Citrus Sinensis ID: 032610

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADNCLNLKKPN
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
MDIISQLQEQINQIAGIafntfgtlqrdappvrlspnypeppanptedaanfaeqPKLMSAALVKAAKQFDALVAAlplaeggeEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADNclnlkkpn
Flexible Loop (DISEMBL)
MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQaadnclnlkkpn
Low Complexity Region (SEG)
MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSAALVKAAKQFDalvaalplaeggeeaQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADNCLNLKKPN
Disordered region (IsUnstruct)
*********QINQIAGIAFNTFGTL************************************ALVKAAKQFDALVAALPL**********************************************************
Disordered Region (DISOPRED)
MDIISQLQEQINQIAGIAFNTFGTLQRDA**************************PKLMSAALVKAAKQFDALVA**********************************EAAEKELKQVQELFSQAADN*L******
Disordered Region (DISEMBL)
MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADNCLNLKKPN
Disordered Region (DISPRO)
MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADNCLNL****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCLNLKKPN
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	137	2.2.26 [Sep-21-2011]
C0LU16	139	Mediator of RNA polymeras	yes	no	0.992	0.978	0.804	3e-54
Q2TBU8	144	Mediator of RNA polymeras	yes	no	0.934	0.888	0.275	3e-06
Q6BER6	130	Mediator of RNA polymeras	yes	no	0.751	0.792	0.281	4e-06
Q9CQ39	144	Mediator of RNA polymeras	yes	no	0.875	0.833	0.284	5e-06
Q4R6N3	144	Mediator of RNA polymeras	N/A	no	0.875	0.833	0.284	6e-06
Q7ZTI5	145	Mediator of RNA polymeras	yes	no	0.934	0.882	0.275	8e-06
Q16RX1	141	Mediator of RNA polymeras	N/A	no	0.919	0.893	0.282	9e-06
Q13503	144	Mediator of RNA polymeras	yes	no	0.875	0.833	0.276	1e-05
Q9W5P1	142	Mediator of RNA polymeras	yes	no	0.817	0.788	0.288	2e-05
Q5RE46	144	Mediator of RNA polymeras	yes	no	0.824	0.784	0.284	4e-05

>sp|C0LU16|MED21_ARATH Mediator of RNA polymerase II transcription subunit 21 OS=Arabidopsis thaliana GN=MED21 PE=1 SV=1

 Score =  209 bits (533), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 118/138 (85%), Gaps = 2/138 (1%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAAN--FAEQPKL 58
           MDIISQLQEQ+N IA I FN FGTLQRDAPPV+LSPNYPEPPA  T       F EQPK 
Sbjct: 1   MDIISQLQEQVNTIAAITFNAFGTLQRDAPPVQLSPNYPEPPATTTVTDDATPFPEQPKQ 60

Query: 59  MSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQ 118
           +SA LVKAAKQFDALVAALPL+EGGE AQLKRIAELQ END VGQ+LQ+QLEAAEKELKQ
Sbjct: 61  LSAGLVKAAKQFDALVAALPLSEGGEGAQLKRIAELQVENDLVGQELQKQLEAAEKELKQ 120

Query: 119 VQELFSQAADNCLNLKKP 136
           VQELF QAADNCLN+KKP
Sbjct: 121 VQELFGQAADNCLNMKKP 138

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Required for embryo development and defense against necrotrophic fungal pathogens.
Arabidopsis thaliana (taxid: 3702)

>sp|Q2TBU8|MED21_BOVIN Mediator of RNA polymerase II transcription subunit 21 OS=Bos taurus GN=MED21 PE=2 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/138 (27%), Positives = 64/138 (46%), Gaps = 10/138 (7%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLS----PNYPEPPANPTEDAANFAEQPK 57
           D ++QLQ+ +N +A    N  G LQ+  PP   S        + PANPTE+ A      +
Sbjct: 3   DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTEEYA------Q 56

Query: 58  LMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
           L +A + + AK  D L+ +LP  E     Q   + +L+ EN      L+  +   +  L+
Sbjct: 57  LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATSLEDVVYRGDMLLE 116

Query: 118 QVQELFSQAADNCLNLKK 135
           ++Q   +  A + L  + 
Sbjct: 117 KIQSALADIAQSQLKTRS 134

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Bos taurus (taxid: 9913)

>sp|Q6BER6|MED21_CAEEL Mediator of RNA polymerase II transcription subunit 21 OS=Caenorhabditis elegans GN=mdt-21 PE=1 SV=1

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 36/128 (28%), Positives = 61/128 (47%), Gaps = 25/128 (19%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSA 61
           D ++QLQ+ IN++AG+  N  G LQ  APP        E      ED  N A    + +A
Sbjct: 3   DRMTQLQDMINEMAGLMTNAIGVLQATAPPCEFGAISQE-----LEDEPNCA----IFAA 53

Query: 62  ALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQE 121
            + KAAK  + L+ + P+  G +EA+++                ++ ++  EK+ ++V E
Sbjct: 54  GIAKAAKNIEILIDSFPIEAGNQEAEVE----------------EKMIKNDEKQREKVNE 97

Query: 122 LFSQAADN 129
           L     D+
Sbjct: 98  LVGLVGDS 105

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Caenorhabditis elegans (taxid: 6239)

>sp|Q9CQ39|MED21_MOUSE Mediator of RNA polymerase II transcription subunit 21 OS=Mus musculus GN=Med21 PE=1 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 37/130 (28%), Positives = 60/130 (46%), Gaps = 10/130 (7%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLS----PNYPEPPANPTEDAANFAEQPK 57
           D ++QLQ+ +N +A    N  G LQ+  PP   S        + PANPTE      E  +
Sbjct: 3   DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTE------EYAQ 56

Query: 58  LMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
           L +A + + AK  D L+ +LP  E     Q   + +L+ EN      L+  +   +  L+
Sbjct: 57  LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATCLEDVVYRGDMLLE 116

Query: 118 QVQELFSQAA 127
           ++Q   +  A
Sbjct: 117 KIQSALADIA 126

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Mus musculus (taxid: 10090)

>sp|Q4R6N3|MED21_MACFA Mediator of RNA polymerase II transcription subunit 21 OS=Macaca fascicularis GN=MED21 PE=2 SV=1

 Score = 49.3 bits (116), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 37/130 (28%), Positives = 61/130 (46%), Gaps = 10/130 (7%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLS----PNYPEPPANPTEDAANFAEQPK 57
           D ++QLQ+ +N +A    N  G LQ+  PP   S        + PANPTE+ A      +
Sbjct: 3   DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTEEYA------Q 56

Query: 58  LMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
           L +A + + AK  D L+ +LP  E     Q   + +L+ EN      L+  +   +  L+
Sbjct: 57  LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATCLEDVVYRGDMLLE 116

Query: 118 QVQELFSQAA 127
           ++Q   +  A
Sbjct: 117 KIQSALADIA 126

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Macaca fascicularis (taxid: 9541)

>sp|Q7ZTI5|MED21_DANRE Mediator of RNA polymerase II transcription subunit 21 OS=Danio rerio GN=med21 PE=2 SV=1

 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 38/138 (27%), Positives = 65/138 (47%), Gaps = 10/138 (7%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLS----PNYPEPPANPTEDAANFAEQPK 57
           D ++QLQ+ +N +A    N  G LQ+ APP   S        + P+NPTE+ A      +
Sbjct: 3   DRLTQLQDAVNSLADQFCNAIGVLQQCAPPASFSNIQTAINKDQPSNPTEEYA------Q 56

Query: 58  LMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
           L +A + + AK  D L+ +LP  E     Q   + +L+ EN      L+  +   +  L+
Sbjct: 57  LFAALIARTAKDVDVLIDSLPSEESTAALQAASLRQLEEENQEAAARLEEVVYRGDALLE 116

Query: 118 QVQELFSQAADNCLNLKK 135
           ++Q   +  A + L  + 
Sbjct: 117 KIQTALADIAQSQLRTRS 134

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Danio rerio (taxid: 7955)

>sp|Q16RX1|MED21_AEDAE Mediator of RNA polymerase II transcription subunit 21 OS=Aedes aegypti GN=MED21 PE=3 SV=1

 Score = 48.9 bits (115), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 39/138 (28%), Positives = 67/138 (48%), Gaps = 12/138 (8%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPE-----PPANPTEDAANFAEQP 56
           D ++QLQ+ +NQ A    N+ G LQ+ + P +  P +       P  N  ED A      
Sbjct: 3   DRLTQLQDTVNQQAEHFCNSIGILQQCSVPSKF-PGFERTGSQTPQQNQQEDYA------ 55

Query: 57  KLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKEL 116
           +L S  + + AK  D L+ +LP  E   E Q++ +  L+ EN    + L+  +   E  L
Sbjct: 56  QLFSTLISRCAKDIDTLIESLPSEESSIELQVQALKRLEIENQESAEKLEEVVRKGELLL 115

Query: 117 KQVQELFSQAADNCLNLK 134
           +++Q   S  A + L+++
Sbjct: 116 EKIQAALSDIAQSQLDMQ 133

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Aedes aegypti (taxid: 7159)

>sp|Q13503|MED21_HUMAN Mediator of RNA polymerase II transcription subunit 21 OS=Homo sapiens GN=MED21 PE=1 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 61/130 (46%), Gaps = 10/130 (7%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRL----SPNYPEPPANPTEDAANFAEQPK 57
           D ++QLQ+ +N +A    N  G LQ+  PP       +    + PANPTE+ A      +
Sbjct: 3   DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFNNIQTAINKDQPANPTEEYA------Q 56

Query: 58  LMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
           L +A + + AK  D L+ +LP  E     Q   + +L+ EN      L+  +   +  L+
Sbjct: 57  LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATCLEDVVYRGDMLLE 116

Query: 118 QVQELFSQAA 127
           ++Q   +  A
Sbjct: 117 KIQSALADIA 126

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Homo sapiens (taxid: 9606)

>sp|Q9W5P1|MED21_DROME Mediator of RNA polymerase II transcription subunit 21 OS=Drosophila melanogaster GN=MED21 PE=1 SV=1

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 36/125 (28%), Positives = 60/125 (48%), Gaps = 13/125 (10%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPV------RLSPNYPEPPANPTEDAANFAEQ 55
           D ++QLQ+ +NQ A    N  G +Q+ + P       R+ P  P  P  P ED A     
Sbjct: 3   DRLTQLQDTVNQQAEHFCNAIGVIQQTSLPSKFVNFERIGPQTP-IPCPPQEDYA----- 56

Query: 56  PKLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKE 115
            +L +  + + AK  D L+ +LP  +   E Q   +  L+ EN    +DL+  ++  E  
Sbjct: 57  -QLFAQLIARCAKDIDTLIESLPNEDSSIELQNSSLKRLEIENQGTARDLEEVVQKGELL 115

Query: 116 LKQVQ 120
           L+++Q
Sbjct: 116 LEKMQ 120

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Required for activated transcription of the MtnA, MtnB and MtnD genes.

Drosophila melanogaster (taxid: 7227)

>sp|Q5RE46|MED21_PONAB Mediator of RNA polymerase II transcription subunit 21 OS=Pongo abelii GN=MED21 PE=2 SV=1

 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 35/123 (28%), Positives = 57/123 (46%), Gaps = 10/123 (8%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLS----PNYPEPPANPTEDAANFAEQPK 57
           D ++QLQ+ +N +A    N  G LQ+  PP   S        + PAN TE      E  +
Sbjct: 3   DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANSTE------EYAQ 56

Query: 58  LMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
           L +A + + AK  D L+ +LP  E     Q   + +L+ EN      L+  +   +  L+
Sbjct: 57  LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATCLEDVVYRGDMLLE 116

Query: 118 QVQ 120
           ++Q
Sbjct: 117 KIQ 119

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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Pongo abelii (taxid: 9601)

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	137
388509762	139	unknown [Lotus japonicus]	1.0	0.985	0.846	1e-60
224076269	137	predicted protein [Populus trichocarpa]	1.0	1.0	0.861	3e-60
255556538	135	conserved hypothetical protein [Ricinus	0.978	0.992	0.876	2e-59
449463842	138	PREDICTED: mediator of RNA polymerase II	0.985	0.978	0.852	2e-58
351720654	139	uncharacterized protein LOC100306480 [Gl	1.0	0.985	0.810	6e-58
449522780	138	PREDICTED: mediator of RNA polymerase II	0.985	0.978	0.845	1e-57
297809651	139	hypothetical protein ARALYDRAFT_352398 [	0.992	0.978	0.811	2e-55
7267236	381	hypothetical protein [Arabidopsis thalia	0.992	0.356	0.804	1e-53
27754568	162	unknown protein [Arabidopsis thaliana]	0.992	0.839	0.804	2e-52
334186358	139	protein mediator 21 [Arabidopsis thalian	0.992	0.978	0.804	2e-52

>gi|388509762|gb|AFK42947.1| unknown [Lotus japonicus]

 Score =  237 bits (604), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 116/137 (84%), Positives = 127/137 (92%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMS 60
           MDIISQLQEQ+N IA +AFNT GTLQRDAPP R+SPNYPEPPA PTED A F+EQPKLMS
Sbjct: 1   MDIISQLQEQVNLIANLAFNTIGTLQRDAPPNRISPNYPEPPAQPTEDGATFSEQPKLMS 60

Query: 61  AALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQ 120
             LVKAAKQFDALVAALP+AEGGEEAQLKRIAELQ+ENDA+GQ+LQ+QLEAAEKEL QVQ
Sbjct: 61  TGLVKAAKQFDALVAALPIAEGGEEAQLKRIAELQAENDAIGQELQKQLEAAEKELHQVQ 120

Query: 121 ELFSQAADNCLNLKKPN 137
           ELFSQA+DNCLNLKKP+
Sbjct: 121 ELFSQASDNCLNLKKPD 137

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224076269|ref|XP_002304917.1| predicted protein [Populus trichocarpa] gi|222847881|gb|EEE85428.1| predicted protein [Populus trichocarpa]

 Score =  236 bits (601), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 118/137 (86%), Positives = 126/137 (91%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMS 60
           MDIISQLQEQ+NQIAG+ FNTFGTLQRDAP  RLS NYPEPP NPTEDAA+F EQPK MS
Sbjct: 1   MDIISQLQEQVNQIAGLTFNTFGTLQRDAPSARLSQNYPEPPPNPTEDAASFPEQPKQMS 60

Query: 61  AALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQ 120
           AALVKAAKQFDALVAALPL+EGGEEAQLKRIAELQ+ENDAVGQ+LQRQLEAAE+ELK VQ
Sbjct: 61  AALVKAAKQFDALVAALPLSEGGEEAQLKRIAELQAENDAVGQELQRQLEAAERELKLVQ 120

Query: 121 ELFSQAADNCLNLKKPN 137
           ELF Q  DNCLNLKKP+
Sbjct: 121 ELFGQTTDNCLNLKKPD 137

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556538|ref|XP_002519303.1| conserved hypothetical protein [Ricinus communis] gi|223541618|gb|EEF43167.1| conserved hypothetical protein [Ricinus communis]

 Score =  233 bits (594), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 121/138 (87%), Positives = 128/138 (92%), Gaps = 4/138 (2%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPA-NPTEDAANFAEQPKLM 59
           MDIISQLQEQ++ IA +AFNT GTLQRDAPPVRLSPNYPEPPA NP ED    A+QPKLM
Sbjct: 1   MDIISQLQEQVDTIASLAFNTIGTLQRDAPPVRLSPNYPEPPASNPAED---IADQPKLM 57

Query: 60  SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQV 119
           SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQ+ENDAVGQ+LQRQLEAAEKELKQV
Sbjct: 58  SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQAENDAVGQELQRQLEAAEKELKQV 117

Query: 120 QELFSQAADNCLNLKKPN 137
           QELFSQA DNCLNLKKP+
Sbjct: 118 QELFSQATDNCLNLKKPD 135

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463842|ref|XP_004149640.1| PREDICTED: mediator of RNA polymerase II transcription subunit 21-like [Cucumis sativus]

 Score =  229 bits (585), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 116/136 (85%), Positives = 125/136 (91%), Gaps = 1/136 (0%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPAN-PTEDAANFAEQPKLM 59
           MDIISQLQEQ+N IA +AFNTFGTLQRDAPPVRLSPNYPEPP+  PTED A  AEQPKLM
Sbjct: 1   MDIISQLQEQVNTIAALAFNTFGTLQRDAPPVRLSPNYPEPPSQEPTEDNATIAEQPKLM 60

Query: 60  SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQV 119
           SAALVKAAKQFDALVAALPL++GGEE QLKRIAELQ+END VGQ+LQ+QL+AAEKEL QV
Sbjct: 61  SAALVKAAKQFDALVAALPLSDGGEEEQLKRIAELQAENDVVGQELQKQLQAAEKELVQV 120

Query: 120 QELFSQAADNCLNLKK 135
           QELFSQ ADNCLNLKK
Sbjct: 121 QELFSQVADNCLNLKK 136

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351720654|ref|NP_001235648.1| uncharacterized protein LOC100306480 [Glycine max] gi|255628677|gb|ACU14683.1| unknown [Glycine max]

 Score =  228 bits (581), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 111/137 (81%), Positives = 125/137 (91%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMS 60
           MDIISQLQEQ+N IA +AFNT GTLQRDAPP RLSPNYPEPPA+ TED +NF+EQPKLMS
Sbjct: 1   MDIISQLQEQVNLIAHLAFNTVGTLQRDAPPNRLSPNYPEPPAHATEDGSNFSEQPKLMS 60

Query: 61  AALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQ 120
             LVKAAKQFDALVAALP++E GEEAQLKRI+ELQ+ENDA+G +LQ+QLEAAEKEL QVQ
Sbjct: 61  TTLVKAAKQFDALVAALPISESGEEAQLKRISELQAENDAIGLELQKQLEAAEKELNQVQ 120

Query: 121 ELFSQAADNCLNLKKPN 137
           ELF QA+DNCLNLKKP+
Sbjct: 121 ELFRQASDNCLNLKKPD 137

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449522780|ref|XP_004168404.1| PREDICTED: mediator of RNA polymerase II transcription subunit 21-like [Cucumis sativus]

 Score =  227 bits (579), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 115/136 (84%), Positives = 124/136 (91%), Gaps = 1/136 (0%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPAN-PTEDAANFAEQPKLM 59
           MDIISQLQEQ+N IA +AFNTFGTLQRDAPPVRLSPNYPEPP+  PTED A  AEQPKLM
Sbjct: 1   MDIISQLQEQVNTIAALAFNTFGTLQRDAPPVRLSPNYPEPPSQEPTEDNATIAEQPKLM 60

Query: 60  SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQV 119
           SAALVKAAKQFDALVAALPL++GGEE QLKRIAELQ+END VGQ+LQ+QL+AAEKEL QV
Sbjct: 61  SAALVKAAKQFDALVAALPLSDGGEEEQLKRIAELQAENDVVGQELQKQLQAAEKELVQV 120

Query: 120 QELFSQAADNCLNLKK 135
           QELFSQ ADNCLNL K
Sbjct: 121 QELFSQVADNCLNLMK 136

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297809651|ref|XP_002872709.1| hypothetical protein ARALYDRAFT_352398 [Arabidopsis lyrata subsp. lyrata] gi|297318546|gb|EFH48968.1| hypothetical protein ARALYDRAFT_352398 [Arabidopsis lyrata subsp. lyrata]

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 122/138 (88%), Gaps = 2/138 (1%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPT--EDAANFAEQPKL 58
           MDIISQLQEQ+N IA I FN FGTLQRDAPPV+LSPNYPEPPA  T  +DA  F EQPK 
Sbjct: 1   MDIISQLQEQVNTIAAITFNAFGTLQRDAPPVQLSPNYPEPPATTTAVDDATPFPEQPKQ 60

Query: 59  MSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQ 118
           +SA LVKAAKQFDALVAALPL+EGGEEAQLKRIA+LQ END VGQ+LQ+QLEAAEKELKQ
Sbjct: 61  LSAGLVKAAKQFDALVAALPLSEGGEEAQLKRIAQLQVENDLVGQELQKQLEAAEKELKQ 120

Query: 119 VQELFSQAADNCLNLKKP 136
           VQELF QAAD+CLN+KKP
Sbjct: 121 VQELFGQAADSCLNMKKP 138

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7267236|emb|CAB80843.1| hypothetical protein [Arabidopsis thaliana]

 Score =  213 bits (543), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 118/138 (85%), Gaps = 2/138 (1%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAAN--FAEQPKL 58
           MDIISQLQEQ+N IA I FN FGTLQRDAPPV+LSPNYPEPPA  T       F EQPK 
Sbjct: 243 MDIISQLQEQVNTIAAITFNAFGTLQRDAPPVQLSPNYPEPPATTTVTDDATPFPEQPKQ 302

Query: 59  MSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQ 118
           +SA LVKAAKQFDALVAALPL+EGGE AQLKRIAELQ END VGQ+LQ+QLEAAEKELKQ
Sbjct: 303 LSAGLVKAAKQFDALVAALPLSEGGEGAQLKRIAELQVENDLVGQELQKQLEAAEKELKQ 362

Query: 119 VQELFSQAADNCLNLKKP 136
           VQELF QAADNCLN+KKP
Sbjct: 363 VQELFGQAADNCLNMKKP 380

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|27754568|gb|AAO22731.1| unknown protein [Arabidopsis thaliana]

 Score =  209 bits (533), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 118/138 (85%), Gaps = 2/138 (1%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAAN--FAEQPKL 58
           MDIISQLQEQ+N IA I FN FGTLQRDAPPV+LSPNYPEPPA  T       F EQPK 
Sbjct: 24  MDIISQLQEQVNTIAAITFNAFGTLQRDAPPVQLSPNYPEPPATTTVTDDATPFPEQPKQ 83

Query: 59  MSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQ 118
           +SA LVKAAKQFDALVAALPL+EGGE AQLKRIAELQ END VGQ+LQ+QLEAAEKELKQ
Sbjct: 84  LSAGLVKAAKQFDALVAALPLSEGGEGAQLKRIAELQVENDLVGQELQKQLEAAEKELKQ 143

Query: 119 VQELFSQAADNCLNLKKP 136
           VQELF QAADNCLN+KKP
Sbjct: 144 VQELFGQAADNCLNMKKP 161

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334186358|ref|NP_192387.2| protein mediator 21 [Arabidopsis thaliana] gi|302425116|sp|C0LU16.1|MED21_ARATH RecName: Full=Mediator of RNA polymerase II transcription subunit 21; AltName: Full=Mediator complex subunit 21; AltName: Full=RNAPII complex component SRB7 gi|225126090|gb|ACN81041.1| MED21/SRB7 [Arabidopsis thaliana] gi|332657025|gb|AEE82425.1| protein mediator 21 [Arabidopsis thaliana]

 Score =  209 bits (533), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 118/138 (85%), Gaps = 2/138 (1%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAAN--FAEQPKL 58
           MDIISQLQEQ+N IA I FN FGTLQRDAPPV+LSPNYPEPPA  T       F EQPK 
Sbjct: 1   MDIISQLQEQVNTIAAITFNAFGTLQRDAPPVQLSPNYPEPPATTTVTDDATPFPEQPKQ 60

Query: 59  MSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQ 118
           +SA LVKAAKQFDALVAALPL+EGGE AQLKRIAELQ END VGQ+LQ+QLEAAEKELKQ
Sbjct: 61  LSAGLVKAAKQFDALVAALPLSEGGEGAQLKRIAELQVENDLVGQELQKQLEAAEKELKQ 120

Query: 119 VQELFSQAADNCLNLKKP 136
           VQELF QAADNCLN+KKP
Sbjct: 121 VQELFGQAADNCLNMKKP 138

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	137
ZFIN|ZDB-GENE-040426-2763	145	med21 "mediator complex subuni	0.927	0.875	0.248	2.9e-07
UNIPROTKB|Q2TBU8	144	MED21 "Mediator of RNA polymer	0.927	0.881	0.248	4.8e-07
UNIPROTKB|E1C1C6	144	MED21 "Uncharacterized protein	0.927	0.881	0.248	6.1e-07
UNIPROTKB|F1SG80	144	MED21 "Uncharacterized protein	0.927	0.881	0.248	1e-06
MGI|MGI:1347064	144	Med21 "mediator complex subuni	0.927	0.881	0.248	1e-06
UNIPROTKB|Q13503	144	MED21 "Mediator of RNA polymer	0.919	0.875	0.246	1.3e-06
FB|FBgn0040020	142	MED21 "Mediator complex subuni	0.919	0.887	0.265	3e-05
WB|WBGene00007704	130	mdt-21 [Caenorhabditis elegans	0.810	0.853	0.289	0.0001
UNIPROTKB|Q6BER6	130	mdt-21 "Mediator of RNA polyme	0.810	0.853	0.289	0.0001

ZFIN|ZDB-GENE-040426-2763 med21 "mediator complex subunit 21" [Danio rerio (taxid:7955)]

 Score = 117 (46.2 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 34/137 (24%), Positives = 59/137 (43%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYP----EPPANPTEDAANFAEQPK 57
             D ++QLQ+ +N +A    N  G LQ+ APP   S        + P+NPTE+ A      +
Sbjct:     3 DRLTQLQDAVNSLADQFCNAIGVLQQCAPPASFSNIQTAINKDQPSNPTEEYA------Q 56

Query:    58 LMSAALVKAAKQFDXXXXXXXXXXXXXXXQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
             L +A + + AK  D               Q   + +L+ EN      L+  +   +  L+
Sbjct:    57 LFAALIARTAKDVDVLIDSLPSEESTAALQAASLRQLEEENQEAAARLEEVVYRGDALLE 116

Query:   118 QVQELFSQAADNCLNLK 134
             ++Q   +  A + L  +
Sbjct:   117 KIQTALADIAQSQLRTR 133

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q2TBU8 MED21 "Mediator of RNA polymerase II transcription subunit 21" [Bos taurus (taxid:9913)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 34/137 (24%), Positives = 58/137 (42%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYP----EPPANPTEDAANFAEQPK 57
             D ++QLQ+ +N +A    N  G LQ+  PP   S        + PANPTE+ A      +
Sbjct:     3 DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTEEYA------Q 56

Query:    58 LMSAALVKAAKQFDXXXXXXXXXXXXXXXQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
             L +A + + AK  D               Q   + +L+ EN      L+  +   +  L+
Sbjct:    57 LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATSLEDVVYRGDMLLE 116

Query:   118 QVQELFSQAADNCLNLK 134
             ++Q   +  A + L  +
Sbjct:   117 KIQSALADIAQSQLKTR 133

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0001824 "blastocyst development" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|E1C1C6 MED21 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 114 (45.2 bits), Expect = 6.1e-07, P = 6.1e-07
 Identities = 34/137 (24%), Positives = 57/137 (41%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYP----EPPANPTEDAANFAEQPK 57
             D ++QLQ+ +N +A    N  G LQ+  PP   S        + PANPTE+ A      +
Sbjct:     3 DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTEEYA------Q 56

Query:    58 LMSAALVKAAKQFDXXXXXXXXXXXXXXXQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
             L +A + + AK  D               Q   +  L+ EN      L+  +   +  L+
Sbjct:    57 LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYRLEEENHEAAARLEEVVYRGDMLLE 116

Query:   118 QVQELFSQAADNCLNLK 134
             ++Q   +  A + L  +
Sbjct:   117 KIQSALADIAQSQLKTR 133

GO:0001824 "blastocyst development" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|F1SG80 MED21 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 112 (44.5 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 34/137 (24%), Positives = 58/137 (42%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYP----EPPANPTEDAANFAEQPK 57
             D ++QLQ+ +N +A    N  G LQ+  PP   S        + PANPTE+ A      +
Sbjct:     3 DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTTINKDQPANPTEEYA------Q 56

Query:    58 LMSAALVKAAKQFDXXXXXXXXXXXXXXXQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
             L +A + + AK  D               Q   + +L+ EN      L+  +   +  L+
Sbjct:    57 LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATCLEDVVYRGDMLLE 116

Query:   118 QVQELFSQAADNCLNLK 134
             ++Q   +  A + L  +
Sbjct:   117 KIQSALADIAQSQLKTR 133

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0001824 "blastocyst development" evidence=IEA

MGI|MGI:1347064 Med21 "mediator complex subunit 21" [Mus musculus (taxid:10090)]

 Score = 112 (44.5 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 34/137 (24%), Positives = 58/137 (42%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYP----EPPANPTEDAANFAEQPK 57
             D ++QLQ+ +N +A    N  G LQ+  PP   S        + PANPTE+ A      +
Sbjct:     3 DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTEEYA------Q 56

Query:    58 LMSAALVKAAKQFDXXXXXXXXXXXXXXXQLKRIAELQSENDAVGQDLQRQLEAAEKELK 117
             L +A + + AK  D               Q   + +L+ EN      L+  +   +  L+
Sbjct:    57 LFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATCLEDVVYRGDMLLE 116

Query:   118 QVQELFSQAADNCLNLK 134
             ++Q   +  A + L  +
Sbjct:   117 KIQSALADIAQSQLKTR 133

GO:0001824 "blastocyst development" evidence=IMP

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IC

GO:0016592 "mediator complex" evidence=ISO;IDA

GO:0019827 "stem cell maintenance" evidence=IMP

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

UNIPROTKB|Q13503 MED21 "Mediator of RNA polymerase II transcription subunit 21" [Homo sapiens (taxid:9606)]

 Score = 111 (44.1 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 34/138 (24%), Positives = 61/138 (44%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPP-----VRLSPNYPEPPANPTEDAANFAEQP 56
             D ++QLQ+ +N +A    N  G LQ+  PP     ++ + N  + PANPTE+ A      
Sbjct:     3 DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFNNIQTAIN-KDQPANPTEEYA------ 55

Query:    57 KLMSAALVKAAKQFDXXXXXXXXXXXXXXXQLKRIAELQSENDAVGQDLQRQLEAAEKEL 116
             +L +A + + AK  D               Q   + +L+ EN      L+  +   +  L
Sbjct:    56 QLFAALIARTAKDIDVLIDSLPSEESTAALQAASLYKLEEENHEAATCLEDVVYRGDMLL 115

Query:   117 KQVQELFSQAADNCLNLK 134
             +++Q   +  A + L  +
Sbjct:   116 EKIQSALADIAQSQLKTR 133

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0001824 "blastocyst development" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

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

GO:0003713 "transcription coactivator activity" evidence=IDA

GO:0016592 "mediator complex" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=TAS

FB|FBgn0040020 MED21 "Mediator complex subunit 21" [Drosophila melanogaster (taxid:7227)]

 Score = 98 (39.6 bits), Expect = 3.0e-05, P = 3.0e-05
 Identities = 38/143 (26%), Positives = 61/143 (42%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPV------RLSPNYPEPPANPTEDAANFAEQ 55
             D ++QLQ+ +NQ A    N  G +Q+ + P       R+ P  P P   P ED A     
Sbjct:     3 DRLTQLQDTVNQQAEHFCNAIGVIQQTSLPSKFVNFERIGPQTPIP-CPPQEDYA----- 56

Query:    56 PKLMSAALVKAAKQFDXXXXXXXXXXXXXXXQLKRIAELQSENDAVGQDLQRQLEAAEKE 115
              +L +  + + AK  D               Q   +  L+ EN    +DL+  ++  E  
Sbjct:    57 -QLFAQLIARCAKDIDTLIESLPNEDSSIELQNSSLKRLEIENQGTARDLEEVVQKGELL 115

Query:   116 LKQVQ---ELFSQAA-DNCLNLK 134
             L+++Q   E  +QA  D  + LK
Sbjct:   116 LEKMQYSLECIAQAQLDMQITLK 138

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISS

GO:0016592 "mediator complex" evidence=ISS;IDA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS

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

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

GO:0003713 "transcription coactivator activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

WB|WBGene00007704 mdt-21 [Caenorhabditis elegans (taxid:6239)]

 Score = 93 (37.8 bits), Expect = 0.00010, P = 0.00010
 Identities = 37/128 (28%), Positives = 56/128 (43%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSA 61
             D ++QLQ+ IN++AG+  N  G LQ  APP        E      ED  N A    + +A
Sbjct:     3 DRMTQLQDMINEMAGLMTNAIGVLQATAPPCEFGAISQE-----LEDEPNCA----IFAA 53

Query:    62 ALVKAAKQFDXXXXXXXXXXXXXXXQL--KRIA--ELQSE--NDAVGQ--DLQRQLEAAE 113
              + KAAK  +               ++  K I   E Q E  N+ VG   D  R +   +
Sbjct:    54 GIAKAAKNIEILIDSFPIEAGNQEAEVEEKMIKNDEKQREKVNELVGLVGDSNRLVGVVQ 113

Query:   114 KELKQVQE 121
             K+L ++ +
Sbjct:   114 KKLAEISK 121

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0007413 "axonal fasciculation" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

UNIPROTKB|Q6BER6 mdt-21 "Mediator of RNA polymerase II transcription subunit 21" [Caenorhabditis elegans (taxid:6239)]

 Score = 93 (37.8 bits), Expect = 0.00010, P = 0.00010
 Identities = 37/128 (28%), Positives = 56/128 (43%)

Query:     2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPANPTEDAANFAEQPKLMSA 61
             D ++QLQ+ IN++AG+  N  G LQ  APP        E      ED  N A    + +A
Sbjct:     3 DRMTQLQDMINEMAGLMTNAIGVLQATAPPCEFGAISQE-----LEDEPNCA----IFAA 53

Query:    62 ALVKAAKQFDXXXXXXXXXXXXXXXQL--KRIA--ELQSE--NDAVGQ--DLQRQLEAAE 113
              + KAAK  +               ++  K I   E Q E  N+ VG   D  R +   +
Sbjct:    54 GIAKAAKNIEILIDSFPIEAGNQEAEVEEKMIKNDEKQREKVNELVGLVGDSNRLVGVVQ 113

Query:   114 KELKQVQE 121
             K+L ++ +
Sbjct:   114 KKLAEISK 121


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        0.312   0.127   0.345    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      137       122   0.00091  102 3  11 23  0.42    31
                                                     29  0.49    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:  9
  No. of states in DFA:  469 (50 KB)
  Total size of DFA:  96 KB (2071 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:  16.76u 0.11s 16.87t   Elapsed:  00:00:01
  Total cpu time:  16.76u 0.11s 16.87t   Elapsed:  00:00:01
  Start:  Thu May  9 18:08:50 2013   End:  Thu May  9 18:08:51 2013

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)
C0LU16	MED21_ARATH	No assigned EC number	0.8043	0.9927	0.9784	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: grail3.0111003501 hypothetical protein (137 aa) (Populus trichocarpa)

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

ID	Length	Definition	E-value
Query	137
pfam11221	132	pfam11221, Med21, Subunit 21 of Mediator complex	9e-34

>gnl|CDD|204614 pfam11221, Med21, Subunit 21 of Mediator complex

 Score =  114 bits (287), Expect = 9e-34
 Identities = 41/131 (31%), Positives = 68/131 (51%), Gaps = 2/131 (1%)

Query: 1   MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPE--PPANPTEDAANFAEQPKL 58
            D ++QLQ+ ++Q+A     T G LQ++  P  LSP+ P    P         F E  + 
Sbjct: 2   ADRLTQLQDCLDQLAEQFCATIGYLQQNHDPSPLSPDEPAVSDPKANAPPPEEFEEGQRE 61

Query: 59  MSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQ 118
           ++  ++  A+Q + L+ +LP  E  EE QL+RI EL+ E   V  + +  ++  EK LK+
Sbjct: 62  LARDIILKAQQIEYLIDSLPGIESSEEEQLRRIKELEEELREVEAEREEAVKEKEKLLKK 121

Query: 119 VQELFSQAADN 129
           V+ L  + A  
Sbjct: 122 VEALLREIARG 132

Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator. Length = 132

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
PF11221	144	Med21: Subunit 21 of Mediator complex; InterPro: I	100.0
KOG1510	139	consensus RNA polymerase II holoenzyme and mediato	100.0
PF07544	83	Med9: RNA polymerase II transcription mediator com	96.67

>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=100.00  E-value=5.1e-47  Score=283.80  Aligned_cols=129  Identities=41%  Similarity=0.583  Sum_probs=108.5

Q ss_pred             CchhhHHHHHHHHHHHHHHHhHhhhcccCCCCCCCCCCCCCCC--------------CCCcchHhhhhhHHHHHHHHHHH
Q 032610            1 MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPA--------------NPTEDAANFAEQPKLMSAALVKA   66 (137)
Q Consensus         1 mDrLTQLQd~ldqLa~~f~~sig~L~~~a~~~~~~~~~~~~~~--------------~~~~~~~~f~~~~~ela~dii~k   66 (137)
                      ||||||||||||+|+++||||||||+++|||++|+++.+....              ..+.+++.|++++++||+|||.|
T Consensus         2 ~DrlTQLQd~ldqL~~~f~~si~~l~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~elA~dIi~k   81 (144)
T PF11221_consen    2 ADRLTQLQDCLDQLAEQFCNSIGYLQRDAPPSPLSPNDPSISDPKPQAPPQQQQQAEPAPDPPEEFEENIKELATDIIRK   81 (144)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGG-----------------------------HHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCcccccCccccchhhhhhhhcccCCChhhHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999887632111              11247899999999999999999


Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032610           67 AKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADN  129 (137)
Q Consensus        67 akqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l~~ia~~  129 (137)
                      +|+|++|||||||+++|+++|+++|++|++||++++++|+++|++||.+|++|+++|+.|++|
T Consensus        82 akqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~i~~ia~~  144 (144)
T PF11221_consen   82 AKQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELLKQVQELIREIARG  144 (144)
T ss_dssp             HHHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999999999999976

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. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.

>KOG1510 consensus RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription]

Probab=100.00  E-value=1e-45  Score=272.52  Aligned_cols=136  Identities=42%  Similarity=0.581  Sum_probs=128.2

Q ss_pred             CchhhHHHHHHHHHHHHHHHhHhhhcccCCCCCCCCCCCCCCC-CCCcchHhhhhhHHHHHHHHHHHHHHHHHHHHhCCC
Q 032610            1 MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPA-NPTEDAANFAEQPKLMSAALVKAAKQFDALVAALPL   79 (137)
Q Consensus         1 mDrLTQLQd~ldqLa~~f~~sig~L~~~a~~~~~~~~~~~~~~-~~~~~~~~f~~~~~ela~dii~kakqIe~LIdsLPg   79 (137)
                      ||||||||||||+||++|||+||||+++|||++|+++.|.+.. ..+.+++.|.++++.||++|++|+||||.||+||||
T Consensus         2 aDRlTQLQd~vn~~A~qf~naig~Lq~~~pp~~l~~~e~~~~~~~~~~pa~p~~~~~~~laa~i~~~akqId~LIdsLP~   81 (139)
T KOG1510|consen    2 ADRLTQLQDTVNEMAEQFCNAIGVLQQTHPPVPLPNNEPESPDKVNPIPAEPFEEYAQLLAADIAKKAKQIDTLIDSLPG   81 (139)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCCCCCCCCCCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            7999999999999999999999999999999999988876543 234566779999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 032610           80 AEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADNCLNLKKP  136 (137)
Q Consensus        80 ~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l~~ia~~~l~~r~~  136 (137)
                      ++++++.|+++|++|++|+++++.+|++.|.++|.|+++|+.+|..|++++++||++
T Consensus        82 ~~~~~e~Ql~~i~kLq~en~e~~~el~~~v~~~e~Ll~~vq~~le~~a~~~l~~k~s  138 (139)
T KOG1510|consen   82 EEGSAEAQLEKIKKLQEENEEVALELEELVSKGEKLLEQVQSLLEDIADLQLNSKKS  138 (139)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            999999999999999999999999999999999999999999999999999999974

>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=96.67  E-value=0.015  Score=39.79  Aligned_cols=50  Identities=20%  Similarity=0.190  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 032610           56 PKLMSAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDL  105 (137)
Q Consensus        56 ~~ela~dii~kakqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el  105 (137)
                      ...-+..|=.|-+....+|.+|||++.|.++|...|+.|+++++...+-+
T Consensus        26 ~~~~~~~lk~Klq~ar~~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L   75 (83)
T PF07544_consen   26 LDTATGSLKHKLQKARAAIRELPGIDRSVEEQEEEIEELEEQIRKKREVL   75 (83)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44456677778888999999999999999999999999999885544433

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

---

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	137
1yke_B	151	RNA polymerase II holoenzyme component SRB7; gene	3e-27
1ykh_B	132	RNA polymerase II holoenzyme component SRB7; gene	4e-24

>1yke_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.30A {Saccharomyces cerevisiae} SCOP: a.252.1.1 Length = 151

 Score = 97.9 bits (243), Expect = 3e-27
 Identities = 32/138 (23%), Positives = 58/138 (42%), Gaps = 2/138 (1%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPE--PPANPTEDAANFAEQPKLM 59
           D ++QLQ  ++Q+      T   + ++    RL+ N P+             F+     +
Sbjct: 3   DRLTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDEL 62

Query: 60  SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQV 119
           S  ++   +Q + L+ +LP  +   E QL++I  LQ +   V  +    ++  EK L+ V
Sbjct: 63  STDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHV 122

Query: 120 QELFSQAADNCLNLKKPN 137
             L     D   N KK  
Sbjct: 123 DSLIEDFVDGIANSKKST 140

>1ykh_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.00A {Saccharomyces cerevisiae} SCOP: a.252.1.1 Length = 132

 Score = 89.3 bits (221), Expect = 4e-24
 Identities = 27/129 (20%), Positives = 54/129 (41%), Gaps = 2/129 (1%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYP--EPPANPTEDAANFAEQPKLM 59
           D ++QLQ  ++Q+      T   + ++    RL+ N P              F+     +
Sbjct: 3   DRMTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDEL 62

Query: 60  SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQV 119
           S  ++   +Q + L+ +LP  +   E QL++I  LQ +   V  +    ++  EK ++ V
Sbjct: 63  STDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLMRHV 122

Query: 120 QELFSQAAD 128
             +     D
Sbjct: 123 DSMIEDFVD 131

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
1yke_B	151	RNA polymerase II holoenzyme component SRB7; gene	100.0
1ykh_B	132	RNA polymerase II holoenzyme component SRB7; gene	100.0
1zxa_A	67	CGMP-dependent protein kinase 1, alpha isozyme; pa	83.28

>1yke_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.30A {Saccharomyces cerevisiae} SCOP: a.252.1.1

Probab=100.00  E-value=1.3e-49  Score=299.54  Aligned_cols=136  Identities=24%  Similarity=0.315  Sum_probs=117.6

Q ss_pred             CchhhHHHHHHHHHHHHHHHhHhhhcccCCCCCCCCCCCCCCCC--CCcchHhhhhhHHHHHHHHHHHHHHHHHHHHhCC
Q 032610            1 MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPAN--PTEDAANFAEQPKLMSAALVKAAKQFDALVAALP   78 (137)
Q Consensus         1 mDrLTQLQd~ldqLa~~f~~sig~L~~~a~~~~~~~~~~~~~~~--~~~~~~~f~~~~~ela~dii~kakqIe~LIdsLP   78 (137)
                      ||||||||||||+|+++||||||||+++|||++|+|+.|.++..  .+.+++.|..++.+||+|||.|+|||++||||||
T Consensus         2 aDrLTQLQd~ldqLa~~f~nsig~Lq~~app~~~~~~~~~~~~~~~~~~~~~~f~~~~~ela~dli~kakqIe~LIdsLP   81 (151)
T 1yke_B            2 TDRLTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQINKLIDSLP   81 (151)
T ss_dssp             -CCHHHHHHHHHHHHHHTTTTHHHHHHTTGGGGCCC------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCCCCCCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            89999999999999999999999999999999999887653322  2357899999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 032610           79 LAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADNCLNLKKP  136 (137)
Q Consensus        79 g~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l~~ia~~~l~~r~~  136 (137)
                      |+++|+++|+++|++|++||++++++|+++|++||.++++|+++|+.|+++++++|++
T Consensus        82 g~~~seeeQ~~ri~~Le~E~~~~~~el~~~v~eae~ll~~v~~~l~~ia~~~l~~r~~  139 (151)
T 1yke_B           82 GVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFVDGIANSKKS  139 (151)
T ss_dssp             TSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCC------
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence            9999999999999999999999999999999999999999999999999999999986

>1ykh_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.00A {Saccharomyces cerevisiae} SCOP: a.252.1.1

Probab=100.00  E-value=3.8e-48  Score=285.87  Aligned_cols=129  Identities=21%  Similarity=0.309  Sum_probs=111.7

Q ss_pred             CchhhHHHHHHHHHHHHHHHhHhhhcccCCCCCCCCCCCCCCCC--CCcchHhhhhhHHHHHHHHHHHHHHHHHHHHhCC
Q 032610            1 MDIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPPAN--PTEDAANFAEQPKLMSAALVKAAKQFDALVAALP   78 (137)
Q Consensus         1 mDrLTQLQd~ldqLa~~f~~sig~L~~~a~~~~~~~~~~~~~~~--~~~~~~~f~~~~~ela~dii~kakqIe~LIdsLP   78 (137)
                      ||||||||||||+|+++||||||||+++|||++|+|+.|.++..  .+.+++.|..++.+||+|||.|+|||++||||||
T Consensus         2 aDrlTQLQd~ldqla~~f~nsig~Lq~~a~p~~~~~~~~~~~~~~~~~~~~~~f~~~~~ela~dli~k~kqIe~LIdsLP   81 (132)
T 1ykh_B            2 TDRMTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQINKLIDSLP   81 (132)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCC---------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHST
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCCCCCCCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            89999999999999999999999999999999999877654322  2357799999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032610           79 LAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQAADN  129 (137)
Q Consensus        79 g~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l~~ia~~  129 (137)
                      |+++|+++|+++|++|++||++++++|+++|++|+.++++|+++|+.|++|
T Consensus        82 ~~~~see~Q~~ri~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l~~i~~~  132 (132)
T 1ykh_B           82 GVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLMRHVDSMIEDFVDG  132 (132)
T ss_dssp             TTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC--
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999875

>1zxa_A CGMP-dependent protein kinase 1, alpha isozyme; parallel coiled coil dimer, transferase; NMR {Homo sapiens}

Probab=83.28  E-value=2.9  Score=26.83  Aligned_cols=46  Identities=15%  Similarity=0.291  Sum_probs=12.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032610           78 PLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELF  123 (137)
Q Consensus        78 Pg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l  123 (137)
                      ||+..|-..+.+.+.+.-..-.+.-.+++..+.+++.....+++.|
T Consensus         3 ~~~~~~~~~~~e~~~~~i~~Kde~I~eLE~~L~~kd~eI~eLr~~L   48 (67)
T 1zxa_A            3 PGIPGSTSELEEDFAKILMLKEERIKELEKRLSEKEEEIQELKRKL   48 (67)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcchHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555444443333333333333344444444444444444433

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	137
d1ykhb1	129	a.252.1.1 (B:2-130) RNA polymerase II holoenzyme c	3e-33

>d1ykhb1 a.252.1.1 (B:2-130) RNA polymerase II holoenzyme component SRB7 (MED21) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 129

class: All alpha proteins
fold: Mediator hinge subcomplex-like
superfamily: Mediator hinge subcomplex-like
family: CSE2-like
domain: RNA polymerase II holoenzyme component SRB7 (MED21)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  111 bits (278), Expect = 3e-33
 Identities = 26/126 (20%), Positives = 54/126 (42%), Gaps = 2/126 (1%)

Query: 2   DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPE--PPANPTEDAANFAEQPKLM 59
           D ++QLQ  ++Q+      T   + ++    RL+ N P+             F+     +
Sbjct: 2   DRMTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDEL 61

Query: 60  SAALVKAAKQFDALVAALPLAEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQV 119
           S  ++   +Q + L+ +LP  +   E QL++I  LQ +   V  +    ++  EK ++ V
Sbjct: 62  STDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLMRHV 121

Query: 120 QELFSQ 125
             +   
Sbjct: 122 DSMIED 127

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	137
d1ykhb1	129	RNA polymerase II holoenzyme component SRB7 (MED21	100.0

>d1ykhb1 a.252.1.1 (B:2-130) RNA polymerase II holoenzyme component SRB7 (MED21) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Mediator hinge subcomplex-like
superfamily: Mediator hinge subcomplex-like
family: CSE2-like
domain: RNA polymerase II holoenzyme component SRB7 (MED21)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=6.6e-47  Score=276.63  Aligned_cols=125  Identities=21%  Similarity=0.302  Sum_probs=109.7

Q ss_pred             chhhHHHHHHHHHHHHHHHhHhhhcccCCCCCCCCCCCCCC--CCCCcchHhhhhhHHHHHHHHHHHHHHHHHHHHhCCC
Q 032610            2 DIISQLQEQINQIAGIAFNTFGTLQRDAPPVRLSPNYPEPP--ANPTEDAANFAEQPKLMSAALVKAAKQFDALVAALPL   79 (137)
Q Consensus         2 DrLTQLQd~ldqLa~~f~~sig~L~~~a~~~~~~~~~~~~~--~~~~~~~~~f~~~~~ela~dii~kakqIe~LIdsLPg   79 (137)
                      |||||||||||+||++||||||||+++|||++|+++.|.+.  ..++.+++.|++.+++||+|||.|+|||++||+||||
T Consensus         2 DrLTQLQd~lnqla~~f~nsig~L~~~a~~~~~~~~~~~~~~~~~~~~~~e~f~~~~~elA~dii~kakqId~LI~sLP~   81 (129)
T d1ykhb1           2 DRMTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQINKLIDSLPG   81 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSSCCC---------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHHHHHHhCCC
Confidence            99999999999999999999999999999999988775533  3345788999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032610           80 AEGGEEAQLKRIAELQSENDAVGQDLQRQLEAAEKELKQVQELFSQA  126 (137)
Q Consensus        80 ~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l~~i  126 (137)
                      +++|+++|+++|++|++||++++++|+++|++++.+|++|+++|++|
T Consensus        82 ~~~see~Q~~~i~~Le~E~~~~~~el~~~v~e~e~ll~~i~~~i~~i  128 (129)
T d1ykhb1          82 VDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLMRHVDSMIEDF  128 (129)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999876