Citrus Sinensis ID: 032437

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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-
Protein Sequence
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL
Secondary Structure (PSIPRED)
ccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHcHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccHHEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccHHHHHccEEEcccccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mkqskdpfeaaleespgdspdeleietqpqtgtaagsataavTGELedefdnlesqapmsvsagpaakmtmsknkdeydeeddenvdvelgkfpsssdpaKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL
Flexible Loop (DISEMBL)
mkqskdpfeaaleespgdspdelEIETQPQTGTAAGSATAAVTGELEDEFDNLEsqapmsvsagpaakMTMSKNKDEYDEEDDENVDVELGkfpsssdpaKMAKMQAILNQFTEDQMNRYESfrrsalqksnmrrlllewl
Low Complexity Region (SEG)
MKQSKDPFEAALEESPGDSPDELEIETQPQtgtaagsataavtgELEDEFDNLESQAPMSVSAGPAAKMTMSknkdeydeeddenvdveLGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL
Disordered region (IsUnstruct)
*********************************************************************************************************************************************
Disordered Region (DISOPRED)
*****DP**************************************************************************************************QAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL
Disordered Region (DISEMBL)
***********************EIETQ***********AAVTGELEDEFDNLESQAP****************************DVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL
Disordered Region (DISPRO)
*****************************************************************************YDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL
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	141	2.2.26 [Sep-21-2011]
Q5RA91	211	Transcription initiation	yes	no	0.255	0.170	0.472	3e-05
Q5U1X0	211	Transcription initiation	yes	no	0.255	0.170	0.472	4e-05
Q15544	211	Transcription initiation	yes	no	0.283	0.189	0.45	4e-05
Q99JX1	211	Transcription initiation	yes	no	0.255	0.170	0.472	4e-05
P49906	196	Transcription initiation	yes	no	0.234	0.168	0.484	0.0008

>sp|Q5RA91|TAF11_PONAB Transcription initiation factor TFIID subunit 11 OS=Pongo abelii GN=TAF11 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 29/36 (80%)

Query: 102 MAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
           + KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct: 103 IQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).
Pongo abelii (taxid: 9601)

>sp|Q5U1X0|TAF11_RAT Transcription initiation factor TFIID subunit 11 OS=Rattus norvegicus GN=Taf11 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 29/36 (80%)

Query: 102 MAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
           + KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct: 103 IQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).

Rattus norvegicus (taxid: 10116)

>sp|Q15544|TAF11_HUMAN Transcription initiation factor TFIID subunit 11 OS=Homo sapiens GN=TAF11 PE=1 SV=1

 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query: 98  DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
           D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct: 99  DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).

Homo sapiens (taxid: 9606)

>sp|Q99JX1|TAF11_MOUSE Transcription initiation factor TFIID subunit 11 OS=Mus musculus GN=Taf11 PE=2 SV=1

 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 29/36 (80%)

Query: 102 MAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
           + KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct: 103 IQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).

Mus musculus (taxid: 10090)

>sp|P49906|TAF11_DROME Transcription initiation factor TFIID subunit 11 OS=Drosophila melanogaster GN=Taf11 PE=1 SV=1

 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 27/33 (81%)

Query: 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
           MQ +++ FTE+Q++RYE +RRSA  K+ ++RL+
Sbjct: 89  MQVLVSNFTEEQLDRYEMYRRSAFPKAAVKRLM 121

TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.

Drosophila melanogaster (taxid: 7227)

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	141
388513279	203	unknown [Medicago truncatula]	0.893	0.620	0.510	3e-26
388491516	203	unknown [Medicago truncatula]	0.893	0.620	0.510	3e-26
225462089	198	PREDICTED: transcription initiation fact	0.858	0.611	0.545	2e-25
217072422	203	unknown [Medicago truncatula]	0.893	0.620	0.503	6e-25
388503812	205	unknown [Lotus japonicus]	0.936	0.643	0.481	1e-21
224072412	186	predicted protein [Populus trichocarpa]	0.730	0.553	0.485	3e-19
224057892	222	predicted protein [Populus trichocarpa]	0.943	0.599	0.477	4e-19
255583916	205	Transcription initiation factor TFIID su	0.836	0.575	0.548	5e-19
351734450	155	uncharacterized protein LOC100305481 [Gl	0.581	0.529	0.445	1e-18
297804116	211	predicted protein [Arabidopsis lyrata su	0.602	0.402	0.616	8e-18

>gi|388513279|gb|AFK44701.1| unknown [Medicago truncatula]

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 72/141 (51%), Positives = 99/141 (70%), Gaps = 15/141 (10%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGT----AAGSATAAVTGELEDEFDNLESQ 56
           MKQSKDPFEAA EESP +SP  +E E  P   T    +  S+    T   E+E +++++ 
Sbjct: 1   MKQSKDPFEAAFEESPPESP--IETEPDPDASTENPNSTNSSLPQSTLTHEEEHNHIKT- 57

Query: 57  APMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQ 116
                   P +  T++K+KDE D+E+++N+DVEL KFP++ DP KMAKMQAIL+QFTE+Q
Sbjct: 58  --------PNSNNTITKHKDEEDDEEEDNMDVELAKFPTAGDPHKMAKMQAILSQFTEEQ 109

Query: 117 MNRYESFRRSALQKSNMRRLL 137
           M+RYESFRR+  QK+NM+RLL
Sbjct: 110 MSRYESFRRAGFQKANMKRLL 130

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388491516|gb|AFK33824.1| unknown [Medicago truncatula]

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 72/141 (51%), Positives = 99/141 (70%), Gaps = 15/141 (10%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGT----AAGSATAAVTGELEDEFDNLESQ 56
           MKQSKDPFEAA EESP +SP  +E E  P   T    +  S+    T   E+E +++++ 
Sbjct: 1   MKQSKDPFEAAFEESPPESP--IETEPDPDASTENPNSTNSSLPQSTLAHEEEHNHIKT- 57

Query: 57  APMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQ 116
                   P +  T++K+KDE D+E+++N+DVEL KFP++ DP KMAKMQAIL+QFTE+Q
Sbjct: 58  --------PNSNNTITKHKDEEDDEEEDNMDVELAKFPTAGDPHKMAKMQAILSQFTEEQ 109

Query: 117 MNRYESFRRSALQKSNMRRLL 137
           M+RYESFRR+  QK+NM+RLL
Sbjct: 110 MSRYESFRRAGFQKANMKRLL 130

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225462089|ref|XP_002277017.1| PREDICTED: transcription initiation factor TFIID subunit 11 [Vitis vinifera] gi|296086768|emb|CBI32917.3| unnamed protein product [Vitis vinifera]

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/143 (54%), Positives = 99/143 (69%), Gaps = 22/143 (15%)

Query: 1   MKQSKDPFEAALEES-PGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFD-NLESQAP 58
           MKQSKDPFE A EES P DSP E EI                V G++EDE D N+     
Sbjct: 1   MKQSKDPFEVAFEESSPPDSPVE-EI----------------VGGQIEDEDDANVNVHPT 43

Query: 59  MSVSAGPAAKMTM---SKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTED 115
            + SA P++  T+   +K+KDE +EE++EN+DVELGK P+S DP KMAKMQAIL+QFTE+
Sbjct: 44  STPSAAPSSGTTVPPTAKSKDEDEEEEEENMDVELGKLPTSGDPHKMAKMQAILSQFTEE 103

Query: 116 QMNRYESFRRSALQKSNMRRLLL 138
           QM+RYESFRRS  QK+NM++LL+
Sbjct: 104 QMSRYESFRRSGFQKANMKKLLV 126

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217072422|gb|ACJ84571.1| unknown [Medicago truncatula]

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 71/141 (50%), Positives = 98/141 (69%), Gaps = 15/141 (10%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGT----AAGSATAAVTGELEDEFDNLESQ 56
           MKQSKDPFEAA EES  +SP  +E E  P   T    +  S+    T   E+E +++++ 
Sbjct: 1   MKQSKDPFEAAFEESLPESP--IETEPDPDASTENPNSTNSSLPQSTLTHEEEHNHIKT- 57

Query: 57  APMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQ 116
                   P +  T++K+KDE D+E+++N+DVEL KFP++ DP KMAKMQAIL+QFTE+Q
Sbjct: 58  --------PNSNNTITKHKDEEDDEEEDNMDVELAKFPTAGDPHKMAKMQAILSQFTEEQ 109

Query: 117 MNRYESFRRSALQKSNMRRLL 137
           M+RYESFRR+  QK+NM+RLL
Sbjct: 110 MSRYESFRRAGFQKANMKRLL 130

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388503812|gb|AFK39972.1| unknown [Lotus japonicus]

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 66/137 (48%), Positives = 89/137 (64%), Gaps = 5/137 (3%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMS 60
           MKQSKDPFEAA  ESP +SP E+E E   +    A S+  A   + +++   L      +
Sbjct: 1   MKQSKDPFEAAFVESPPESPVEIEAEPDGEAQNPASSSGVAQVTQAQEDGKKLSKTGTGT 60

Query: 61  VSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRY 120
                +      KNKD+ +EE+++N+DVEL K   + DP KMAKMQAIL+QFTE+QM+RY
Sbjct: 61  -----SGGGGGGKNKDDEEEEEEDNMDVELTKLQPTGDPQKMAKMQAILSQFTEEQMSRY 115

Query: 121 ESFRRSALQKSNMRRLL 137
           ESFRR+  QK+NM+RLL
Sbjct: 116 ESFRRAGFQKANMKRLL 132

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224072412|ref|XP_002303723.1| predicted protein [Populus trichocarpa] gi|222841155|gb|EEE78702.1| predicted protein [Populus trichocarpa]

 Score = 99.8 bits (247), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 67/138 (48%), Positives = 80/138 (57%), Gaps = 35/138 (25%)

Query: 1   MKQSKDPFEAAL---EESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQA 57
           MK SKDPFEAA    EESP +SP                          +D++D   S A
Sbjct: 1   MKHSKDPFEAAYVEQEESPPESPIA------------------------QDDYDTQTSNA 36

Query: 58  PMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQM 117
                AG   K    KNK + +EE D N+DVEL K  S++DP KMA MQAIL QFTE+QM
Sbjct: 37  ----YAGLCKK---GKNKQDEEEEQD-NMDVELWKLASTADPDKMANMQAILAQFTEEQM 88

Query: 118 NRYESFRRSALQKSNMRR 135
           +RYESFRRSALQK+NM+R
Sbjct: 89  SRYESFRRSALQKTNMKR 106

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224057892|ref|XP_002299376.1| predicted protein [Populus trichocarpa] gi|222846634|gb|EEE84181.1| predicted protein [Populus trichocarpa]

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 74/155 (47%), Positives = 93/155 (60%), Gaps = 22/155 (14%)

Query: 1   MKQSKDPFEAAL---EESPGDSP---DELEIETQPQTGTAAGSATAAVTGE--------- 45
           MKQSKDPFEAA    EESP +SP   D+ + +       A  S  A V  +         
Sbjct: 1   MKQSKDPFEAAYVEQEESPPESPVAQDDYDTQASNAAAAADDSQGAVVGQDDDDLGGGGR 60

Query: 46  --LEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMA 103
                  D+  +  PM  SA   AK     NKD+ +EE+++N+DVEL K  S++DP KMA
Sbjct: 61  NDFAHSSDHPSASRPMLGSARSKAK-----NKDDDEEEEEDNMDVELSKLASTADPDKMA 115

Query: 104 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLL 138
           KMQ IL QFTE QM+RYESFRRSALQK+NM+RLL+
Sbjct: 116 KMQTILAQFTEGQMSRYESFRRSALQKTNMKRLLV 150

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583916|ref|XP_002532706.1| Transcription initiation factor TFIID subunit, putative [Ricinus communis] gi|223527552|gb|EEF29673.1| Transcription initiation factor TFIID subunit, putative [Ricinus communis]

 Score = 99.0 bits (245), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/144 (54%), Positives = 98/144 (68%), Gaps = 26/144 (18%)

Query: 1   MKQSKDPFEAALEE---SPGDSP---DELEIETQPQTGTAAGSATAAVTGELEDEFDNLE 54
           MKQSKDPFEAA EE   +P +SP   DEL +++Q    T A    AAV  E +D      
Sbjct: 10  MKQSKDPFEAAYEEQEETPPESPLGADEL-LDSQ-TAATTAQDPDAAVLQEDDD------ 61

Query: 55  SQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTE 114
               +  S G         +++E+DEE++ENVDVEL KFPS++DP KMAKMQAIL+QFTE
Sbjct: 62  ----IGSSGG--------GSREEFDEEEEENVDVELAKFPSTADPDKMAKMQAILSQFTE 109

Query: 115 DQMNRYESFRRSALQKSNMRRLLL 138
           +QM RYESFRRSALQK+NMRRLL+
Sbjct: 110 NQMTRYESFRRSALQKANMRRLLV 133

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351734450|ref|NP_001236012.1| uncharacterized protein LOC100305481 [Glycine max] gi|255625637|gb|ACU13163.1| unknown [Glycine max]

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/137 (44%), Positives = 72/137 (52%), Gaps = 55/137 (40%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMS 60
           MKQSKDPFEAA EESP            P++ TA                          
Sbjct: 1   MKQSKDPFEAAFEESP------------PESPTAT------------------------- 23

Query: 61  VSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRY 120
                           E +EED  N+DVEL K PS+ DP KMAKMQAIL+QFTE+QM+RY
Sbjct: 24  ----------------ETEEED--NMDVELAKLPSTGDPHKMAKMQAILSQFTEEQMSRY 65

Query: 121 ESFRRSALQKSNMRRLL 137
           ESFRR+  QK+NM+RLL
Sbjct: 66  ESFRRAGFQKANMKRLL 82

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804116|ref|XP_002869942.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297315778|gb|EFH46201.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score = 95.1 bits (235), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 53/86 (61%), Positives = 71/86 (82%), Gaps = 1/86 (1%)

Query: 53  LESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQF 112
           ++ + PM   A  +  +T +KNKDE DEE++EN++VEL K+P+SSDPAKMAKMQ IL+QF
Sbjct: 55  VDVRRPMK-KAKTSVVVTEAKNKDEDDEEEEENMEVELTKYPTSSDPAKMAKMQTILSQF 113

Query: 113 TEDQMNRYESFRRSALQKSNMRRLLL 138
           TEDQM+RYESFRRSALQ+  M++LL+
Sbjct: 114 TEDQMSRYESFRRSALQRPQMKKLLI 139

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	141
TAIR|locus:2120422	210	TAF11 "TBP-associated factor 1	0.347	0.233	0.755	6e-22
TAIR|locus:2198671	204	TAF11b "TBP-associated factor	0.304	0.210	0.590	9.2e-15
UNIPROTKB|Q15544	211	TAF11 "Transcription initiatio	0.283	0.189	0.45	2.7e-07
RGD|1305626	211	Taf11 "TAF11 RNA polymerase II	0.283	0.189	0.45	2.7e-07
ZFIN|ZDB-GENE-040718-283	206	taf11 "TAF11 RNA polymerase II	0.283	0.194	0.45	1.4e-05
RGD|1562272	207	RGD1562272 "similar to TAF11 R	0.283	0.193	0.45	1.8e-05
UNIPROTKB|Q3ZBP7	210	TAF11 "TAF11 RNA polymerase II	0.283	0.190	0.45	1.9e-05
UNIPROTKB|E2RFN3	211	TAF11 "Uncharacterized protein	0.283	0.189	0.45	1.9e-05
UNIPROTKB|F1RZ14	211	TAF11 "Uncharacterized protein	0.283	0.189	0.45	1.9e-05
MGI|MGI:1916026	211	Taf11 "TAF11 RNA polymerase II	0.283	0.189	0.45	1.9e-05

TAIR|locus:2120422 TAF11 "TBP-associated factor 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 6.0e-22, Sum P(2) = 6.0e-22
 Identities = 37/49 (75%), Positives = 45/49 (91%)

Query:    90 LGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLL 138
             L K+P+SSDPAKMAKMQ IL+QFTEDQM+RYESFRRSALQ+  M++LL+
Sbjct:    90 LTKYPTSSDPAKMAKMQTILSQFTEDQMSRYESFRRSALQRPQMKKLLI 138

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

GO:0009086 "methionine biosynthetic process" evidence=RCA

TAIR|locus:2198671 TAF11b "TBP-associated factor 11B" [Arabidopsis thaliana (taxid:3702)]

 Score = 129 (50.5 bits), Expect = 9.2e-15, Sum P(2) = 9.2e-15
 Identities = 26/44 (59%), Positives = 35/44 (79%)

Query:    95 SSSDPAKMA-KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             + +DP   A KMQ IL+QFTE+QM+RYESFRRS  +KS+M +L+
Sbjct:    88 TGADPVTRANKMQKILSQFTEEQMSRYESFRRSGFKKSDMEKLV 131

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

UNIPROTKB|Q15544 TAF11 "Transcription initiation factor TFIID subunit 11" [Homo sapiens (taxid:9606)]

 Score = 103 (41.3 bits), Expect = 2.7e-07, Sum P(2) = 2.7e-07
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0042809 "vitamin D receptor binding" evidence=IPI

GO:0046966 "thyroid hormone receptor binding" evidence=IPI

GO:0043923 "positive regulation by host of viral transcription" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=IDA

GO:0005669 "transcription factor TFIID complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

GO:0047485 "protein N-terminus binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

RGD|1305626 Taf11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]

 Score = 103 (41.3 bits), Expect = 2.7e-07, Sum P(2) = 2.7e-07
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

GO:0003674 "molecular_function" evidence=ND

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

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO

GO:0005669 "transcription factor TFIID complex" evidence=IEA;ISO

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

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

GO:0008150 "biological_process" evidence=ND

GO:0042809 "vitamin D receptor binding" evidence=IEA;ISO

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA;ISO

GO:0046966 "thyroid hormone receptor binding" evidence=IEA;ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0047485 "protein N-terminus binding" evidence=IEA;ISO

ZFIN|ZDB-GENE-040718-283 taf11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Danio rerio (taxid:7955)]

 Score = 104 (41.7 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    94 DEDEIQKMQVLVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 133

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

RGD|1562272 RGD1562272 "similar to TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]

 Score = 103 (41.3 bits), Expect = 1.8e-05, P = 1.8e-05
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    95 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 134

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q3ZBP7 TAF11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" [Bos taurus (taxid:9913)]

 Score = 103 (41.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    98 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 137

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA

GO:0042809 "vitamin D receptor binding" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

UNIPROTKB|E2RFN3 TAF11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 103 (41.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA

GO:0042809 "vitamin D receptor binding" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

UNIPROTKB|F1RZ14 TAF11 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 103 (41.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA

GO:0042809 "vitamin D receptor binding" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

MGI|MGI:1916026 Taf11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)]

 Score = 103 (41.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLI 138

GO:0003677 "DNA binding" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO

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

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

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

GO:0042809 "vitamin D receptor binding" evidence=ISO

GO:0043923 "positive regulation by host of viral transcription" evidence=ISO

GO:0046966 "thyroid hormone receptor binding" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0047485 "protein N-terminus binding" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	141
pfam04719	89	pfam04719, TAFII28, hTAFII28-like protein conserve	8e-13
cd08048	85	cd08048, TAF11, TATA Binding Protein (TBP) Associa	3e-09
COG5251	199	COG5251, TAF40, Transcription initiation factor TF	0.003

>gnl|CDD|218227 pfam04719, TAFII28, hTAFII28-like protein conserved region

 Score = 59.7 bits (145), Expect = 8e-13
 Identities = 17/33 (51%), Positives = 29/33 (87%)

Query: 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137
           MQ +++ FTE+Q+NRYE FRRS+L+K+ +++L+
Sbjct: 1   MQVLVSNFTEEQLNRYEVFRRSSLKKAQVKKLI 33

The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C-terminal of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3. Length = 89

>gnl|CDD|173967 cd08048, TAF11, TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

 Score = 50.3 bits (121), Expect = 3e-09
 Identities = 15/25 (60%), Positives = 21/25 (84%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRL 136
           F+E+QMNRYE FRRS+  K+ ++RL
Sbjct: 1   FSEEQMNRYEMFRRSSFPKAAIKRL 25

The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone. TAF11 also directly interacts with TFIIA, acting as a bridging factor that stabilizes the TFIIA-TBP-DNA complex. Each TAF, with the help of a specific activator, is required only for the expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. The TAF11 domain is structurally analogous to histone H3 and interacts with TAF13, making a novel histone-like heterodimer. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex. Length = 85

>gnl|CDD|227576 COG5251, TAF40, Transcription initiation factor TFIID, subunit TAF11 [Transcription]

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 13/37 (35%), Positives = 25/37 (67%)

Query: 100 AKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRL 136
           A+  + + ++    E+Q NRYE FRR++L K+ +++L
Sbjct: 88  AQDERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKL 124

Length = 199

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	141
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	99.61
KOG3219	195	consensus Transcription initiation factor TFIID, s	99.6
COG5251	199	TAF40 Transcription initiation factor TFIID, subun	99.21
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	99.19

>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex

Probab=99.61  E-value=2.1e-16  Score=114.66  Aligned_cols=37  Identities=43%  Similarity=0.843  Sum_probs=23.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032437          105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL  141 (141)
Q Consensus       105 m~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL  141 (141)
                      |++||++||+||++|||+||||+|+|++||||||+++
T Consensus         1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~   37 (90)
T PF04719_consen    1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVL   37 (90)
T ss_dssp             ---------HHHHHHHHHHHH----HHHHHHHHHHHH
T ss_pred             ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHc
Confidence            6899999999999999999999999999999999874

The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.

>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]

Probab=99.60  E-value=1.1e-15  Score=124.35  Aligned_cols=48  Identities=35%  Similarity=0.681  Sum_probs=43.2

Q ss_pred             CCCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032437           94 PSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL  141 (141)
Q Consensus        94 ~sT~dEee~~km~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL  141 (141)
                      ..+.++++..+|+.||++||+|||+|||+||||+|||++|||||++|.
T Consensus        79 ~~~~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~it  126 (195)
T KOG3219|consen   79 KPTVDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSIT  126 (195)
T ss_pred             CCCcCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence            334467788899999999999999999999999999999999999874

>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]

Probab=99.21  E-value=1.4e-11  Score=100.35  Aligned_cols=39  Identities=31%  Similarity=0.621  Sum_probs=36.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032437          103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL  141 (141)
Q Consensus       103 ~km~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL  141 (141)
                      .+++.|+.+||+|||+|||+|||++|||.+||||+++||
T Consensus        91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~  129 (199)
T COG5251          91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVA  129 (199)
T ss_pred             HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHh
Confidence            677889999999999999999999999999999999885

>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=99.19  E-value=1.6e-11  Score=88.01  Aligned_cols=30  Identities=50%  Similarity=0.857  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032437          112 FTEDQMNRYESFRRSALQKSNMRRLLLEWL  141 (141)
Q Consensus       112 FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL  141 (141)
                      ||+|||+|||+||||+|+|+.||||||+++
T Consensus         1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~   30 (85)
T cd08048           1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVT   30 (85)
T ss_pred             CCHHHHHHHHHHHHhhccHHHHHHHHHHHc
Confidence            899999999999999999999999999875

The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	141
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	7e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05

>1bh9_B TAFII28; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_B* Length = 89

 Score = 46.3 bits (110), Expect = 7e-08
 Identities = 14/26 (53%), Positives = 22/26 (84%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLL 137
           F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLI 26

>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 = 41.4 bits (96), Expect = 4e-05
 Identities = 20/139 (14%), Positives = 47/139 (33%), Gaps = 16/139 (11%)

Query: 2   KQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSV 61
            + K      L+  P D P E+ + T P+      S  A    +    +DN +      +
Sbjct: 301 DEVKSLLLKYLDCRPQDLPREV-LTTNPR----RLSIIAESIRDGLATWDNWKHVNCDKL 355

Query: 62  SAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSD-PAKMAKM--QAILNQFTEDQMN 118
           +        +  + +  +  +   +   L  FP S+  P  +  +    ++       +N
Sbjct: 356 T------TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVN 409

Query: 119 RYESFRRSALQKSNMRRLL 137
             +  + S ++K      +
Sbjct: 410 --KLHKYSLVEKQPKESTI 426

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	141
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	99.24

>1bh9_B TAFII28; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_B*

Probab=99.24  E-value=3e-12  Score=91.43  Aligned_cols=30  Identities=47%  Similarity=0.843  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032437          112 FTEDQMNRYESFRRSALQKSNMRRLLLEWL  141 (141)
Q Consensus       112 FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL  141 (141)
                      ||+|||+|||+||||+|+|+.||||||+++
T Consensus         1 ft~eQ~~Rye~~Rrs~f~k~~vKrl~~~~~   30 (89)
T 1bh9_B            1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSIT   30 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHc
Confidence            899999999999999999999999999874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	141
d1bh9b_	89	a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [Tax	4e-09

>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)28
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (116), Expect = 4e-09
 Identities = 14/26 (53%), Positives = 22/26 (84%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLL 137
           F+E+Q+NRYE +RRSA  K+ ++RL+
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLI 26

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	141
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	99.4

>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)28
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=5.3e-14  Score=99.62  Aligned_cols=30  Identities=47%  Similarity=0.843  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032437          112 FTEDQMNRYESFRRSALQKSNMRRLLLEWL  141 (141)
Q Consensus       112 FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL  141 (141)
                      ||+|||+|||+||||+|+|++||||||+|+
T Consensus         1 Fs~eQ~~RyE~fRRs~~~K~~vkrl~~~~~   30 (89)
T d1bh9b_           1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSIT   30 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCCHHHHHHHHHHHc
Confidence            899999999999999999999999999874