Citrus Sinensis ID: 025523

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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-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-
Protein Sequence
MATPPPGANLEGAPPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQGPAKRMKI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccEEccHHHHHccccccHHHHHHHHHcccccccccHHHHHHHHccccHHHHHccccccEEEEEEEccccEEEEEEEEEccccccEEEEEEEEEccEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccEEEccHHHHHHccccccHHHHHHcccccccccccHHHHHHHHHccccHHHHHHcccEEEEEEEcccccEEEEEEEccccccccEEHEEEEEEcccEEccccHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccHHccccccccccccccccccccccccccccHcccc
Coil and Loop (DISEMBL)
matpppganlegappaappppgtdmtgicfrdqlwlntypldrnmifDYFTLSLFYDrtcnneqlrmrsihpldisqlskmTGIEYMLSEVMEPHLFVIRKqkrdgpekvtpMLTYYVLdgsiyqapqlCNVFSARIGRALHYIQKAFTTAASKLEKigyvdaendggtplhskagketidlkevKRVDQILASLQrklppapppppfpegyappqteeaekdpetqqtaepqppaidpiidqgpakrmki
Flexible Loop (DISEMBL)
matpppganlegappaapPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRmrsihpldisqlSKMTGIEYMLSEVMEPHLFVIrkqkrdgpekVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVdaendggtplhskagketidlkeVKRVDQILASLQrklppapppppFPEGYAPPQTEEAEKDPEtqqtaepqppaidpiidqgpakrmki
Low Complexity Region (SEG)
MATpppganlegappaappppgTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLppapppppfpegyappQTEEAEKDpetqqtaepqppaidpiidqgpaKRMKI
Disordered region (IsUnstruct)
*************************TGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDA****************************************************************************************
Disordered Region (DISOPRED)
*************************TGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRD***KVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEK***********************************ASLQR******************************************************
Disordered Region (DISEMBL)
*************PPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAP******************QPPAIDPIIDQGPAKRMKI
Disordered Region (DISPRO)
**********************TDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVD*****************IDLKEVKRVDQILASLQRKLPPAPP***********************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATPPPGANLEGAPPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQGPAKRMKI
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	251	2.2.26 [Sep-21-2011]
F4IXJ7	298	Mediator of RNA polymeras	no	no	0.916	0.771	0.604	1e-79
Q54PN3	267	Putative mediator of RNA	yes	no	0.756	0.711	0.378	5e-30
O75586	246	Mediator of RNA polymeras	yes	no	0.852	0.869	0.346	6e-28
Q921D4	246	Mediator of RNA polymeras	yes	no	0.852	0.869	0.338	1e-27
Q5RD94	246	Mediator of RNA polymeras	yes	no	0.848	0.865	0.353	1e-27
Q3SZY9	246	Mediator of RNA polymeras	yes	no	0.852	0.869	0.334	5e-27
Q7Q107	267	Mediator of RNA polymeras	yes	no	0.760	0.715	0.350	3e-25
Q6IQ63	254	Mediator of RNA polymeras	yes	no	0.693	0.685	0.356	2e-24
Q8MSX2	249	Mediator of RNA polymeras	yes	no	0.625	0.630	0.382	9e-24
Q6C3T0	227	Mediator of RNA polymeras	yes	no	0.605	0.669	0.317	6e-18

>sp|F4IXJ7|MED6_ARATH Mediator of RNA polymerase II transcription subunit 6 OS=Arabidopsis thaliana GN=MED6 PE=1 SV=1

 Score =  296 bits (757), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 165/273 (60%), Positives = 183/273 (67%), Gaps = 43/273 (15%)

Query: 20  PPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLS 79
           PPGTDMTGI FRDQLW+N+YPLDRN IFDYF LS FYD TCNNE LR RSIHPLD+S LS
Sbjct: 28  PPGTDMTGISFRDQLWINSYPLDRNYIFDYFALSPFYDTTCNNEILRRRSIHPLDLSHLS 87

Query: 80  KMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGR 139
           KMTG+EYML++  EP+LFV RKQKRDGPEKVTPMLTYY+LDGSIYQAPQLC+VF+AR+ R
Sbjct: 88  KMTGLEYMLTDATEPNLFVFRKQKRDGPEKVTPMLTYYILDGSIYQAPQLCSVFAARVSR 147

Query: 140 ALHYIQKAFTTAASKLEKI-------------------------------------GY-- 160
            ++ I KAFT AASKLE I                                     G+  
Sbjct: 148 TIYNISKAFTDAASKLETIRQDLQVCLVAIVLSLSVNLGSYFLLIFKLMANGEQVYGFNK 207

Query: 161 --VDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTE 218
              D EN    P  SK   ET+DLKE+KRVD IL SL RKL P PPPPPFPEGY   Q  
Sbjct: 208 FLFDTENQ-NEPAESKPASETVDLKEMKRVDVILTSLYRKLAPPPPPPPFPEGYV-SQEA 265

Query: 219 EAEKDPETQQTAEPQPPAIDPIIDQGPAKRMKI 251
             EK+    Q  E QPP +DPIIDQGPAKRMK 
Sbjct: 266 LGEKEELGTQGGESQPPQVDPIIDQGPAKRMKF 298

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 (By similarity).
Arabidopsis thaliana (taxid: 3702)

>sp|Q54PN3|MED6_DICDI Putative mediator of RNA polymerase II transcription subunit 6 OS=Dictyostelium discoideum GN=med6 PE=3 SV=1

 Score =  131 bits (329), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 76/201 (37%), Positives = 112/201 (55%), Gaps = 11/201 (5%)

Query: 24  DMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTG 83
           D+T + +RD LWL  YPL+   I  YF+ S FYD+ CNNEQL+M+    LD+S L  M G
Sbjct: 65  DLTQVMWRDPLWLQMYPLNPQTILQYFSYSQFYDKNCNNEQLKMQR---LDLSALKNMDG 121

Query: 84  IEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHY 143
           +EY L + +EP  F+I KQ R  P  V     YYV++G+IYQAP+L  VF +R+ +++ +
Sbjct: 122 LEYELIKFVEPSFFLIAKQTRISPTDVLINTLYYVINGNIYQAPELHVVFKSRVSQSISH 181

Query: 144 IQKAFTTAASKLEK---IGYVDAENDGGTPLHSK-AGKETIDLKEVKRVDQILASLQRKL 199
           + +AF + +S +      GY    +       SK A      +++ KR+DQ++ SL  K 
Sbjct: 182 LSEAFNSISSIVNWDIVNGYSLNLDPSNQQEKSKLAAYSRKQIEDTKRLDQLINSLFIKF 241

Query: 200 PPAPPPPPFPE----GYAPPQ 216
           P    P   P+    G  P Q
Sbjct: 242 PAINRPVENPQQMGGGITPQQ 262

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.

Dictyostelium discoideum (taxid: 44689)

>sp|O75586|MED6_HUMAN Mediator of RNA polymerase II transcription subunit 6 OS=Homo sapiens GN=MED6 PE=1 SV=2

 Score =  124 bits (311), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 87/251 (34%), Positives = 125/251 (49%), Gaps = 37/251 (14%)

Query: 24  DMTGICFRDQLWLNTYPLDRNMIFDYFTLSL--FYDRTCNNEQLRMRSIHPLDISQLSKM 81
           ++ GI + D  W+    L+   + DYF+     FYDRTCNNE ++M+    L +  L++M
Sbjct: 9   NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query: 82  TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
            GIEY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct: 64  VGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query: 142 HYIQKAFTTAA-------SKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
           H IQ AF  A        SK     + D E        +K  +E   + + +RVD +L  
Sbjct: 124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVRPKAKRKEEPSSIFQRQRVDALLLD 183

Query: 195 LQRKLPP-----APPPPPFP------EGYAPPQT---EEAEKDPETQQTAEPQPPAIDPI 240
           L++K PP      P   P P      E    P+T   EE E     QQT   + P     
Sbjct: 184 LRQKFPPKFVQLKPGEKPVPVDQTKKEAEPIPETVKPEEKETTKNVQQTVSAKGP----- 238

Query: 241 IDQGPAKRMKI 251
               P KRM++
Sbjct: 239 ----PEKRMRL 245

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|Q921D4|MED6_MOUSE Mediator of RNA polymerase II transcription subunit 6 OS=Mus musculus GN=Med6 PE=2 SV=2

 Score =  123 bits (309), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 125/251 (49%), Gaps = 37/251 (14%)

Query: 24  DMTGICFRDQLWLNTYPLDRNMIFDYFTLSL--FYDRTCNNEQLRMRSIHPLDISQLSKM 81
           ++ GI + D  W+    L+   + DYF+     FYDRTCNNE ++M+    L +  L++M
Sbjct: 9   NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query: 82  TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
            GIEY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct: 64  VGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query: 142 HYIQKAFTTAA-------SKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
           H IQ AF  A        SK     + D E        +K  +E   + + +RVD +L  
Sbjct: 124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQEKVKPKAKRKEEPSSIFQRQRVDALLID 183

Query: 195 LQRKLPP---------APPPPPFPEGYAPP-----QTEEAEKDPETQQTAEPQPPAIDPI 240
           L++K PP          P P    +  A P     ++EE E     QQT   + P     
Sbjct: 184 LRQKFPPRFVQQKSGEKPVPVDQAKKEAEPLPETVKSEEKESTKNIQQTVSTKGP----- 238

Query: 241 IDQGPAKRMKI 251
               P KRM++
Sbjct: 239 ----PEKRMRL 245

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|Q5RD94|MED6_PONAB Mediator of RNA polymerase II transcription subunit 6 OS=Pongo abelii GN=MED6 PE=2 SV=1

 Score =  123 bits (308), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 126/252 (50%), Gaps = 39/252 (15%)

Query: 24  DMTGICFRDQLWLNTYPLDRNMIFDYFTLSL--FYDRTCNNEQLRMRSIHPLDISQLSKM 81
           ++ GI + D  W+    L+   + DYF+     FYDRTCNNE ++M+    L +  L++M
Sbjct: 9   NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query: 82  TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
            GIEY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct: 64  VGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query: 142 HYIQKAFTTAASKLE---KIGYV-----DAENDGGTPLHSKAGKETIDLKEVKRVDQILA 193
           H IQ AF  A S        GY        E D   P  +K  +E   + + +RVD +L 
Sbjct: 124 HGIQSAFDEAMSYCRYHPSKGYWWHFKEHEEQDKVRP-KAKRKEEPSSIFQRQRVDALLL 182

Query: 194 SLQRKLPP-----APPPPPFP------EGYAPPQT---EEAEKDPETQQTAEPQPPAIDP 239
            L++K PP      P   P P      E    P+T   EE E     QQT   + P    
Sbjct: 183 DLRQKFPPKFVQLKPGEKPVPVDQTKKEAEPVPETVKPEEKETTKNVQQTVSAKGP---- 238

Query: 240 IIDQGPAKRMKI 251
                P KRM++
Sbjct: 239 -----PEKRMRL 245

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)

>sp|Q3SZY9|MED6_BOVIN Mediator of RNA polymerase II transcription subunit 6 OS=Bos taurus GN=MED6 PE=2 SV=1

 Score =  121 bits (303), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 37/251 (14%)

Query: 24  DMTGICFRDQLWLNTYPLDRNMIFDYFTLSL--FYDRTCNNEQLRMRSIHPLDISQLSKM 81
           ++ GI + D  W+    L+   + DYF+     FYDRTCNNE ++M+    L +  L++M
Sbjct: 9   NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query: 82  TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
            G+EY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct: 64  VGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query: 142 HYIQKAFTTAA-------SKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
           H IQ AF  A        SK     + D E         K  +E   + + +RVD +L  
Sbjct: 124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVKPKVKRKEEPSSIFQRQRVDALLLD 183

Query: 195 LQRKLPP---------APPPPPFPEGYAPP-----QTEEAEKDPETQQTAEPQPPAIDPI 240
           L++K PP          P P    +  A P     ++EE E     QQT   + P     
Sbjct: 184 LRQKFPPKFVQQKSGEKPVPVDQTKKEAEPLPETVKSEEKETAKNVQQTVGTKGP----- 238

Query: 241 IDQGPAKRMKI 251
               P KRM++
Sbjct: 239 ----PEKRMRL 245

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|Q7Q107|MED6_ANOGA Mediator of RNA polymerase II transcription subunit 6 OS=Anopheles gambiae GN=MED6 PE=3 SV=3

 Score =  115 bits (288), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 74/211 (35%), Positives = 108/211 (51%), Gaps = 20/211 (9%)

Query: 28  ICFRDQLWLNTYPLDRNMIFDYFTLSL--FYDRTCNNEQLRMRSIHPLDISQLSKMTGIE 85
           I + D  W+    L+   + DYF+     FYDRTCNNE +RM+      +  L+ MTG+E
Sbjct: 19  ISWHDSNWIPV--LNPGNVMDYFSEKSNPFYDRTCNNEIVRMQR---QSLELLNNMTGVE 73

Query: 86  YMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQ 145
           Y+   V +P L+VIRKQ R  P + TPM  YY++ G++YQAP L +VF++RI   +H++Q
Sbjct: 74  YIPLHVQDPILYVIRKQHRHSPTEATPMADYYIIAGTVYQAPDLASVFNSRILSTVHHLQ 133

Query: 146 KAFTTAASKLE---KIGY---------VDAENDGGTPLHSKAGKETIDLKEVKRVDQILA 193
            AF  A+S        GY         +  +    T   +   +E   + + +RVD +L 
Sbjct: 134 TAFDEASSYSRYHPSKGYSWDFSSNKAIAEKTKTQTKKEAPVKEEPSSIFQRQRVDMLLG 193

Query: 194 SLQRKLP-PAPPPPPFPEGYAPPQTEEAEKD 223
            L RK P P P     P G  P  T  A  +
Sbjct: 194 DLLRKFPLPLPQMTNNPTGGNPSDTANASNN 224

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.

Anopheles gambiae (taxid: 7165)

>sp|Q6IQ63|MED6_DANRE Mediator of RNA polymerase II transcription subunit 6 OS=Danio rerio GN=med6 PE=2 SV=1

 Score =  113 bits (282), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 67/188 (35%), Positives = 102/188 (54%), Gaps = 14/188 (7%)

Query: 24  DMTGICFRDQLWLNTYPLDRNMIFDYFTLSL--FYDRTCNNEQLRMRSIHPLDISQLSKM 81
           ++ GI + D  W+    L+ + + +YF+     FYDRTCNNE ++M+      +  L+++
Sbjct: 9   NLLGISWVDSGWVPI--LNPSNVLEYFSERSNPFYDRTCNNEVVKMQRS---TLDHLTQL 63

Query: 82  TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
            G+EY+L    EP L++IRKQ+R  P +V P+  YY++ G +YQAP L +V S+R   A+
Sbjct: 64  VGVEYILLHTQEPILYIIRKQQRQSPTQVIPLADYYIIAGVVYQAPDLGSVISSRALSAV 123

Query: 142 HYIQKAFTTAA-------SKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
           H IQ AF  A        SK     + D E        SK  +E   L + +RVD +L  
Sbjct: 124 HGIQSAFDEAMSFCRYHPSKGYWWHFKDQEEKERVKPKSKRKEEPSSLFQRQRVDTLLLD 183

Query: 195 LQRKLPPA 202
           L+ K PP 
Sbjct: 184 LRNKFPPT 191

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|Q8MSX2|MED6_DROME Mediator of RNA polymerase II transcription subunit 6 OS=Drosophila melanogaster GN=MED6 PE=1 SV=1

 Score =  110 bits (275), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 67/175 (38%), Positives = 94/175 (53%), Gaps = 18/175 (10%)

Query: 46  IFDYFTLSL--FYDRTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQK 103
           + DYF      FYD  CNNE +RM+ + P     L  M G+EY+L  V EP L+VIRKQ 
Sbjct: 29  VMDYFCRKSNPFYDHMCNNETVRMQRLGP---EHLHNMIGLEYILLHVAEPILYVIRKQH 85

Query: 104 RDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE---KIGY 160
           R  P + TP+  YY++ G++Y+AP L NV ++RI   +  +Q AF  A+S        GY
Sbjct: 86  RHNPSEATPIADYYIIGGTVYKAPDLANVINSRILNTVVNLQSAFEEASSYARYHPNKGY 145

Query: 161 V-DAENDGGTPLHSKAGKETID---------LKEVKRVDQILASLQRKLPPAPPP 205
             D  ++      SK+ K+  +         L + +RVD +LA L RK PP  PP
Sbjct: 146 TWDFSSNKVFSDRSKSDKKDANSAKDENSGTLFQKQRVDMLLAELLRKFPPPIPP 200

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|Q6C3T0|MED6_YARLI Mediator of RNA polymerase II transcription subunit 6 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=MED6 PE=3 SV=1

 Score = 91.3 bits (225), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 93/173 (53%), Gaps = 21/173 (12%)

Query: 24  DMTGICFRDQLWLNTYP-LDRNMIFDYFTLSLFYDRTCNNEQLRMRS---------IHPL 73
           ++  + +R   W+  +  L  + + DYF  S FYDR  NN+ LRM++         + P 
Sbjct: 3   NLDEVQWRSPEWIQAHQGLRTDNVLDYFAESPFYDRVSNNQVLRMQTQFNQQQTGQLTPQ 62

Query: 74  DISQ-LSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNV 132
              Q L KMTGIE++++ V EP L+VI+KQ R  P++ TP+ TY+V++ ++Y AP +  +
Sbjct: 63  HFEQELQKMTGIEFVITHVREPDLWVIKKQNRLNPQQTTPISTYFVINENVYMAPTVAAI 122

Query: 133 FSARIGRALHYIQKAFTTAA-----SKLEKIGYVDAE-----NDGGTPLHSKA 175
             +R+     ++++A   A      S  +   Y D++     +D  TP  SKA
Sbjct: 123 MQSRVLSTSMFLKRALEEAIELPSYSPSQGYTYEDSQLTTAGDDDSTPQASKA 175

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.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

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	251
225442396	258	PREDICTED: putative mediator of RNA poly	0.996	0.968	0.818	1e-109
147800916	253	hypothetical protein VITISV_044247 [Viti	0.996	0.988	0.818	1e-104
297743145	226	unnamed protein product [Vitis vinifera]	0.900	1.0	0.845	1e-102
255549722	251	RNA polymerase II mediator complex subun	0.992	0.992	0.790	1e-101
449462906	260	PREDICTED: LOW QUALITY PROTEIN: mediator	0.952	0.919	0.797	1e-101
356526061	252	PREDICTED: putative mediator of RNA poly	0.992	0.988	0.787	1e-100
224116560	235	predicted protein [Populus trichocarpa]	0.920	0.982	0.806	1e-99
388518953	248	unknown [Medicago truncatula]	0.988	1.0	0.764	4e-99
449517269	226	PREDICTED: mediator of RNA polymerase II	0.888	0.986	0.810	6e-97
357124816	260	PREDICTED: putative mediator of RNA poly	0.920	0.888	0.728	6e-88

>gi|225442396|ref|XP_002282496.1| PREDICTED: putative mediator of RNA polymerase II transcription subunit 6 [Vitis vinifera]

 Score =  400 bits (1027), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 208/254 (81%), Positives = 221/254 (87%), Gaps = 4/254 (1%)

Query: 1   MATPPPGA---NLEGAPPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYD 57
           MA P P A   N +G PPA P PPGTDMTGICFRDQLWLN+YPLDRN++FDYF LS FYD
Sbjct: 6   MAPPNPAAGNPNFDGNPPAVPTPPGTDMTGICFRDQLWLNSYPLDRNLVFDYFALSPFYD 65

Query: 58  RTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYY 117
            TCNNEQLR+RSIHPLD S LSKMTG EYML+EVMEPHLFVIRKQKRDGPEKVTPMLTYY
Sbjct: 66  WTCNNEQLRLRSIHPLDTSHLSKMTGTEYMLNEVMEPHLFVIRKQKRDGPEKVTPMLTYY 125

Query: 118 VLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGK 177
           +LDGSIYQAPQLCNVF+ARIGRAL++I KAFTTAASKLEKIGYVDAEN+    L SK GK
Sbjct: 126 ILDGSIYQAPQLCNVFTARIGRALYHISKAFTTAASKLEKIGYVDAENENPA-LESKVGK 184

Query: 178 ETIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAI 237
           ETID KEV RVDQILASLQRKLPPAPPPP FPEGYAPP T E EK PETQQ AEPQ PA+
Sbjct: 185 ETIDFKEVMRVDQILASLQRKLPPAPPPPQFPEGYAPPPTAEGEKGPETQQAAEPQLPAL 244

Query: 238 DPIIDQGPAKRMKI 251
           DPIIDQGP+KRMK 
Sbjct: 245 DPIIDQGPSKRMKF 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147800916|emb|CAN68925.1| hypothetical protein VITISV_044247 [Vitis vinifera]

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 208/254 (81%), Positives = 221/254 (87%), Gaps = 4/254 (1%)

Query: 1   MATPPPGA---NLEGAPPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYD 57
           MA P P A   N +G PPAAP PPGTDMTGICFRDQLWLN+YPLDRN++FDYF LS FYD
Sbjct: 1   MAPPNPAAGNPNFDGNPPAAPTPPGTDMTGICFRDQLWLNSYPLDRNLVFDYFALSPFYD 60

Query: 58  RTCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYY 117
            TCNNEQLR+RSIHPLD S LSKMTG EYML+EVMEPHLFVIRKQKRDGPEKVTPMLTYY
Sbjct: 61  WTCNNEQLRLRSIHPLDTSHLSKMTGTEYMLNEVMEPHLFVIRKQKRDGPEKVTPMLTYY 120

Query: 118 VLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGK 177
           +LDGSIYQAPQLCNVF+ARIGRAL++I KAFTTAASKLEKIGYVDAEN+    L SK GK
Sbjct: 121 ILDGSIYQAPQLCNVFTARIGRALYHISKAFTTAASKLEKIGYVDAENENPA-LESKVGK 179

Query: 178 ETIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAI 237
           ETID KEV RVDQILASLQRKLPPAPP P FPEGYAPP T E EK PETQQ AEPQ PA+
Sbjct: 180 ETIDFKEVMRVDQILASLQRKLPPAPPAPQFPEGYAPPPTAEGEKGPETQQAAEPQLPAL 239

Query: 238 DPIIDQGPAKRMKI 251
           DPIIDQGP+KRMK 
Sbjct: 240 DPIIDQGPSKRMKF 253

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743145|emb|CBI36012.3| unnamed protein product [Vitis vinifera]

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 192/227 (84%), Positives = 204/227 (89%), Gaps = 1/227 (0%)

Query: 25  MTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGI 84
           MTGICFRDQLWLN+YPLDRN++FDYF LS FYD TCNNEQLR+RSIHPLD S LSKMTG 
Sbjct: 1   MTGICFRDQLWLNSYPLDRNLVFDYFALSPFYDWTCNNEQLRLRSIHPLDTSHLSKMTGT 60

Query: 85  EYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYI 144
           EYML+EVMEPHLFVIRKQKRDGPEKVTPMLTYY+LDGSIYQAPQLCNVF+ARIGRAL++I
Sbjct: 61  EYMLNEVMEPHLFVIRKQKRDGPEKVTPMLTYYILDGSIYQAPQLCNVFTARIGRALYHI 120

Query: 145 QKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLPPAPP 204
            KAFTTAASKLEKIGYVDAEN+    L SK GKETID KEV RVDQILASLQRKLPPAPP
Sbjct: 121 SKAFTTAASKLEKIGYVDAENE-NPALESKVGKETIDFKEVMRVDQILASLQRKLPPAPP 179

Query: 205 PPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQGPAKRMKI 251
           PP FPEGYAPP T E EK PETQQ AEPQ PA+DPIIDQGP+KRMK 
Sbjct: 180 PPQFPEGYAPPPTAEGEKGPETQQAAEPQLPALDPIIDQGPSKRMKF 226

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549722|ref|XP_002515912.1| RNA polymerase II mediator complex subunit, putative [Ricinus communis] gi|223544817|gb|EEF46332.1| RNA polymerase II mediator complex subunit, putative [Ricinus communis]

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 200/253 (79%), Positives = 215/253 (84%), Gaps = 4/253 (1%)

Query: 1   MATPPPGANLEG--APPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDR 58
           MAT PPGAN +G    PA P PPGTDMTGICFRDQLWLNTYPLDRN+IFDYF LS FYD 
Sbjct: 1   MATVPPGANFDGNPLAPAPPQPPGTDMTGICFRDQLWLNTYPLDRNLIFDYFALSPFYDW 60

Query: 59  TCNNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYV 118
           TCNNEQLR++SIHPLD+S LSKMTG EYML+EV+EP+LFVIRKQKRD PEKVTPMLTYYV
Sbjct: 61  TCNNEQLRLQSIHPLDLSHLSKMTGTEYMLNEVIEPNLFVIRKQKRDSPEKVTPMLTYYV 120

Query: 119 LDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKE 178
           LDGSIYQAPQLCNVF+ARIGRAL++I KAFTTAASKLEKIGYVD     G    SK GKE
Sbjct: 121 LDGSIYQAPQLCNVFAARIGRALYHISKAFTTAASKLEKIGYVDEGE--GVASESKVGKE 178

Query: 179 TIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAID 238
            ID KEVKR+D ILAS+QRKLPPAPPPPPFPEGY PP T EAEK  ET+Q  E QPP +D
Sbjct: 179 VIDFKEVKRIDHILASIQRKLPPAPPPPPFPEGYVPPATVEAEKGSETRQAVETQPPPVD 238

Query: 239 PIIDQGPAKRMKI 251
           PIIDQGPAKRMK 
Sbjct: 239 PIIDQGPAKRMKF 251

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462906|ref|XP_004149176.1| PREDICTED: LOW QUALITY PROTEIN: mediator of RNA polymerase II transcription subunit 6-like [Cucumis sativus]

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 197/247 (79%), Positives = 211/247 (85%), Gaps = 8/247 (3%)

Query: 9   NLEGAP-PAAPPPPGTDMT---GICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQ 64
           N EG P PAAP PPGTDMT   GICFRDQLWLNTYPLDRN++FDYF LS FYD TCNNEQ
Sbjct: 15  NFEGGPLPAAPQPPGTDMTNLPGICFRDQLWLNTYPLDRNLVFDYFALSPFYDWTCNNEQ 74

Query: 65  LRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIY 124
           LRMRSIHPLD+SQLSKMTGIEYML+EVMEPHLFV RKQKRDGPEKVTPMLTYY+LDGSIY
Sbjct: 75  LRMRSIHPLDLSQLSKMTGIEYMLNEVMEPHLFVFRKQKRDGPEKVTPMLTYYILDGSIY 134

Query: 125 QAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKE 184
           QAPQLC+VF+AR+ RAL+YI KAFTTA+SKLEKIGYVD+EN+       K  KETI+ KE
Sbjct: 135 QAPQLCSVFAARVSRALYYISKAFTTASSKLEKIGYVDSENESE---EVKPAKETINFKE 191

Query: 185 VKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQG 244
           VKRVD ILASLQRKLPPAPPPPPFPEGYAP  T E EK PE QQ  E Q P+ DPIIDQG
Sbjct: 192 VKRVDHILASLQRKLPPAPPPPPFPEGYAPAATAETEKGPENQQ-GESQQPSADPIIDQG 250

Query: 245 PAKRMKI 251
           PAKRMK 
Sbjct: 251 PAKRMKF 257

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526061|ref|XP_003531638.1| PREDICTED: putative mediator of RNA polymerase II transcription subunit 6-like [Glycine max]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 200/254 (78%), Positives = 212/254 (83%), Gaps = 5/254 (1%)

Query: 1   MATPPPGANLEGAPPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTC 60
           MAT P    LEG   A  PP  TDMTGICFRDQLWLN++PLDRN++FDYF LS FYD TC
Sbjct: 1   MATAPGNQMLEGGGGAPQPPG-TDMTGICFRDQLWLNSFPLDRNLVFDYFALSPFYDWTC 59

Query: 61  NNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLD 120
           NNEQLRMRS+HPLDISQLSKMTG EYMLSEVMEPHLFVIRKQKRD P+KVTPML YYVLD
Sbjct: 60  NNEQLRMRSVHPLDISQLSKMTGTEYMLSEVMEPHLFVIRKQKRDSPDKVTPMLAYYVLD 119

Query: 121 GSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGY---VDAENDGGTPLHSKAGK 177
           GSIYQAPQLCNVF+ARIGRAL+YIQKAFTTAASKLEKIGY    D+EN+    L SK  K
Sbjct: 120 GSIYQAPQLCNVFAARIGRALYYIQKAFTTAASKLEKIGYAGSADSENETAL-LESKTAK 178

Query: 178 ETIDLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAI 237
           ETID+KEVKRVD ILASLQRKLPPAPPPPPFPEGY PP T E EK  ETQ+ AE Q P  
Sbjct: 179 ETIDIKEVKRVDHILASLQRKLPPAPPPPPFPEGYVPPPTAETEKGTETQEAAETQAPTA 238

Query: 238 DPIIDQGPAKRMKI 251
           DPIIDQGPAKRMK 
Sbjct: 239 DPIIDQGPAKRMKF 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116560|ref|XP_002331927.1| predicted protein [Populus trichocarpa] gi|222874599|gb|EEF11730.1| predicted protein [Populus trichocarpa]

 Score =  368 bits (945), Expect = e-99,   Method: Compositional matrix adjust.
 Identities = 187/232 (80%), Positives = 200/232 (86%), Gaps = 1/232 (0%)

Query: 20  PPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLS 79
           PPGTDMTGICFRDQLWLNTYPLDRN++FDYF LS FYD TCNNEQLR +SIHPLD+S L 
Sbjct: 5   PPGTDMTGICFRDQLWLNTYPLDRNLVFDYFALSPFYDWTCNNEQLRSQSIHPLDLSHLL 64

Query: 80  KMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGR 139
           KMTG EYMLSEVMEPHLFV RKQKRD  EKVTPMLTYYVLDGSIYQAPQLC+VF+AR+GR
Sbjct: 65  KMTGTEYMLSEVMEPHLFVFRKQKRDSAEKVTPMLTYYVLDGSIYQAPQLCSVFAARVGR 124

Query: 140 ALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKL 199
           AL+YI KAF TAASKLEKIGYVD+EN+G     SK GKE ID KEVKR+D ILASLQRKL
Sbjct: 125 ALYYISKAFGTAASKLEKIGYVDSENEGAAS-ESKTGKEVIDFKEVKRIDHILASLQRKL 183

Query: 200 PPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQGPAKRMKI 251
           PPAPPPP FPEGY P  T E EK PETQQ  EPQ P++DPIIDQGPAKRMK 
Sbjct: 184 PPAPPPPSFPEGYVPQPTTEEEKGPETQQGGEPQLPSVDPIIDQGPAKRMKF 235

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388518953|gb|AFK47538.1| unknown [Medicago truncatula]

 Score =  366 bits (940), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 192/251 (76%), Positives = 212/251 (84%), Gaps = 3/251 (1%)

Query: 1   MATPPPGANLEGAPPAAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTC 60
           MATP  G  L+G  P A PP GTDMTGICFRDQLWLNTYPLDR+++FDYF LS FYD T 
Sbjct: 1   MATPGMGM-LDGGVPTAQPP-GTDMTGICFRDQLWLNTYPLDRDLVFDYFALSPFYDWTS 58

Query: 61  NNEQLRMRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLD 120
           NNEQLRMRS HPLD SQL+KM GIEY+LSEVMEPHLF+++KQKRD P+KVTPML YY+LD
Sbjct: 59  NNEQLRMRSHHPLDSSQLTKMIGIEYVLSEVMEPHLFIMKKQKRDSPDKVTPMLAYYILD 118

Query: 121 GSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETI 180
           GSIYQAPQL NVF+ARIGRAL+YI+KAFTTAASKLEKIGYVD+EN+   P   K  KETI
Sbjct: 119 GSIYQAPQLSNVFAARIGRALYYIEKAFTTAASKLEKIGYVDSENETTIP-EPKVAKETI 177

Query: 181 DLKEVKRVDQILASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPI 240
           DLKE+KRVD ILASLQRKLPPAPPPPPFPEGY PP T E EK PETQ+ AE   P +DPI
Sbjct: 178 DLKEIKRVDHILASLQRKLPPAPPPPPFPEGYVPPSTAETEKGPETQEAAESLAPTVDPI 237

Query: 241 IDQGPAKRMKI 251
           +DQGPAKRMK 
Sbjct: 238 LDQGPAKRMKF 248

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449517269|ref|XP_004165668.1| PREDICTED: mediator of RNA polymerase II transcription subunit 6-like [Cucumis sativus]

 Score =  359 bits (921), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 184/227 (81%), Positives = 198/227 (87%), Gaps = 4/227 (1%)

Query: 25  MTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTGI 84
           MTGICFRDQLWLNTYPLDRN++FDYF LS FYD TCNNEQLRMRSIHPLD+SQLSKMTGI
Sbjct: 1   MTGICFRDQLWLNTYPLDRNLVFDYFALSPFYDWTCNNEQLRMRSIHPLDLSQLSKMTGI 60

Query: 85  EYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYI 144
           EYML+EVMEPHLFV RKQKRDGPEKVTPMLTYY+LDGSIYQAPQLC+VF+AR+ RAL+YI
Sbjct: 61  EYMLNEVMEPHLFVFRKQKRDGPEKVTPMLTYYILDGSIYQAPQLCSVFAARVSRALYYI 120

Query: 145 QKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLPPAPP 204
            KAFTTA+SKLEKIGYVD+EN+       K  KETI+ KEVKRVD ILASLQRKLPPAPP
Sbjct: 121 SKAFTTASSKLEKIGYVDSENESE---EVKPAKETINFKEVKRVDHILASLQRKLPPAPP 177

Query: 205 PPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQGPAKRMKI 251
           PPPFPEGYAP  T E EK PE QQ  E Q P+ DPIIDQGPAKRMK 
Sbjct: 178 PPPFPEGYAPAATAETEKGPENQQ-GESQQPSADPIIDQGPAKRMKF 223

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357124816|ref|XP_003564093.1| PREDICTED: putative mediator of RNA polymerase II transcription subunit 6-like [Brachypodium distachyon]

 Score =  329 bits (844), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 172/236 (72%), Positives = 193/236 (81%), Gaps = 5/236 (2%)

Query: 16  AAPPPPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDI 75
           A PPPPGTDMTGICFRDQLWLNTYPLDRN++FDYF LS FYD TCNNE LR R IHPLD+
Sbjct: 23  ALPPPPGTDMTGICFRDQLWLNTYPLDRNLVFDYFALSPFYDITCNNESLRSRQIHPLDM 82

Query: 76  SQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEK---VTPMLTYYVLDGSIYQAPQLCNV 132
           SQL+KMTG+EY+LS+V EPHLFVIRKQKR   EK   + PML YY+LDGSIYQAPQLCNV
Sbjct: 83  SQLTKMTGMEYVLSDVQEPHLFVIRKQKRLSSEKSDPMLPMLAYYILDGSIYQAPQLCNV 142

Query: 133 FSARIGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKETIDLKEVKRVDQIL 192
           F++RI RA+H+I KAFTTA SKLEKIG V+ E+D      SK  KE IDLKE+KRVD IL
Sbjct: 143 FASRISRAMHHISKAFTTACSKLEKIGNVETESDAAAS-ESKTQKEAIDLKELKRVDHIL 201

Query: 193 ASLQRKLPPAPPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQGPAKR 248
            SLQRKLPPAPPPPPFPEGY PP   + EK P+   ++E  PP+IDPIIDQGPAKR
Sbjct: 202 MSLQRKLPPAPPPPPFPEGYVPPSASDQEKAPD-DLSSEALPPSIDPIIDQGPAKR 256

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

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	251
TAIR|locus:2089488	298	MED6 [Arabidopsis thaliana (ta	0.541	0.456	0.779	2.3e-64
DICTYBASE|DDB_G0284421	267	med6 "putative mediator comple	0.673	0.632	0.397	5e-28
RGD|1310296	246	Med6 "mediator complex subunit	0.677	0.691	0.375	9.7e-25
UNIPROTKB|E2R2L6	246	MED6 "Mediator of RNA polymera	0.677	0.691	0.369	1.2e-24
UNIPROTKB|G3V4A5	249	MED6 "Mediator of RNA polymera	0.677	0.682	0.375	1.2e-24
UNIPROTKB|O75586	246	MED6 "Mediator of RNA polymera	0.677	0.691	0.375	1.2e-24
MGI|MGI:1917042	246	Med6 "mediator of RNA polymera	0.677	0.691	0.375	1.2e-24
UNIPROTKB|Q3SZY9	246	MED6 "Mediator of RNA polymera	0.677	0.691	0.369	2.6e-24
UNIPROTKB|E1BZ92	246	MED6 "Mediator of RNA polymera	0.677	0.691	0.375	3.3e-24
UNIPROTKB|H9KYN6	190	H9KYN6 "Uncharacterized protei	0.677	0.894	0.375	3.3e-24

TAIR|locus:2089488 MED6 [Arabidopsis thaliana (taxid:3702)]

 Score = 572 (206.4 bits), Expect = 2.3e-64, Sum P(2) = 2.3e-64
 Identities = 106/136 (77%), Positives = 119/136 (87%)

Query:    23 TDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMT 82
             TDMTGI FRDQLW+N+YPLDRN IFDYF LS FYD TCNNE LR RSIHPLD+S LSKMT
Sbjct:    31 TDMTGISFRDQLWINSYPLDRNYIFDYFALSPFYDTTCNNEILRRRSIHPLDLSHLSKMT 90

Query:    83 GIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALH 142
             G+EYML++  EP+LFV RKQKRDGPEKVTPMLTYY+LDGSIYQAPQLC+VF+AR+ R ++
Sbjct:    91 GLEYMLTDATEPNLFVFRKQKRDGPEKVTPMLTYYILDGSIYQAPQLCSVFAARVSRTIY 150

Query:   143 YIQKAFTTAASKLEKI 158
              I KAFT AASKLE I
Sbjct:   151 NISKAFTDAASKLETI 166

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0016592 "mediator complex" evidence=IEA

DICTYBASE|DDB_G0284421 med6 "putative mediator complex subunit 6" [Dictyostelium discoideum (taxid:44689)]

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 70/176 (39%), Positives = 105/176 (59%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDISQLSKMTG 83
             D+T + +RD LWL  YPL+   I  YF+ S FYD+ CNNEQL+M+    LD+S L  M G
Sbjct:    65 DLTQVMWRDPLWLQMYPLNPQTILQYFSYSQFYDKNCNNEQLKMQR---LDLSALKNMDG 121

Query:    84 IEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHY 143
             +EY L + +EP  F+I KQ R  P  V     YYV++G+IYQAP+L  VF +R+ +++ +
Sbjct:   122 LEYELIKFVEPSFFLIAKQTRISPTDVLINTLYYVINGNIYQAPELHVVFKSRVSQSISH 181

Query:   144 IQKAFTTAASKLE-KI--GYVDAENDGGTPLHSK-AGKETIDLKEVKRVDQILASL 195
             + +AF + +S +   I  GY    +       SK A      +++ KR+DQ++ SL
Sbjct:   182 LSEAFNSISSIVNWDIVNGYSLNLDPSNQQEKSKLAAYSRKQIEDTKRLDQLINSL 237

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

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

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

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

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

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

GO:0005634 "nucleus" evidence=IEA

RGD|1310296 Med6 "mediator complex subunit 6" [Rattus norvegicus (taxid:10116)]

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 69/184 (37%), Positives = 103/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+    L +  L++M
Sbjct:     9 NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              GIEY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E        +K  +E   + + +RVD +L  
Sbjct:   124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVKPKAKRKEEPSSIFQRQRVDALLID 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0003713 "transcription coactivator activity" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO

GO:0008134 "transcription factor binding" evidence=IEA;ISO

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

GO:0019827 "stem cell maintenance" evidence=IEA;ISO

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

UNIPROTKB|E2R2L6 MED6 "Mediator of RNA polymerase II transcription subunit 6" [Canis lupus familiaris (taxid:9615)]

 Score = 281 (104.0 bits), Expect = 1.2e-24, P = 1.2e-24
 Identities = 68/184 (36%), Positives = 103/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+    L +  L++M
Sbjct:     9 NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              G+EY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E        +K  +E   + + +RVD +L  
Sbjct:   124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVKPKAKRKEEPSSIFQRQRVDALLLD 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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:0008134 "transcription factor binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|G3V4A5 MED6 "Mediator of RNA polymerase II transcription subunit 6" [Homo sapiens (taxid:9606)]

 Score = 281 (104.0 bits), Expect = 1.2e-24, P = 1.2e-24
 Identities = 69/184 (37%), Positives = 103/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+    L +  L++M
Sbjct:     9 NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              GIEY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E        +K  +E   + + +RVD +L  
Sbjct:   124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVRPKAKRKEEPSSIFQRQRVDALLLD 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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

GO:0016592 "mediator complex" evidence=IEA

UNIPROTKB|O75586 MED6 "Mediator of RNA polymerase II transcription subunit 6" [Homo sapiens (taxid:9606)]

 Score = 281 (104.0 bits), Expect = 1.2e-24, P = 1.2e-24
 Identities = 69/184 (37%), Positives = 103/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+    L +  L++M
Sbjct:     9 NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              GIEY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E        +K  +E   + + +RVD +L  
Sbjct:   124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVRPKAKRKEEPSSIFQRQRVDALLLD 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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

GO:0003677 "DNA binding" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IPI

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

GO:0005634 "nucleus" evidence=TAS

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

GO:0003713 "transcription coactivator activity" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

MGI|MGI:1917042 Med6 "mediator of RNA polymerase II transcription, subunit 6 homolog (yeast)" [Mus musculus (taxid:10090)]

 Score = 281 (104.0 bits), Expect = 1.2e-24, P = 1.2e-24
 Identities = 69/184 (37%), Positives = 103/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+    L +  L++M
Sbjct:     9 NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              GIEY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E        +K  +E   + + +RVD +L  
Sbjct:   124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQEKVKPKAKRKEEPSSIFQRQRVDALLID 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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

GO:0003677 "DNA binding" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

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

GO:0008134 "transcription factor binding" evidence=ISO

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|Q3SZY9 MED6 "Mediator of RNA polymerase II transcription subunit 6" [Bos taurus (taxid:9913)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 68/184 (36%), Positives = 102/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+    L +  L++M
Sbjct:     9 NLLGISWVDSSWIPI--LNSGSVLDYFSERSNPFYDRTCNNEVVKMQR---LTLEHLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              G+EY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E         K  +E   + + +RVD +L  
Sbjct:   124 HGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVKPKVKRKEEPSSIFQRQRVDALLLD 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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:0008134 "transcription factor binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|E1BZ92 MED6 "Mediator of RNA polymerase II transcription subunit 6" [Gallus gallus (taxid:9031)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 69/184 (37%), Positives = 103/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+ +  LD   L++M
Sbjct:     9 NLLGISWVDSAWIPI--LNNGSVLDYFSERSNPFYDRTCNNEVVKMQRM-TLD--HLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              G+EY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E        +K  +E   + +  RVD +L  
Sbjct:   124 HGIQSAFEEAMSYCRYHPSKGYWWHFKDQEEREKAKPKAKKKEEPSSIFQRHRVDALLLD 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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

GO:0016592 "mediator complex" evidence=IEA

UNIPROTKB|H9KYN6 H9KYN6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 69/184 (37%), Positives = 103/184 (55%)

Query:    24 DMTGICFRDQLWLNTYPLDRNMIFDYFT--LSLFYDRTCNNEQLRMRSIHPLDISQLSKM 81
             ++ GI + D  W+    L+   + DYF+   + FYDRTCNNE ++M+ +  LD   L++M
Sbjct:     9 NLLGISWVDSAWIPI--LNNGSVLDYFSERSNPFYDRTCNNEVVKMQRM-TLD--HLNQM 63

Query:    82 TGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRAL 141
              G+EY+L    EP LF+IRKQ+R  P +V P+  YY++ G IYQAP L +V ++R+  A+
Sbjct:    64 VGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAV 123

Query:   142 HYIQKAFTTAASKLE---KIGY----VDAENDGGTPLHSKAGKETIDLKEVKRVDQILAS 194
             H IQ AF  A S        GY     D E        +K  +E   + +  RVD +L  
Sbjct:   124 HGIQSAFEEAMSYCRYHPSKGYWWHFKDQEEREKAKPKAKKKEEPSSIFQRHRVDALLLD 183

Query:   195 LQRK 198
             L++K
Sbjct:   184 LRQK 187

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

GO:0016592 "mediator complex" evidence=IEA

---

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)
Q921D4	MED6_MOUSE	No assigned EC number	0.3386	0.8525	0.8699	yes	no
O75586	MED6_HUMAN	No assigned EC number	0.3466	0.8525	0.8699	yes	no
Q3SZY9	MED6_BOVIN	No assigned EC number	0.3346	0.8525	0.8699	yes	no
Q5RD94	MED6_PONAB	No assigned EC number	0.3531	0.8486	0.8658	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	251
pfam04934	134	pfam04934, Med6, MED6 mediator sub complex compone	2e-58
COG5097	210	COG5097, MED6, RNA polymerase II transcriptional r	3e-29

>gnl|CDD|218335 pfam04934, Med6, MED6 mediator sub complex component

 Score =  181 bits (462), Expect = 2e-58
 Identities = 63/128 (49%), Positives = 90/128 (70%), Gaps = 2/128 (1%)

Query: 28  ICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDI--SQLSKMTGIE 85
           I +RD  WL ++ L+ N + DYF+ S FYD+T NNE LRM+         S+L KMTGIE
Sbjct: 1   IQWRDPEWLQSFGLNTNNVLDYFSESPFYDKTSNNEVLRMQRQFNQIAFESRLKKMTGIE 60

Query: 86  YMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQ 145
           Y+L+ V EP L+VIRKQ+R  P++VTP+  YY++ G+IYQAP L +V S+R+  A+ +++
Sbjct: 61  YVLAHVREPDLWVIRKQRRHNPDEVTPLADYYIIGGNIYQAPTLYSVLSSRLLSAVLHLE 120

Query: 146 KAFTTAAS 153
           KAF T +S
Sbjct: 121 KAFDTLSS 128

Component of RNA polymerase II holoenzyme and mediator sub complex. Length = 134

>gnl|CDD|227428 COG5097, MED6, RNA polymerase II transcriptional regulation mediator [Transcription]

 Score =  108 bits (272), Expect = 3e-29
 Identities = 42/140 (30%), Positives = 70/140 (50%), Gaps = 5/140 (3%)

Query: 22  GTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRS-IHPLDI----S 76
              +T I + D  WL +  L    + +YF+ S FYD++ NNE L+M++    LD+     
Sbjct: 3   ERPLTSIQWVDPEWLQSKGLRTENVLEYFSGSPFYDKSSNNEILKMQTQFRGLDLGQLSK 62

Query: 77  QLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSAR 136
            LS + G   + S   EP L+VIRKQ R    + TP++ Y +   +IY AP   +++  R
Sbjct: 63  LLSMLGGFYEVESSNREPTLWVIRKQYRHNDTEETPLMYYIIHGHNIYAAPTNYSIYRCR 122

Query: 137 IGRALHYIQKAFTTAASKLE 156
           +G +++ +         K  
Sbjct: 123 MGDSMYQLNSFLDRMMEKRR 142

Length = 210

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	251
KOG3169	208	consensus RNA polymerase II transcriptional regula	100.0
PF04934	140	Med6: MED6 mediator sub complex component; InterPr	100.0
COG5097	210	MED6 RNA polymerase II transcriptional regulation	100.0

>KOG3169 consensus RNA polymerase II transcriptional regulation mediator [Transcription]

Probab=100.00  E-value=4.1e-59  Score=407.25  Aligned_cols=179  Identities=34%  Similarity=0.547  Sum_probs=152.7

Q ss_pred             CCCCCCCceeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCC--CChhhhhhcCCceeEEeeecCCceE
Q 025523           20 PPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHP--LDISQLSKMTGIEYMLSEVMEPHLF   97 (251)
Q Consensus        20 ~p~~d~~~i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~--l~~~~L~~m~GiEY~l~~~~ep~Lf   97 (251)
                      ++.+|+++|+||||+|++.++|+++|||||||+|||||++||||+||||++.+  +..++|.+|.||||+|.|++||.||
T Consensus         1 ~~~~~l~~isw~dp~wi~~~~L~~~nVLdYFs~sPFYd~scNNe~lkMQ~qf~~~~~~e~L~~m~GieYvl~~~~~P~Lf   80 (208)
T KOG3169|consen    1 PMEDDLLSISWRDPEWIQSKGLRTENVLDYFSSSPFYDKSCNNEVLKMQTQFRGRDLEEHLFSMVGIEYVLLHSREPILF   80 (208)
T ss_pred             CCCCCccceeeeCcccccccCCCcchHHHHhhcCccccccccHHHHHHHHHHhccchHHHHhhCcCeEEEEEecCCCeEE
Confidence            35789999999999999999999999999999999999999999999997652  3468999999999999999999999


Q ss_pred             EEEEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCcCCCCCC---CCCC
Q 025523           98 VIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYVDAENDG---GTPL  171 (251)
Q Consensus        98 VIrKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~~~~~~~---~~~~  171 (251)
                      |||||+|+++++++||++||||||+|||||++|+|++|||++++++|++||+++.++.+   .+||+|.....   ++++
T Consensus        81 VIrKQ~R~n~tev~PLa~YYII~g~VYqAPd~ysiv~sRml~a~~~lqsa~~e~~~~~rynP~kGy~~~~~s~~~~~~~~  160 (208)
T KOG3169|consen   81 VIRKQRRHNPTEVIPLADYYIINGNVYQAPDLYSIVQSRMLNAVYQLQSAFDEAMSYRRYNPSKGYTWRFLSKSLEDSKD  160 (208)
T ss_pred             EEehhhcCCCccceeeeeEEEECceeeeCccHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCcccccCCchhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999988   89999854433   1122


Q ss_pred             CCCCCCC--CcchHHHhhHHHHHHHHHHhCCCCCC
Q 025523          172 HSKAGKE--TIDLKEVKRVDQILASLQRKLPPAPP  204 (251)
Q Consensus       172 ~~k~~~e--~~~~fQ~~RvD~lL~~L~~kfPp~~~  204 (251)
                      ..|+.++  ....+|      |++.|..+||+..+
T Consensus       161 ~~~~~~~~~~~~~~s------l~n~~~~~~p~~~~  189 (208)
T KOG3169|consen  161 LDNKNEIFNKFKKSS------LLNALYSFSPEDFS  189 (208)
T ss_pred             ccccccccccchhHH------HHhhccccCCCccc
Confidence            2222221  122223      78888877775533

>PF04934 Med6: MED6 mediator sub complex component; InterPro: IPR007018 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=100.00  E-value=8.2e-54  Score=356.83  Aligned_cols=129  Identities=49%  Similarity=0.785  Sum_probs=55.2

Q ss_pred             eeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCCC--------ChhhhhhcCCceeEEeeecCCceEEE
Q 025523           28 ICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPL--------DISQLSKMTGIEYMLSEVMEPHLFVI   99 (251)
Q Consensus        28 i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~l--------~~~~L~~m~GiEY~l~~~~ep~LfVI   99 (251)
                      |+||||+||++++||.+||||||++|||||++||||+||||++++.        .+++|++|.|+||+|+|++||+||||
T Consensus         1 i~w~dp~~l~~~~l~~~nvL~YF~~SPFyd~~snNe~lrmQ~~~~~~~~~~~~~~~~~L~~m~GiEY~l~~~~eP~l~vI   80 (140)
T PF04934_consen    1 IQWRDPEWLQQNGLNSNNVLDYFSESPFYDRTSNNEVLRMQRQFNQQNLPTREAFEQQLRNMKGIEYVLAHVQEPGLFVI   80 (140)
T ss_dssp             -------SHHHHHH---STTSSTTTHHHH----SSSSSSTTTSHHHTT-SSSHHHHHTTTS-------------------
T ss_pred             CcccCHHHHHhcCCChhHHHHHHccCcccCCCCCCceeeeccccCccccchhHHHHHHHhhcCCeEEEEeccCCCCEEEE
Confidence            7999999999999999999999999999999999999999987532        23579999999999999999999999


Q ss_pred             EEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025523          100 RKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE  156 (251)
Q Consensus       100 rKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~  156 (251)
                      |||+|+++++++||++||||||+|||||||++||++||++++++|++||+.+.++.+
T Consensus        81 ~Kq~r~~~~~~~~la~YYIi~g~IYqAPsl~~vl~sRl~~~~~~l~~a~~~~~~~~~  137 (140)
T PF04934_consen   81 RKQRRQSPDEVTPLAYYYIINGNIYQAPSLYSVLSSRLLSAVSSLSKAFDEANSMSR  137 (140)
T ss_dssp             -------------------------------SSSSSTTTHHHHHHHHHHHTT-----
T ss_pred             EEeeccCCCcceEeEEEEEECCEEEeCCCHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            999999999999999999999999999999999999999999999999999988654

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. Regulation of mRNA synthesis requires intermediary proteins that transduce regulatory signals from upstream transcriptional activator proteins to basal transcription machinery at the core promoter. Three types of intermediary factors that enable the basal transcription machinery to respond to transcriptional activator proteins bound to regulatory DNA sequences have been identified: (i) TAFIIs, which associate with TATA-binding protein (TBP) to form TFIID; (ii) mediator, which associates with RNA polymerase II to form a holo-polymerase; and (iii) coactivators such as human upstream stimulatory activity (USA), mammalian CBP/P300, yeast ADA complex, and HMG proteins. The interaction of these multiprotein complexes with activators and general transcription factors is essential for transcriptional regulation. This family of proteins represent the transcriptional mediator protein subunit 6 that is required for activation of many RNA polymerase II promoters and which are conserved from yeast to humans []..; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3RJ1_N.

>COG5097 MED6 RNA polymerase II transcriptional regulation mediator [Transcription]

Probab=100.00  E-value=1e-42  Score=301.71  Aligned_cols=137  Identities=31%  Similarity=0.513  Sum_probs=127.0

Q ss_pred             CCceeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCC-CCh----hhhhhcCCceeEEeeecCCceEEE
Q 025523           25 MTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHP-LDI----SQLSKMTGIEYMLSEVMEPHLFVI   99 (251)
Q Consensus        25 ~~~i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~-l~~----~~L~~m~GiEY~l~~~~ep~LfVI   99 (251)
                      +++|+|+||+||+.+||..+||||||+.|||||++||||+||||+..+ ||.    ++|+.+.|++||+.|+.||.||||
T Consensus         6 l~siqw~~pew~qs~gLrteNVLeYFs~SPFydk~sNNeilKMQ~QF~~LdL~ql~~~l~~l~g~~~V~ss~rep~lwVI   85 (210)
T COG5097           6 LTSIQWVDPEWLQSKGLRTENVLEYFSGSPFYDKSSNNEILKMQTQFRGLDLGQLSKLLSMLGGFYEVESSNREPTLWVI   85 (210)
T ss_pred             ccceeecCHHHHhccCCcchhHHHHhcCCCccccccchHHHHHHHHhhccChHHHHHHHHhccCEEEEEecCCCCcEEEE
Confidence            889999999999999999999999999999999999999999998543 553    557788999999999999999999


Q ss_pred             EEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCc
Q 025523          100 RKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYV  161 (251)
Q Consensus       100 rKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~  161 (251)
                      |||+|++.++++||.+|||+|.+|||||+.|+|+++||++++++|+++++.+...-+   ..||.
T Consensus        86 rKq~r~n~~e~~pl~~Y~i~g~NIY~aPt~y~i~~~Rm~~s~y~lns~l~~~~~~~~fnP~~g~~  150 (210)
T COG5097          86 RKQYRHNDTEETPLMYYIIHGHNIYAAPTNYSIYRCRMGDSMYQLNSFLDRMMEKRRFNPFSGPK  150 (210)
T ss_pred             ehhhhcCCcccccceEEEEecCceeeCcchhhhhhhhhhhhHHHHHHHHHHHHHhhccCCCCCCC
Confidence            999999999999999999999999999999999999999999999999999888655   55654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	251
4h63_F	183	Structure Of The Schizosaccharomyces Pombe Mediator		2e-15
4h61_A	175	Structure Of The Schizosaccharomyces Pombe Mediator		2e-15
4gwp_G	295	Structure Of The Mediator Head Module From S. Cerev		9e-10
3rj1_G	295	Architecture Of The Mediator Head Module Length = 2		1e-08

>pdb|4H63|F Chain F, Structure Of The Schizosaccharomyces Pombe Mediator Head Module Length = 183

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 78/141 (55%), Gaps = 10/141 (7%)
Query: 24  DMTGICFRDQLWLNTYP-LDRNMIFDYFTLSLFYDRTCNNEQLRMRS-IHPLDI----SQ 77
           D+T I +R   W+ +   L    + +YF+ S FY    NNE L+M+S  + LD+    SQ
Sbjct: 13  DLTSIQWRMPEWVQSMGGLRTENVLEYFSQSPFYSHKSNNEMLKMQSQFNALDLGDLNSQ 72
Query: 78  LSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARI 137
           L ++TGI++++     P L+VI+KQ R    +V P+  Y+V + +IY AP    + + R+
Sbjct: 73  LKRLTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRM 132
Query: 138 GRALHYIQKAFTTAASKLEKI 158
             A +  QKA T    K+EK 
Sbjct: 133 LNATYCFQKALT----KIEKF 149

>pdb|4H61|A Chain A, Structure Of The Schizosaccharomyces Pombe Mediator Subunit Med6 Length = 175

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 78/141 (55%), Gaps = 10/141 (7%)
Query: 24  DMTGICFRDQLWLNTYP-LDRNMIFDYFTLSLFYDRTCNNEQLRMRS-IHPLDI----SQ 77
           D+T I +R   W+ +   L    + +YF+ S FY    NNE L+M+S  + LD+    SQ
Sbjct: 5   DLTSIQWRMPEWVQSMGGLRTENVLEYFSQSPFYSHKSNNEMLKMQSQFNALDLGDLNSQ 64
Query: 78  LSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARI 137
           L ++TGI++++     P L+VI+KQ R    +V P+  Y+V + +IY AP    + + R+
Sbjct: 65  LKRLTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRM 124
Query: 138 GRALHYIQKAFTTAASKLEKI 158
             A +  QKA T    K+EK 
Sbjct: 125 LNATYCFQKALT----KIEKF 141

>pdb|4GWP|G Chain G, Structure Of The Mediator Head Module From S. Cerevisiae Length = 295

Iteration: 1
 Score = 60.5 bits (145), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 42/160 (26%), Positives = 68/160 (42%), Gaps = 58/160 (36%)
Query: 35  WLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRM--------------------------- 67
           W+  + L    + DYF  S F+D+T NN+ ++M                           
Sbjct: 16  WIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNAAVNMTQNIMTLPDGK 75
Query: 68  ---------------RSI---HPLDI---SQLSKMTGIEYMLSEVMEPHLFVIRKQKR-- 104
                          R I   +P+ +    +L K+ G EY+LS V EP  +VIRKQ+R  
Sbjct: 76  NGNLEEEFAYVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTN 135
Query: 105 -------DGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARI 137
                   GPE + P+  YY++  +IYQ+P +  +  +R+
Sbjct: 136 NSGVGSAKGPE-IIPLQDYYIIGANIYQSPTIFKIVQSRL 174

>pdb|3RJ1|G Chain G, Architecture Of The Mediator Head Module Length = 295

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 10/81 (12%)
Query: 77  QLSKMTGIEYMLSEVMEPHLFVIRKQKR---------DGPEKVTPMLTYYVLDGSIYQAP 127
           +L K+ G EY+LS V EP  +VIRKQ+R          GPE + P+  YY++  +IYQ+P
Sbjct: 106 ELXKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPE-IIPLQDYYIIGANIYQSP 164
Query: 128 QLCNVFSARIGRALHYIQKAF 148
            +  +  +R+    +++    
Sbjct: 165 TIFKIVQSRLXSTSYHLNSTL 185

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	251
3rj1_G	295	Mediator of RNA polymerase II transcription subun;	5e-36
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

>3rj1_G Mediator of RNA polymerase II transcription subun; RNA polymeras II, POL II, head module, head, regulator, helical bundle; 4.30A {Saccharomyces cerevisiae} Length = 295

 Score =  128 bits (322), Expect = 5e-36
 Identities = 48/289 (16%), Positives = 91/289 (31%), Gaps = 64/289 (22%)

Query: 23  TDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPLDI------- 75
           T +  + ++   W+  + L    + DYF  S F+D+T NN+ ++M+              
Sbjct: 4   TPLDELQWKSPEWIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNAAVN 63

Query: 76  -----------------------------------------SQLSKMTGIEYMLSEVMEP 94
                                                     +L K+ G EY+LS V EP
Sbjct: 64  MTQNIMTLPDGKNGNLEEEFAYVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSVREP 123

Query: 95  HLFVIRKQKRDGPEK--------VTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQK 146
             +VIRKQ+R             + P+  YY++  +IYQ+P +  +  +R+    +++  
Sbjct: 124 DFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSPTIFKIVQSRLMSTSYHLNS 183

Query: 147 AFTTAASKLE---KIGYV--DAENDGGTPLHSKAGKETIDLKEVKRVDQILASLQRKLPP 201
              +    +E     G       +   T   +  G           V     +    +P 
Sbjct: 184 TLESLYDLIEFQPSQGVHYKVPTDTSTTATAATNGNNAGGGSNKSSVRPTGGANMATVPS 243

Query: 202 APPPPPFPEGYAPPQTEEAEKDPETQQTAEPQPPAIDPIIDQGPAKRMK 250
                          T     D  T +T          ++D+     ++
Sbjct: 244 TTNVNMTV---NTMGTGGQTIDNGTGRTGNGNMGITTEMLDKLMVTSIR 289

>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 = 46.4 bits (109), Expect = 5e-06
 Identities = 32/253 (12%), Positives = 74/253 (29%), Gaps = 57/253 (22%)

Query: 29  CFRDQLWLNTYP----LDRNMIFDYFTLSLFYDRTCN------NEQLRMRSIHPLDISQL 78
            ++D L +         D   + D    S+      +      +       +        
Sbjct: 17  QYKDILSVFEDAFVDNFDCKDVQD-MPKSILSKEEIDHIIMSKDAVSGTLRL--FWTLLS 73

Query: 79  SKMTGIEYMLSEVMEP-HLFV---IRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFS 134
            +   ++  + EV+   + F+   I+ ++R  P  +T M         +Y   Q   VF+
Sbjct: 74  KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQ-PSMMTRMYIEQR--DRLYNDNQ---VFA 127

Query: 135 AR-IGRALHYIQKAFTTAASKLEKIGYVDAENDGGTPLHSKAGKET-------------- 179
              + R   Y++     A  +L     V  +   G      +GK                
Sbjct: 128 KYNVSRLQPYLK--LRQALLELRPAKNVLIDGVLG------SGKTWVALDVCLSYKVQCK 179

Query: 180 -------IDLKEVKRVDQILASLQR---KLPPAPPPPPFPEGYAPPQTEEAEKDPETQQT 229
                  ++LK     + +L  LQ+   ++ P              +    + +      
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 230 AEPQPPAIDPIID 242
           ++P    +  ++ 
Sbjct: 240 SKPYENCLL-VLL 251

>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 = 39.5 bits (91), Expect = 8e-04
 Identities = 32/186 (17%), Positives = 65/186 (34%), Gaps = 40/186 (21%)

Query: 51  TLSLFYDRT-CNNEQLR--MRSIHPLDISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGP 107
             SL      C  + L   + + +P  +S          +++E +   L      K    
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRLS----------IIAESIRDGLATWDNWKHVNC 352

Query: 108 EKVTPML--TYYVLDGSIYQAP-QLCNVF--SARIGRALHYI---QKAFTTA---ASKLE 156
           +K+T ++  +  VL+ + Y+      +VF  SA I   L  +       +      +KL 
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH 412

Query: 157 KIGYVDAENDGGT-PLHSKAGKETIDLKEVKRVDQILA---------SLQRKLPPAPPPP 206
           K   V+ +    T  + S      I L+   +++   A         ++ +        P
Sbjct: 413 KYSLVEKQPKESTISIPS------IYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466

Query: 207 PFPEGY 212
           P+ + Y
Sbjct: 467 PYLDQY 472

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	251
4h61_A	175	Mediator of RNA polymerase II transcription subun;	100.0
4gwp_G	295	Mediator of RNA polymerase II transcription subun;	100.0

>4h61_A Mediator of RNA polymerase II transcription subun; mediator complex, nucleus; 2.70A {Schizosaccharomyces pombe} PDB: 4h63_F

Probab=100.00  E-value=9.9e-58  Score=392.08  Aligned_cols=144  Identities=33%  Similarity=0.559  Sum_probs=124.1

Q ss_pred             CCCCceeeeCchhhccC-CCCcchHHHhhhcCCCcccCCChHHHHhhhCCC-CC----hhhhhhcCCceeEEeeecCCce
Q 025523           23 TDMTGICFRDQLWLNTY-PLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHP-LD----ISQLSKMTGIEYMLSEVMEPHL   96 (251)
Q Consensus        23 ~d~~~i~wrDp~wL~~~-~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~-l~----~~~L~~m~GiEY~l~~~~ep~L   96 (251)
                      -|+++|+||||+||+.+ |||++||||||++||||||+||||+||||++++ ++    +++|++|+|+||+|+|++||+|
T Consensus         4 ~dl~~i~wr~p~wi~~~~~L~~~nvLdYF~~SPFyD~tsnNe~lrmQ~~~~~~~~~~~e~~L~~m~GiEy~l~~~~~p~l   83 (175)
T 4h61_A            4 MDLTSIQWRMPEWVQSMGGLRTENVLEYFSQSPFYSHKSNNEMLKMQSQFNALDLGDLNSQLKRLTGIQFVIIHERPPFL   83 (175)
T ss_dssp             CCGGGCCBCCHHHHHHTTSCCTTTHHHHHHTSTTCCTTSHHHHHHHHHHHTTCCCCCHHHHHHTCCEEEEEEEEEETTTE
T ss_pred             CCccccEEcCHHHHHhcCCCCccHHHHHhhcCCcccccchHHHHHHhhccCccchHHHHHHHhcCCCceEEEeecCCCce
Confidence            58999999999999997 799999999999999999999999999998643 32    4789999999999999999999


Q ss_pred             EEEEEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCcCCCCC
Q 025523           97 FVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYVDAEND  166 (251)
Q Consensus        97 fVIrKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~~~~~~  166 (251)
                      ||||||+|+++++++||++||||||+|||||||++||++||++++++|++||+++.++.+   +.||+|....
T Consensus        84 fvI~Kq~R~~~~~~~~la~YyIi~g~IYqAP~l~~vl~sRl~s~~~~L~~a~~~~~~~~~~~ps~Gy~~~~~~  156 (175)
T 4h61_A           84 WVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLNATYCFQKALTKIEKFPQYNPQEGYTYPKLS  156 (175)
T ss_dssp             EEEEEEEECSSSCEEEEEEEEEETTEEEECCHHHHHHHHHHHHHHHHHHHHHTTCC-----------------
T ss_pred             EEEEEEEEcCCCcceEEEEEEEECCEEccCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCccCcCCeeCCCCC
Confidence            999999999999999999999999999999999999999999999999999999998766   7999996444

>4gwp_G Mediator of RNA polymerase II transcription subun; binding sites, mediator complex, models, molecular, phosphor protein structure; 4.20A {Saccharomyces cerevisiae S288C} PDB: 3rj1_G 4gwq_G

Probab=100.00  E-value=1.4e-58  Score=423.90  Aligned_cols=182  Identities=23%  Similarity=0.427  Sum_probs=123.7

Q ss_pred             CCCceeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCCC------------------------------
Q 025523           24 DMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPL------------------------------   73 (251)
Q Consensus        24 d~~~i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~l------------------------------   73 (251)
                      -|.+|+||||+||+.+|||++||||||++||||||+||||+||||++++.                              
T Consensus         5 PLdEiqWr~P~wiq~~gL~s~NVLdYFa~SPFyDktSNNevlrmQ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (295)
T 4gwp_G            5 PLDELQWKSPEWIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNAAVNMTQNIMTLPDGKNGNLEEEFA   84 (295)
T ss_dssp             CSSCCBCCSTTTTTCCSSTHHHHHHHHHHSCCCSHHHHHHHHHHHCCSCCCCCSCC----------------------CC
T ss_pred             CCcceeecCHHHHHhcCCCcchHHHHhhcCCccccccchHHHHHHHHhccccccccchhccccccccccccccchhhccc
Confidence            36789999999999999999999999999999999999999999986542                              


Q ss_pred             ------------------ChhhhhhcCCceeEEeeecCCceEEEEEeeecCCC--------ccccceeEEEEcCeEeeCC
Q 025523           74 ------------------DISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPE--------KVTPMLTYYVLDGSIYQAP  127 (251)
Q Consensus        74 ------------------~~~~L~~m~GiEY~l~~~~ep~LfVIrKQ~R~s~~--------~v~pLa~YYIi~G~IYQAP  127 (251)
                                        .+++|++|.||||+|+|++||+|||||||+|++++        +++||++||||||+|||||
T Consensus        85 ~~~~~r~~i~~~~~~~~~~e~~L~~m~GiEyvl~~~~eP~lwVIrKQ~R~s~~~~~~~~~~ev~pLa~YYIig~~IYqAP  164 (295)
T 4gwp_G           85 YVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSP  164 (295)
T ss_dssp             CCCCHHHHHHCCCSTHHHHHHHHHHHSCEEETTEEECSSEEEEEEETTEEEEEEEEECCCTTCCCEEEEEEEEETTEEEC
T ss_pred             cccchhhhhhhhcchhhhhHHHHhhCCCeEEEEeecCCCceEEEEeeeccCCcccccccCcceeEeEEEEEECCEEecCC
Confidence                              14789999999999999999999999999999864        7899999999999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCcCCCCCCCCCC--CCCCCCCCcchHHHhhHHHHHHHHHHhCCCC
Q 025523          128 QLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYVDAENDGGTPL--HSKAGKETIDLKEVKRVDQILASLQRKLPPA  202 (251)
Q Consensus       128 sl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~~~~~~~~~~~--~~k~~~e~~~~fQ~~RvD~lL~~L~~kfPp~  202 (251)
                      +|++||++||+++++||+++|+.+.++.+   +.||+|.....+...  ..+......+.+++.|++.....+.+++|.+
T Consensus       165 sl~~Vl~sRlls~~~~L~~a~~~~~~~~~f~Ps~G~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~  244 (295)
T 4gwp_G          165 TIFKIVQSRLMSTSYHLNSTLESLYDLIEFQPSQGVHYKVPTDTSTTATAATNGNNAGGGSNKSSVRPTGGANMATVPST  244 (295)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHTCCC----------------------------------------------------
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHccCcccCCCCccccCCCCCccccccccCCCCCCccccccCCCCccccccccCCCC
Confidence            99999999999999999999999998766   899999644432222  2223345678999999999999999999887


Q ss_pred             CCC
Q 025523          203 PPP  205 (251)
Q Consensus       203 ~~~  205 (251)
                      .++
T Consensus       245 ~~~  247 (295)
T 4gwp_G          245 TNV  247 (295)
T ss_dssp             ---
T ss_pred             CCc
Confidence            554

---

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