013   End:  Mon May 20 18:03:21 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	148
PF11594	106	Med28: Mediator complex subunit 28; InterPro: IPR0	97.38

>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=97.38  E-value=0.00022  Score=53.85  Aligned_cols=63  Identities=27%  Similarity=0.405  Sum_probs=54.5

Q ss_pred             ccCCCCccchhhhhh---hhh-----hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 040074           80 SDDFPPPLDHQKLYF---RLT-----IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHN  142 (148)
Q Consensus        80 ~rDFmeaakklqlYF---~lq-----~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~  142 (148)
                      +--|...|+....||   |+.     -+..++.||..+.+||--|++|++||.-.|..|++.|-|.-+.|.
T Consensus        10 ~~~FlD~aRq~e~~FlqKr~~LS~~kpe~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d~~~~~k   80 (106)
T PF11594_consen   10 IQSFLDVARQMEAFFLQKRFELSAYKPEQVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLSDAQNQHK   80 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            356888899988888   332     667789999999999999999999999999999999998877764

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 [].

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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

ID	Length	Definition	E-value
Query	148
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.5 bits (104), Expect = 4e-06
 Identities = 26/156 (16%), Positives = 60/156 (38%), Gaps = 34/156 (21%)

Query: 23  QAEIEDMIA-CVNVMDDALLP---CLTE---LDLNKAIMPDFEAPLTDFDEPAVQPAVET 75
             E++ ++   ++      LP     T    L +    + D  A   ++        + T
Sbjct: 300 PDEVKSLLLKYLD-CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD-KLTT 357

Query: 76  ELQASDDFPPPLDHQKLYFRLTI----VKEP------------RHEIDAMEEELKIKDEL 119
            +++S +   P +++K++ RL++       P            + ++  +  +L  K  L
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL-HKYSL 416

Query: 120 VQKQEK--------VIQELKKELRDRLDKHNAELER 147
           V+KQ K        +  ELK +L +    H + ++ 
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH 452

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 37.5 bits (86), Expect = 8e-04
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 19/93 (20%)

Query: 44  LTELDL-NKAIMPDFEAPLT-DFDEPAVQPAVETELQASDDFPPPLDHQKLYFRLTIVKE 101
             E     K I+  FE     +FD   VQ   ++ L   +     +DH        I+  
Sbjct: 11  TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEE-----IDH--------IIMS 57

Query: 102 PRHEIDAMEEELKIKDELVQKQEKVIQELKKEL 134
                DA+   L++   L+ KQE+++Q+  +E+
Sbjct: 58  K----DAVSGTLRLFWTLLSKQEEMVQKFVEEV 86

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