Psyllid ID: psy7121

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------8
Protein Sequence
MTGLEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTGS
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHccccccEEEEEEEcccccEEEEEEEEEcccccccEEEEEEEEccEEEEcccHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccHHHHEEEHHHHHHHcccEEEEEEEcccccEEEEEEcccccccccccHHEEEEEcccEEccccHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
MTGLEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHrhsmeqttpiADYYIIAGVvyqapdlasvissrlvgtgs
Flexible Loop (DISEMBL)
MTGLEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTGS
Low Complexity Region (SEG)
MTGLEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTGS
Disordered region (IsUnstruct)
***LEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVIS********
Disordered Region (DISOPRED)
********LHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRH*M*QTTPIADYYIIAGVVYQAPDLASVISSRLVG***
Disordered Region (DISEMBL)
MTGLEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTGS
Disordered Region (DISPRO)
*TGLEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLV****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTGLEYIVLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTGS
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	79	2.2.26 [Sep-21-2011]
Q7Q107	267	Mediator of RNA polymeras	yes	N/A	0.822	0.243	0.738	1e-22
Q8MSX2	249	Mediator of RNA polymeras	yes	N/A	0.822	0.261	0.707	1e-21
Q6IQ63	254	Mediator of RNA polymeras	yes	N/A	0.746	0.232	0.711	1e-18
Q921D4	246	Mediator of RNA polymeras	yes	N/A	0.797	0.256	0.650	3e-18
O75586	246	Mediator of RNA polymeras	yes	N/A	0.797	0.256	0.650	3e-18
Q5RD94	246	Mediator of RNA polymeras	yes	N/A	0.734	0.235	0.689	5e-18
Q3SZY9	246	Mediator of RNA polymeras	yes	N/A	0.734	0.235	0.689	6e-18
Q6C3T0	227	Mediator of RNA polymeras	yes	N/A	0.873	0.303	0.434	4e-13
Q4PHA6	254	Mediator of RNA polymeras	N/A	N/A	0.835	0.259	0.424	3e-11
Q5A2Z1	263	Mediator of RNA polymeras	N/A	N/A	0.860	0.258	0.411	4e-11

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

 Score =  104 bits (260), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 48/65 (73%), Positives = 56/65 (86%)

Query: 13  EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
           E + NMTG+EYI LHVQ+PILYVIRKQHRHS  + TP+ADYYIIAG VYQAPDLASV +S
Sbjct: 64  ELLNNMTGVEYIPLHVQDPILYVIRKQHRHSPTEATPMADYYIIAGTVYQAPDLASVFNS 123

Query: 73  RLVGT 77
           R++ T
Sbjct: 124 RILST 128

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

 Score =  101 bits (252), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 46/65 (70%), Positives = 55/65 (84%)

Query: 13  EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
           E + NM GLEYI+LHV EPILYVIRKQHRH+  + TPIADYYII G VY+APDLA+VI+S
Sbjct: 58  EHLHNMIGLEYILLHVAEPILYVIRKQHRHNPSEATPIADYYIIGGTVYKAPDLANVINS 117

Query: 73  RLVGT 77
           R++ T
Sbjct: 118 RILNT 122

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

 Score = 91.3 bits (225), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query: 15  ILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSR 73
           +  + G+EYI+LH QEPILY+IRKQ R S  Q  P+ADYYIIAGVVYQAPDL SVISSR
Sbjct: 60  LTQLVGVEYILLHTQEPILYIIRKQQRQSPTQVIPLADYYIIAGVVYQAPDLGSVISSR 118

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

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query: 13  EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
           E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct: 58  EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query: 73  RLV 75
           R++
Sbjct: 118 RVL 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.

Mus musculus (taxid: 10090)

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

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query: 13  EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
           E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct: 58  EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query: 73  RLV 75
           R++
Sbjct: 118 RVL 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.

Homo sapiens (taxid: 9606)

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

 Score = 89.7 bits (221), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 49/58 (84%)

Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLV 75
           M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+SR++
Sbjct: 63  MVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVL 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.

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 = 89.4 bits (220), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 49/58 (84%)

Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLV 75
           M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+SR++
Sbjct: 63  MVGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINSRVL 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.

Bos taurus (taxid: 9913)

>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 = 73.6 bits (179), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 52/69 (75%)

Query: 10  HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASV 69
           H ++ +  MTG+E+++ HV+EP L+VI+KQ+R + +QTTPI+ Y++I   VY AP +A++
Sbjct: 63  HFEQELQKMTGIEFVITHVREPDLWVIKKQNRLNPQQTTPISTYFVINENVYMAPTVAAI 122

Query: 70  ISSRLVGTG 78
           + SR++ T 
Sbjct: 123 MQSRVLSTS 131

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)

>sp|Q4PHA6|MED6_USTMA Mediator of RNA polymerase II transcription subunit 6 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=MED6 PE=3 SV=1

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 28/66 (42%), Positives = 48/66 (72%)

Query: 12  QEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVIS 71
           ++ +   TGLE++++H +EP  +V++K+ R S  +TTP+A YY+I   +YQAPDL S+++
Sbjct: 101 EQELKRFTGLEFVLVHSREPTCFVVQKRWRTSPTETTPLAAYYVINDSIYQAPDLYSILA 160

Query: 72  SRLVGT 77
           +RL  T
Sbjct: 161 TRLQST 166

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.

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

>sp|Q5A2Z1|MED6_CANAL Mediator of RNA polymerase II transcription subunit 6 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=MED6 PE=3 SV=1

 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 44/68 (64%)

Query: 10  HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASV 69
           + Q  +  MTG+E+++ + +EP  ++IRKQ R   + T  + DYYII   VYQAP +  V
Sbjct: 64  YFQSRLSEMTGIEFVIAYTKEPDFWIIRKQKRQDPQNTVTLQDYYIIGANVYQAPRIYDV 123

Query: 70  ISSRLVGT 77
           +SSRL+ +
Sbjct: 124 LSSRLLAS 131

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.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

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	79
443709640	238	hypothetical protein CAPTEDRAFT_168225 [	0.835	0.277	0.803	6e-24
242021515	237	conserved hypothetical protein [Pediculu	0.822	0.274	0.8	3e-23
91087181	250	PREDICTED: similar to AGAP010034-PA [Tri	0.746	0.236	0.847	1e-22
156543394	229	PREDICTED: mediator of RNA polymerase II	0.810	0.279	0.781	2e-22
383854247	229	PREDICTED: mediator of RNA polymerase II	0.772	0.266	0.836	3e-22
260831182	246	hypothetical protein BRAFLDRAFT_202253 [	0.797	0.256	0.761	5e-22
270010564	179	hypothetical protein TcasGA2_TC009982 [T	0.746	0.329	0.830	6e-22
322801480	230	hypothetical protein SINV_10332 [Solenop	0.797	0.273	0.793	8e-22
307176282	229	Mediator of RNA polymerase II transcript	0.772	0.266	0.819	9e-22
241149340	281	mediator of RNA polymerase II transcript	0.772	0.217	0.737	2e-21

>gi|443709640|gb|ELU04232.1| hypothetical protein CAPTEDRAFT_168225 [Capitella teleta]

 Score =  114 bits (286), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 53/66 (80%), Positives = 58/66 (87%)

Query: 12  QEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVIS 71
           QE + NMTGLEYI+LHVQEPILYVIRKQHRHS  Q  P+ADYYIIAG+VYQAPDL SVIS
Sbjct: 52  QEQLGNMTGLEYILLHVQEPILYVIRKQHRHSQSQVAPLADYYIIAGIVYQAPDLGSVIS 111

Query: 72  SRLVGT 77
           SRL+ T
Sbjct: 112 SRLLNT 117

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|242021515|ref|XP_002431190.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212516439|gb|EEB18452.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  112 bits (279), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/65 (80%), Positives = 59/65 (90%)

Query: 13  EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
           E + NMTGLEYI+LHVQEPILYVIRKQHRHS  Q TP+ADYYI+AG+VYQAPDLASVI+S
Sbjct: 59  EQLNNMTGLEYILLHVQEPILYVIRKQHRHSPTQATPLADYYIVAGIVYQAPDLASVINS 118

Query: 73  RLVGT 77
           RL+ T
Sbjct: 119 RLLST 123

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91087181|ref|XP_975417.1| PREDICTED: similar to AGAP010034-PA [Tribolium castaneum]

 Score =  110 bits (275), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 50/59 (84%), Positives = 57/59 (96%)

Query: 17  NMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLV 75
           NMTGLEY++LHVQEPILYVIRKQHRHS +Q TP+ADYYIIAGVVYQAPDLASV++SRL+
Sbjct: 71  NMTGLEYVLLHVQEPILYVIRKQHRHSPQQVTPLADYYIIAGVVYQAPDLASVLNSRLL 129

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156543394|ref|XP_001600142.1| PREDICTED: mediator of RNA polymerase II transcription subunit 6-like [Nasonia vitripennis]

 Score =  109 bits (272), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/64 (78%), Positives = 57/64 (89%)

Query: 13  EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
           E ++NMTG EYI+LHVQEPILYVIRKQHRH   Q TP+ADYYIIAGVVYQAPDLASV++S
Sbjct: 60  EQLMNMTGFEYILLHVQEPILYVIRKQHRHGPTQATPVADYYIIAGVVYQAPDLASVVNS 119

Query: 73  RLVG 76
           RL+ 
Sbjct: 120 RLLS 123

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383854247|ref|XP_003702633.1| PREDICTED: mediator of RNA polymerase II transcription subunit 6-like [Megachile rotundata]

 Score =  108 bits (271), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 51/61 (83%), Positives = 56/61 (91%)

Query: 17  NMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVG 76
           NMTGLEY++LHVQEPILYVIRKQHRHS    TP+ADYYIIAGVVYQAPDLASV+SSRL+ 
Sbjct: 64  NMTGLEYMLLHVQEPILYVIRKQHRHSPTLATPLADYYIIAGVVYQAPDLASVVSSRLLS 123

Query: 77  T 77
           T
Sbjct: 124 T 124

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260831182|ref|XP_002610538.1| hypothetical protein BRAFLDRAFT_202253 [Branchiostoma floridae] gi|229295905|gb|EEN66548.1| hypothetical protein BRAFLDRAFT_202253 [Branchiostoma floridae]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 48/63 (76%), Positives = 57/63 (90%)

Query: 13  EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
           E + NMTG+EYI+LH QEPILYV+RKQHRHS +Q TP+ADYYIIAGVVYQAPDL SV++S
Sbjct: 51  EQLNNMTGMEYILLHAQEPILYVVRKQHRHSQQQVTPLADYYIIAGVVYQAPDLYSVLNS 110

Query: 73  RLV 75
           RL+
Sbjct: 111 RLL 113

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|270010564|gb|EFA07012.1| hypothetical protein TcasGA2_TC009982 [Tribolium castaneum]

 Score =  108 bits (269), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 56/59 (94%)

Query: 18 MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVG 76
          MTGLEY++LHVQEPILYVIRKQHRHS +Q TP+ADYYIIAGVVYQAPDLASV++SRL+ 
Sbjct: 1  MTGLEYVLLHVQEPILYVIRKQHRHSPQQVTPLADYYIIAGVVYQAPDLASVLNSRLLS 59

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322801480|gb|EFZ22141.1| hypothetical protein SINV_10332 [Solenopsis invicta]

 Score =  107 bits (268), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 50/63 (79%), Positives = 56/63 (88%)

Query: 15  ILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRL 74
           + NMTGLEYI+LHVQEPILYVIRKQHRHS    +P+ADYYIIAGVVYQAPDL SV+SSRL
Sbjct: 67  LTNMTGLEYILLHVQEPILYVIRKQHRHSPTLASPVADYYIIAGVVYQAPDLGSVVSSRL 126

Query: 75  VGT 77
           + T
Sbjct: 127 LST 129

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307176282|gb|EFN65913.1| Mediator of RNA polymerase II transcription subunit 6 [Camponotus floridanus]

 Score =  107 bits (267), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 50/61 (81%), Positives = 55/61 (90%)

Query: 17  NMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVG 76
           NMTGLEYI+LHVQEPILYVIRKQHRHS    +P+ADYYIIAGVVYQAPDL SV+SSRL+ 
Sbjct: 64  NMTGLEYILLHVQEPILYVIRKQHRHSPTVASPVADYYIIAGVVYQAPDLGSVVSSRLLS 123

Query: 77  T 77
           T
Sbjct: 124 T 124

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241149340|ref|XP_002406081.1| mediator of RNA polymerase II transcription subunit, putative [Ixodes scapularis] gi|215493804|gb|EEC03445.1| mediator of RNA polymerase II transcription subunit, putative [Ixodes scapularis]

 Score =  105 bits (263), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 45/61 (73%), Positives = 54/61 (88%)

Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGT 77
           MTGLEYI+LH QEPILYV+RKQHRHS  Q TP+ADYY++AGVVYQAPDL +V++SRL+ T
Sbjct: 125 MTGLEYILLHAQEPILYVVRKQHRHSPSQVTPLADYYVLAGVVYQAPDLGAVLNSRLLAT 184

Query: 78  G 78
            
Sbjct: 185 A 185

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

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	79
FB|FBgn0024330	249	MED6 "Mediator complex subunit	0.822	0.261	0.707	1e-20
ZFIN|ZDB-GENE-040625-61	254	med6 "mediator complex subunit	0.746	0.232	0.711	3.6e-18
UNIPROTKB|B4E2P0	181	MED6 "cDNA FLJ59149, highly si	0.797	0.348	0.650	4.6e-18
UNIPROTKB|G3V4A5	249	MED6 "Mediator of RNA polymera	0.797	0.253	0.650	4.6e-18
UNIPROTKB|O75586	246	MED6 "Mediator of RNA polymera	0.797	0.256	0.650	4.6e-18
MGI|MGI:1917042	246	Med6 "mediator of RNA polymera	0.797	0.256	0.650	4.6e-18
RGD|1310296	246	Med6 "mediator complex subunit	0.797	0.256	0.650	4.6e-18
UNIPROTKB|Q3SZY9	246	MED6 "Mediator of RNA polymera	0.797	0.256	0.650	5.8e-18
UNIPROTKB|E2R2L6	246	MED6 "Mediator of RNA polymera	0.797	0.256	0.650	5.8e-18
UNIPROTKB|B4DU17	253	MED6 "Mediator of RNA polymera	0.784	0.245	0.661	5.8e-18

FB|FBgn0024330 MED6 "Mediator complex subunit 6" [Drosophila melanogaster (taxid:7227)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/65 (70%), Positives = 55/65 (84%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E + NM GLEYI+LHV EPILYVIRKQHRH+  + TPIADYYII G VY+APDLA+VI+S
Sbjct:    58 EHLHNMIGLEYILLHVAEPILYVIRKQHRHNPSEATPIADYYIIGGTVYKAPDLANVINS 117

Query:    73 RLVGT 77
             R++ T
Sbjct:   118 RILNT 122

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

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

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS;IMP

GO:0005634 "nucleus" evidence=ISS;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=IDA

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

GO:0046331 "lateral inhibition" evidence=IMP

ZFIN|ZDB-GENE-040625-61 med6 "mediator complex subunit 6" [Danio rerio (taxid:7955)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query:    15 ILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSR 73
             +  + G+EYI+LH QEPILY+IRKQ R S  Q  P+ADYYIIAGVVYQAPDL SVISSR
Sbjct:    60 LTQLVGVEYILLHTQEPILYIIRKQQRQSPTQVIPLADYYIIAGVVYQAPDLGSVISSR 118

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

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

GO:0016592 "mediator complex" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|B4E2P0 MED6 "cDNA FLJ59149, highly similar to RNA polymerase transcriptional regulation mediator, subunit 6 homolog" [Homo sapiens (taxid:9606)]

 Score = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RLV 75
             R++
Sbjct:   118 RVL 120

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

GO:0016592 "mediator complex" evidence=IEA

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

 Score = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RLV 75
             R++
Sbjct:   118 RVL 120

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 = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RLV 75
             R++
Sbjct:   118 RVL 120

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 = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RLV 75
             R++
Sbjct:   118 RVL 120

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

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

 Score = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RLV 75
             R++
Sbjct:   118 RVL 120

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

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RLV 75
             R++
Sbjct:   118 RVL 120

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

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 41/63 (65%), Positives = 51/63 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGVEYILLHAQEPILFIIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RLV 75
             R++
Sbjct:   118 RVL 120

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|B4DU17 MED6 "Mediator of RNA polymerase II transcription subunit 6" [Homo sapiens (taxid:9606)]

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 41/62 (66%), Positives = 50/62 (80%)

Query:    13 EPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISS 72
             E +  M G+EYI+LH QEPIL++IRKQ R S  Q  P+ADYYIIAGV+YQAPDL SVI+S
Sbjct:    58 EHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINS 117

Query:    73 RL 74
             R+
Sbjct:   118 RV 119

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	0.6507	0.7974	0.2560	yes	N/A
O75586	MED6_HUMAN	No assigned EC number	0.6507	0.7974	0.2560	yes	N/A
Q3SZY9	MED6_BOVIN	No assigned EC number	0.6896	0.7341	0.2357	yes	N/A
Q7Q107	MED6_ANOGA	No assigned EC number	0.7384	0.8227	0.2434	yes	N/A
Q6IQ63	MED6_DANRE	No assigned EC number	0.7118	0.7468	0.2322	yes	N/A
Q8MSX2	MED6_DROME	No assigned EC number	0.7076	0.8227	0.2610	yes	N/A
Q5RD94	MED6_PONAB	No assigned EC number	0.6896	0.7341	0.2357	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	79
pfam04934	134	pfam04934, Med6, MED6 mediator sub complex compone	6e-29
COG5097	210	COG5097, MED6, RNA polymerase II transcriptional r	8e-14

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

 Score = 99.6 bits (249), Expect = 6e-29
 Identities = 37/58 (63%), Positives = 48/58 (82%)

Query: 17  NMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRL 74
            MTG+EY++ HV+EP L+VIRKQ RH+ ++ TP+ADYYII G +YQAP L SV+SSRL
Sbjct: 55  KMTGIEYVLAHVREPDLWVIRKQRRHNPDEVTPLADYYIIGGNIYQAPTLYSVLSSRL 112

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 = 62.7 bits (152), Expect = 8e-14
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGT 77
           + G   +    +EP L+VIRKQ+RH+  + TP+  Y I    +Y AP   S+   R+  +
Sbjct: 67  LGGFYEVESSNREPTLWVIRKQYRHNDTEETPLMYYIIHGHNIYAAPTNYSIYRCRMGDS 126

Length = 210

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	79
KOG3169|consensus	208		100.0
PF04934	140	Med6: MED6 mediator sub complex component; InterPr	99.97
COG5097	210	MED6 RNA polymerase II transcriptional regulation	99.9

>KOG3169|consensus

Probab=100.00  E-value=3.4e-34  Score=210.64  Aligned_cols=69  Identities=52%  Similarity=0.961  Sum_probs=66.9

Q ss_pred             hhhhhcccCcceeEEEeecCCCceEEEEEeeecCCCCceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121          10 HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTG   78 (79)
Q Consensus        10 ~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~   78 (79)
                      .++++|.+|+||||+|.|++||.|||||||+|+++++++|||+||||||+||||||+|+|++|||++|+
T Consensus        56 ~~~e~L~~m~GieYvl~~~~~P~LfVIrKQ~R~n~tev~PLa~YYII~g~VYqAPd~ysiv~sRml~a~  124 (208)
T KOG3169|consen   56 DLEEHLFSMVGIEYVLLHSREPILFVIRKQRRHNPTEVIPLADYYIINGNVYQAPDLYSIVQSRMLNAV  124 (208)
T ss_pred             chHHHHhhCcCeEEEEEecCCCeEEEEehhhcCCCccceeeeeEEEECceeeeCccHHHHHHHHHHHHH
Confidence            368999999999999999999999999999999999999999999999999999999999999999874

>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=99.97  E-value=4.1e-34  Score=197.97  Aligned_cols=71  Identities=52%  Similarity=0.820  Sum_probs=18.0

Q ss_pred             hhhhhhhcccCcceeEEEeecCCCceEEEEEeeecCCCCceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121           8 VLHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTG   78 (79)
Q Consensus         8 ~~~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~   78 (79)
                      ...++++|++|+|+||+|+|++||+|||||||+|++|++++|+|+|||+||+||||||+++|++|||++++
T Consensus        52 ~~~~~~~L~~m~GiEY~l~~~~eP~l~vI~Kq~r~~~~~~~~la~YYIi~g~IYqAPsl~~vl~sRl~~~~  122 (140)
T PF04934_consen   52 REAFEQQLRNMKGIEYVLAHVQEPGLFVIRKQRRQSPDEVTPLAYYYIINGNIYQAPSLYSVLSSRLLSAV  122 (140)
T ss_dssp             SHHHHHTTTS--------------------------------------------------SSSSSTTTHHH
T ss_pred             hHHHHHHHhhcCCeEEEEeccCCCCEEEEEEeeccCCCcceEeEEEEEECCEEEeCCCHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999999999999999999999999999999999999999864

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=99.90  E-value=3.8e-24  Score=157.01  Aligned_cols=69  Identities=29%  Similarity=0.416  Sum_probs=66.6

Q ss_pred             hhhhhcccCcceeEEEeecCCCceEEEEEeeecCCCCceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121          10 HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTG   78 (79)
Q Consensus        10 ~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~   78 (79)
                      +++++|+...|++||+.|.+||.|||||||+|+..++++|+.+|||+|.||||||+.|+++.+||++++
T Consensus        59 ql~~~l~~l~g~~~V~ss~rep~lwVIrKq~r~n~~e~~pl~~Y~i~g~NIY~aPt~y~i~~~Rm~~s~  127 (210)
T COG5097          59 QLSKLLSMLGGFYEVESSNREPTLWVIRKQYRHNDTEETPLMYYIIHGHNIYAAPTNYSIYRCRMGDSM  127 (210)
T ss_pred             HHHHHHHhccCEEEEEecCCCCcEEEEehhhhcCCcccccceEEEEecCceeeCcchhhhhhhhhhhhH
Confidence            578899999999999999999999999999999999999999999999999999999999999999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	79
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
4h61_A	175	Structure Of The Schizosaccharomyces Pombe Mediator		4e-07
4h63_F	183	Structure Of The Schizosaccharomyces Pombe Mediator		4e-07

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 8/77 (10%)
Query: 9   LHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVV 60
           + ++E ++ + G EY++  V+EP  +VIRKQ R +          +  P+ DYYII   +
Sbjct: 101 MQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANI 160
Query: 61  YQAPDLASVISSRLVGT 77
           YQ+P +  ++ SRL+ T
Sbjct: 161 YQSPTIFKIVQSRLMST 177

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 8/76 (10%)
Query: 10  HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVVY 61
            ++E +  + G EY++  V+EP  +VIRKQ R +          +  P+ DYYII   +Y
Sbjct: 102 QLEEELXKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIY 161
Query: 62  QAPDLASVISSRLVGT 77
           Q+P +  ++ SRL  T
Sbjct: 162 QSPTIFKIVQSRLXST 177

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 41/59 (69%)
Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVG 76
           +TG++++++H + P L+VI+KQ+R +  +  P+  Y++    +Y AP+  +++++R++ 
Sbjct: 68  LTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLN 126

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 41/59 (69%)
Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVG 76
           +TG++++++H + P L+VI+KQ+R +  +  P+  Y++    +Y AP+  +++++R++ 
Sbjct: 76  LTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLN 134

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	79
3rj1_G	295	Mediator of RNA polymerase II transcription subun;	2e-22

>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 = 86.4 bits (212), Expect = 2e-22
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 8/74 (10%)

Query: 12  QEPILNMTGLEYIVLHVQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVVYQA 63
           +E ++ + G EY++  V+EP  +VIRKQ R +          +  P+ DYYII   +YQ+
Sbjct: 104 EEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQS 163

Query: 64  PDLASVISSRLVGT 77
           P +  ++ SRL+ T
Sbjct: 164 PTIFKIVQSRLMST 177

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	79
4h61_A	175	Mediator of RNA polymerase II transcription subun;	100.0
4gwp_G	295	Mediator of RNA polymerase II transcription subun;	99.97

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

Probab=100.00  E-value=2.4e-34  Score=204.94  Aligned_cols=70  Identities=23%  Similarity=0.612  Sum_probs=67.2

Q ss_pred             hhhhhhcccCcceeEEEeecCCCceEEEEEeeecCCCCceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121           9 LHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVGTG   78 (79)
Q Consensus         9 ~~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~   78 (79)
                      ..++++|++|+|+||+|+|++||+|||||||+|++|++++|+|+||||||+||||||+++|++|||++++
T Consensus        59 ~~~e~~L~~m~GiEy~l~~~~~p~lfvI~Kq~R~~~~~~~~la~YyIi~g~IYqAP~l~~vl~sRl~s~~  128 (175)
T 4h61_A           59 GDLNSQLKRLTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLNAT  128 (175)
T ss_dssp             CCHHHHHHTCCEEEEEEEEEETTTEEEEEEEEECSSSCEEEEEEEEEETTEEEECCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCceEEEeecCCCceEEEEEEEEcCCCcceEEEEEEEECCEEccCCCHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999999999999999999999999999999999874

>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=99.97  E-value=4.1e-34  Score=216.55  Aligned_cols=70  Identities=37%  Similarity=0.773  Sum_probs=66.2

Q ss_pred             hhhhhhcccCcceeEEEeecCCCceEEEEEeeecCCC--------CceeeeEEEEecCeEeeCCChHHHHhhhhccCC
Q psy7121           9 LHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVVYQAPDLASVISSRLVGTG   78 (79)
Q Consensus         9 ~~~~~~L~~m~GiEy~l~~~~eP~lfVIrKq~R~sp~--------~~~~la~YYIi~g~VYQAP~l~~vl~sRl~s~~   78 (79)
                      ..++++|++|+||||+|+|++||+|||||||+|+||+        +++|||+||||||+||||||+++||+|||++++
T Consensus       101 ~~~e~~L~~m~GiEyvl~~~~eP~lwVIrKQ~R~s~~~~~~~~~~ev~pLa~YYIig~~IYqAPsl~~Vl~sRlls~~  178 (295)
T 4gwp_G          101 MQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSPTIFKIVQSRLMSTS  178 (295)
T ss_dssp             HHHHHHHHHHSCEEETTEEECSSEEEEEEETTEEEEEEEEECCCTTCCCEEEEEEEEETTEEECCCTTHHHHHHHHHH
T ss_pred             hhhHHHHhhCCCeEEEEeecCCCceEEEEeeeccCCcccccccCcceeEeEEEEEECCEEecCCCHHHHHHHHHHHHH
Confidence            3579999999999999999999999999999999874        899999999999999999999999999999874

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00