Psyllid ID: psy7895

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------11
Protein Sequence
MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSDDRK
Secondary Structure (PSIPRED)
ccHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcccccEEccccEEEEcccEEEEEEEccEEEEEccEEEEEccEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcccEEEEcccccEEEEcccEEEEEEEcEEEEEccEEEEEcEEEEEEEccccccccc
Coil and Loop (DISEMBL)
MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKsingalpskvksrltfksgklntyrfcDNVWTFVLTDVEFREVAEIARVNKLKIVacdgkssddrk
Flexible Loop (DISEMBL)
MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSIngalpskvksrltfksgklntyrfcDNVWTFVLTDVEFREVaeiarvnklkivacdgkssddrk
Low Complexity Region (SEG)
MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSDDRK
Disordered region (IsUnstruct)
*****YRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVAC*********
Disordered Region (DISOPRED)
MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVA**********
Disordered Region (DISEMBL)
MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVAC*********
Disordered Region (DISPRO)
*SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGK******
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSDDRK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	108	2.2.26 [Sep-21-2011]
P52656	106	Transcription initiation	yes	N/A	0.972	0.990	0.809	2e-45
B7Q1Q9	118	Transcription initiation	N/A	N/A	0.944	0.864	0.794	2e-43
Q9IA78	111	Transcription initiation	N/A	N/A	0.944	0.918	0.737	4e-40
P52657	109	Transcription initiation	yes	N/A	0.953	0.944	0.721	7e-40
O08950	109	Transcription initiation	yes	N/A	0.953	0.944	0.721	7e-40
Q80ZM7	109	Transcription initiation	yes	N/A	0.953	0.944	0.721	7e-40
Q90YG6	108	Transcription initiation	N/A	N/A	0.953	0.953	0.721	1e-39
Q0DLD3	106	Transcription initiation	yes	N/A	0.925	0.943	0.524	4e-27
A2XZI2	106	Transcription initiation	N/A	N/A	0.925	0.943	0.524	4e-27
Q39236	106	Transcription initiation	yes	N/A	0.925	0.943	0.524	9e-27

>sp|P52656|T2AG_DROME Transcription initiation factor IIA subunit 2 OS=Drosophila melanogaster GN=TfIIA-S PE=1 SV=1

 Score =  181 bits (458), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 85/105 (80%), Positives = 94/105 (89%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA KVLLQFDKSIN AL  +VK+R+TFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPGLAFKVLLQFDKSINNALNQRVKARVTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWT +L DVEFREV EI +V+K+KIVACDGKS +
Sbjct: 61  GKLNTYRFCDNVWTLMLNDVEFREVHEIVKVDKVKIVACDGKSGE 105

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.
Drosophila melanogaster (taxid: 7227)

>sp|B7Q1Q9|T2AG_IXOSC Transcription initiation factor IIA subunit 2 OS=Ixodes scapularis GN=IscW_ISCW010050 PE=3 SV=1

 Score =  174 bits (440), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 81/102 (79%), Positives = 92/102 (90%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQ G ITP LA+KVLLQFDK+IN AL ++VK+RLTFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQCGQITPHLALKVLLQFDKAINNALANRVKTRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGK 102
           G L+TYRFCDNVWTFVL DVEFREV E+ + +K+KIVACDGK
Sbjct: 61  GHLSTYRFCDNVWTFVLKDVEFREVQELVKADKVKIVACDGK 102

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with Tbp mediates transcriptional activity.

Ixodes scapularis (taxid: 6945)

>sp|Q9IA78|T2AG_PAROL Transcription initiation factor IIA subunit 2 OS=Paralichthys olivaceus GN=gtf2a2 PE=3 SV=1

 Score =  163 bits (412), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 76/103 (73%), Positives = 91/103 (88%), Gaps = 1/103 (0%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL S+V++R+ F+ 
Sbjct: 1   MAYQLYRNTTLGNSLQESLDELIQTQQITPQLALQVLLQFDKAINTALASRVRNRVNFR- 59

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKS 103
           G LNTYRFCDNVWTFVL DVEFREV ++ +V+K+KIVACDGKS
Sbjct: 60  GSLNTYRFCDNVWTFVLNDVEFREVTDLVKVDKVKIVACDGKS 102

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Paralichthys olivaceus (taxid: 8255)

>sp|P52657|T2AG_HUMAN Transcription initiation factor IIA subunit 2 OS=Homo sapiens GN=GTF2A2 PE=1 SV=1

 Score =  162 bits (409), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 75/104 (72%), Positives = 91/104 (87%), Gaps = 1/104 (0%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct: 1   MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFR- 59

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
           G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct: 60  GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Homo sapiens (taxid: 9606)

>sp|O08950|T2AG_RAT Transcription initiation factor IIA subunit 2 OS=Rattus norvegicus GN=Gtf2a2 PE=2 SV=1

 Score =  162 bits (409), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 75/104 (72%), Positives = 91/104 (87%), Gaps = 1/104 (0%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct: 1   MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFR- 59

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
           G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct: 60  GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Rattus norvegicus (taxid: 10116)

>sp|Q80ZM7|T2AG_MOUSE Transcription initiation factor IIA subunit 2 OS=Mus musculus GN=Gtf2a2 PE=2 SV=2

 Score =  162 bits (409), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 75/104 (72%), Positives = 91/104 (87%), Gaps = 1/104 (0%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct: 1   MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFR- 59

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
           G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct: 60  GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Mus musculus (taxid: 10090)

>sp|Q90YG6|T2AG_ONCMY Transcription initiation factor IIA subunit 2 OS=Oncorhynchus mykiss GN=gtf2a2 PE=3 SV=1

 Score =  161 bits (407), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 75/104 (72%), Positives = 92/104 (88%), Gaps = 1/104 (0%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL ++V++R+ FK 
Sbjct: 1   MAYQLYRNTTLGNSLQESLDELIQTQQITPQLALQVLLQFDKAINTALANRVRNRVNFK- 59

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
           G LNTYRFCDNVWTFVL DVEFREV ++ +V+K+KIVACDGK++
Sbjct: 60  GSLNTYRFCDNVWTFVLNDVEFREVTDLVKVDKVKIVACDGKNT 103

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Oncorhynchus mykiss (taxid: 8022)

>sp|Q0DLD3|T2AG_ORYSJ Transcription initiation factor IIA subunit 2 OS=Oryza sativa subsp. japonica GN=TFIIAy PE=3 SV=1

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 53/101 (52%), Positives = 78/101 (77%), Gaps = 1/101 (0%)

Query: 2   SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSG 61
           +++LYR +T+G  L E+LDE++  GT++P LA++VL+QFDKS+  AL ++VKS+++ K G
Sbjct: 3   TFELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEALENQVKSKVSIK-G 61

Query: 62  KLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGK 102
            L+TYRFCDNVWTF+LT+  F+      +V K+KIVACD K
Sbjct: 62  HLHTYRFCDNVWTFILTEASFKNEETTEQVGKVKIVACDSK 102

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity (By similarity). Protein involved in the resistance to X.oryzae.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2XZI2|T2AG_ORYSI Transcription initiation factor IIA subunit 2 OS=Oryza sativa subsp. indica GN=TFIIAy PE=3 SV=2

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 53/101 (52%), Positives = 78/101 (77%), Gaps = 1/101 (0%)

Query: 2   SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSG 61
           +++LYR +T+G  L E+LDE++  GT++P LA++VL+QFDKS+  AL ++VKS+++ K G
Sbjct: 3   TFELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEALENQVKSKVSIK-G 61

Query: 62  KLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGK 102
            L+TYRFCDNVWTF+LT+  F+      +V K+KIVACD K
Sbjct: 62  HLHTYRFCDNVWTFILTEASFKNEETTEQVGKVKIVACDSK 102

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity (By similarity). Protein involved in the resistance to X.oryzae.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q39236|T2AG_ARATH Transcription initiation factor IIA subunit 2 OS=Arabidopsis thaliana GN=TFIIA-S PE=2 SV=2

 Score =  118 bits (296), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 53/101 (52%), Positives = 78/101 (77%), Gaps = 1/101 (0%)

Query: 2   SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSG 61
           +++LYR +T+G  L E+LDE++Q GT++P LA++VL+QFDKS+  AL S+VK++++ K G
Sbjct: 3   TFELYRRSTIGMCLTETLDEMVQSGTLSPELAIQVLVQFDKSMTEALESQVKTKVSIK-G 61

Query: 62  KLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGK 102
            L+TYRFCDNVWTF+L D  F+       V+++KIVACD K
Sbjct: 62  HLHTYRFCDNVWTFILQDAMFKSDDRQENVSRVKIVACDSK 102

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	108
114052188	108	transcription initiation factor IIA gamm	1.0	1.0	0.824	5e-47
357617974	106	transcription initiation factor IIA gamm	0.953	0.971	0.854	4e-46
383847845	112	PREDICTED: transcription initiation fact	0.972	0.937	0.828	1e-45
66504876	112	PREDICTED: transcription initiation fact	0.972	0.937	0.828	3e-45
332022639	112	Transcription initiation factor IIA subu	0.972	0.937	0.828	3e-45
380014682	112	PREDICTED: transcription initiation fact	0.972	0.937	0.828	3e-45
307190250	112	Transcription initiation factor IIA subu	0.972	0.937	0.828	3e-45
307208051	170	Transcription initiation factor IIA subu	0.953	0.605	0.844	4e-45
340709907	112	PREDICTED: transcription initiation fact	0.972	0.937	0.828	6e-45
195054706	107	GH10565 [Drosophila grimshawi] gi|193896	0.972	0.981	0.819	1e-44

>gi|114052188|ref|NP_001040463.1| transcription initiation factor IIA gamma chain [Bombyx mori] gi|95102994|gb|ABF51438.1| transcription initiation factor IIA gamma chain [Bombyx mori]

 Score =  191 bits (485), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 89/108 (82%), Positives = 100/108 (92%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTT+GNTLQESLDELIQYG ITP LA+KVLLQFDKSIN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTIGNTLQESLDELIQYGQITPALAVKVLLQFDKSINQALSNRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSDDRK 108
           GKLNTYRFCDNVWTF+L DVEFREV E+A+V K+KIVACDGK+ DDR+
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQELAKVEKVKIVACDGKNVDDRR 108

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357617974|gb|EHJ71090.1| transcription initiation factor IIA gamma chain [Danaus plexippus]

 Score =  188 bits (477), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 88/103 (85%), Positives = 98/103 (95%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTT+GNTLQESLDELIQYG ITPTLA+KVLLQFDKSIN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTIGNTLQESLDELIQYGQITPTLAVKVLLQFDKSINTALSNRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKS 103
           GKLNTYRFCDNVWTF+L DVEFREV E+A+V+K+KIVACDGKS
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEVAKVDKVKIVACDGKS 103

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847845|ref|XP_003699563.1| PREDICTED: transcription initiation factor IIA subunit 2-like [Megachile rotundata]

 Score =  186 bits (473), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 97/105 (92%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA+KVLLQFDK+IN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPQLALKVLLQFDKAINQALATRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWTF+L DVEFREV E+A V+K+KIVACDGK+ D
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEVAMVDKVKIVACDGKTLD 105

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66504876|ref|XP_623063.1| PREDICTED: transcription initiation factor IIA subunit 2 [Apis mellifera]

 Score =  185 bits (470), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 97/105 (92%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA+KVLLQFDK+IN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPQLAIKVLLQFDKAINQALATRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWTF+L DVEFREV E+A V+K+KIVACDGK+ D
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEVAIVDKVKIVACDGKTLD 105

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022639|gb|EGI62927.1| Transcription initiation factor IIA subunit 2 [Acromyrmex echinatior]

 Score =  185 bits (470), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 97/105 (92%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA+KVLLQFDK+IN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPQLAIKVLLQFDKAINQALATRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWTF+L DVEFREV E+A V+K+KIVACDGK+ D
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEVAIVDKVKIVACDGKTLD 105

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380014682|ref|XP_003691351.1| PREDICTED: transcription initiation factor IIA subunit 2-like [Apis florea]

 Score =  185 bits (469), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 97/105 (92%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA+KVLLQFDK+IN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPQLAIKVLLQFDKAINQALATRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWTF+L DVEFREV E+A V+K+KIVACDGK+ D
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEVAIVDKVKIVACDGKTLD 105

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307190250|gb|EFN74357.1| Transcription initiation factor IIA subunit 2 [Camponotus floridanus]

 Score =  185 bits (469), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 97/105 (92%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA+KVLLQFDK+IN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPQLAIKVLLQFDKAINQALATRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWTF+L DVEFREV E+A V+K+KIVACDGK+ D
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEVAIVDKVKIVACDGKTLD 105

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307208051|gb|EFN85582.1| Transcription initiation factor IIA subunit 2 [Harpegnathos saltator]

 Score =  184 bits (468), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 87/103 (84%), Positives = 95/103 (92%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA+KVLLQFDK IN AL ++VKSRLTFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPQLAIKVLLQFDKVINQALATRVKSRLTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKS 103
           GKLNTYRFCDNVWTF+L DVEFREV E+A V+K+KIVACDGKS
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEVAMVDKVKIVACDGKS 103

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340709907|ref|XP_003393541.1| PREDICTED: transcription initiation factor IIA subunit 2-like [Bombus terrestris] gi|350398694|ref|XP_003485276.1| PREDICTED: transcription initiation factor IIA subunit 2-like [Bombus impatiens]

 Score =  184 bits (467), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 96/105 (91%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITP LA+KVLLQFDK+IN AL ++VKSRL FK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPQLAIKVLLQFDKAINQALAARVKSRLIFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWTF+L DVEFREV EIA V+K+KIVACDGK+ D
Sbjct: 61  GKLNTYRFCDNVWTFMLNDVEFREVQEIAIVDKVKIVACDGKTLD 105

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195054706|ref|XP_001994264.1| GH10565 [Drosophila grimshawi] gi|193896134|gb|EDV95000.1| GH10565 [Drosophila grimshawi]

 Score =  183 bits (464), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 86/105 (81%), Positives = 94/105 (89%)

Query: 1   MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
           MSYQLYRNTTLGNTLQESLDELIQYG ITPTLA KVLLQFDKSIN AL  +VK+R+TFK+
Sbjct: 1   MSYQLYRNTTLGNTLQESLDELIQYGQITPTLAFKVLLQFDKSINNALNQRVKARVTFKA 60

Query: 61  GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
           GKLNTYRFCDNVWT +L DVEFREV E  +V+K+KIVACDGKS D
Sbjct: 61  GKLNTYRFCDNVWTLMLNDVEFREVHEFVKVDKVKIVACDGKSGD 105

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

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	108
FB|FBgn0013347	106	TfIIA-S "Transcription-factor-	0.972	0.990	0.809	1.1e-41
UNIPROTKB|Q32L01	109	GTF2A2 "Transcription initiati	0.953	0.944	0.721	1.7e-36
UNIPROTKB|E2R3G8	109	GTF2A2 "Transcription initiati	0.953	0.944	0.721	1.7e-36
UNIPROTKB|P52657	109	GTF2A2 "Transcription initiati	0.953	0.944	0.721	1.7e-36
UNIPROTKB|F2Z4Z2	109	GTF2A2 "Transcription initiati	0.953	0.944	0.721	1.7e-36
MGI|MGI:1933289	109	Gtf2a2 "general transcription	0.953	0.944	0.721	1.7e-36
RGD|620720	109	Gtf2a2 "general transcription	0.953	0.944	0.721	1.7e-36
ZFIN|ZDB-GENE-050522-513	109	gtf2a2 "general transcription	0.953	0.944	0.711	3.5e-36
UNIPROTKB|F1NE94	86	GTF2A2 "Transcription initiati	0.703	0.883	0.688	3.6e-25
TAIR|locus:2136017	106	AT4G24440 [Arabidopsis thalian	0.925	0.943	0.524	4.6e-25

FB|FBgn0013347 TfIIA-S "Transcription-factor-IIA-S" [Drosophila melanogaster (taxid:7227)]

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 85/105 (80%), Positives = 94/105 (89%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             MSYQLYRNTTLGNTLQESLDELIQYG ITP LA KVLLQFDKSIN AL  +VK+R+TFK+
Sbjct:     1 MSYQLYRNTTLGNTLQESLDELIQYGQITPGLAFKVLLQFDKSINNALNQRVKARVTFKA 60

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSD 105
             GKLNTYRFCDNVWT +L DVEFREV EI +V+K+KIVACDGKS +
Sbjct:    61 GKLNTYRFCDNVWTLMLNDVEFREVHEIVKVDKVKIVACDGKSGE 105

GO:0005672 "transcription factor TFIIA complex" evidence=ISS;IDA

GO:0001128 "RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly" evidence=IPI

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

GO:0001129 "TBP-class protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" evidence=IPI

GO:0005634 "nucleus" evidence=NAS;IDA

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

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

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|Q32L01 GTF2A2 "Transcription initiation factor IIA subunit 2" [Bos taurus (taxid:9913)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 75/104 (72%), Positives = 91/104 (87%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct:     1 MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFR- 59

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
             G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct:    60 GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IEA

UNIPROTKB|E2R3G8 GTF2A2 "Transcription initiation factor IIA subunit 2" [Canis lupus familiaris (taxid:9615)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 75/104 (72%), Positives = 91/104 (87%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct:     1 MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFR- 59

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
             G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct:    60 GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IEA

UNIPROTKB|P52657 GTF2A2 "Transcription initiation factor IIA subunit 2" [Homo sapiens (taxid:9606)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 75/104 (72%), Positives = 91/104 (87%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct:     1 MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFR- 59

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
             G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct:    60 GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

GO:0019048 "virus-host interaction" evidence=IEA

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0006367 "transcription initiation from RNA polymerase II promoter" 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

GO:0005515 "protein binding" evidence=IPI

GO:0005672 "transcription factor TFIIA complex" evidence=IDA

GO:0017025 "TBP-class protein binding" evidence=IPI

GO:0008134 "transcription factor binding" evidence=IPI

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0003713 "transcription coactivator activity" evidence=IDA

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

UNIPROTKB|F2Z4Z2 GTF2A2 "Transcription initiation factor IIA subunit 2" [Sus scrofa (taxid:9823)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 75/104 (72%), Positives = 91/104 (87%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct:     1 MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFR- 59

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
             G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct:    60 GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IEA

MGI|MGI:1933289 Gtf2a2 "general transcription factor II A, 2" [Mus musculus (taxid:10090)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 75/104 (72%), Positives = 91/104 (87%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct:     1 MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFR- 59

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
             G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct:    60 GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IPI

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005672 "transcription factor TFIIA complex" evidence=ISO

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

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

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

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

GO:0008134 "transcription factor binding" evidence=ISO

GO:0017025 "TBP-class protein binding" evidence=ISO

GO:0042803 "protein homodimerization activity" evidence=ISO

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

GO:0046982 "protein heterodimerization activity" evidence=ISO

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=ISO

RGD|620720 Gtf2a2 "general transcription factor IIA, 2" [Rattus norvegicus (taxid:10116)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 75/104 (72%), Positives = 91/104 (87%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ 
Sbjct:     1 MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFR- 59

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
             G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct:    60 GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 103

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IEA;ISO

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

GO:0005672 "transcription factor TFIIA complex" evidence=IEA;ISO

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

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

GO:0008134 "transcription factor binding" evidence=ISO

GO:0017025 "TBP-class protein binding" evidence=IEA;ISO

GO:0042803 "protein homodimerization activity" evidence=IEA;ISO

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

GO:0046982 "protein heterodimerization activity" evidence=IEA;ISO

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA;ISO

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA;ISO

ZFIN|ZDB-GENE-050522-513 gtf2a2 "general transcription factor IIA, 2" [Danio rerio (taxid:7955)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 74/104 (71%), Positives = 92/104 (88%)

Query:     1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKS 60
             M+YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL ++V++R+ F+ 
Sbjct:     1 MAYQLYRNTTLGNSLQESLDELIQTQQITPQLALQVLLQFDKAINTALANRVRNRVNFR- 59

Query:    61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
             G LNTYRFCDNVWTFVL DVEFREV ++ +V+K+KIVACDGK++
Sbjct:    60 GSLNTYRFCDNVWTFVLNDVEFREVTDLVKVDKVKIVACDGKNT 103

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|F1NE94 GTF2A2 "Transcription initiation factor IIA subunit 2" [Gallus gallus (taxid:9031)]

 Score = 286 (105.7 bits), Expect = 3.6e-25, P = 3.6e-25
 Identities = 53/77 (68%), Positives = 67/77 (87%)

Query:    28 ITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAE 87
             ITP LA++VLLQFDK+IN AL  +V++R+ F+ G LNTYRFCDNVWTFVL DVEFREV E
Sbjct:     5 ITPQLALQVLLQFDKAINSALAQRVRNRVNFR-GSLNTYRFCDNVWTFVLNDVEFREVTE 63

Query:    88 IARVNKLKIVACDGKSS 104
             + +V+K+KIVACDGK++
Sbjct:    64 LVKVDKVKIVACDGKNT 80

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

TAIR|locus:2136017 AT4G24440 [Arabidopsis thaliana (taxid:3702)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 53/101 (52%), Positives = 78/101 (77%)

Query:     2 SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSG 61
             +++LYR +T+G  L E+LDE++Q GT++P LA++VL+QFDKS+  AL S+VK++++ K G
Sbjct:     3 TFELYRRSTIGMCLTETLDEMVQSGTLSPELAIQVLVQFDKSMTEALESQVKTKVSIK-G 61

Query:    62 KLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGK 102
              L+TYRFCDNVWTF+L D  F+       V+++KIVACD K
Sbjct:    62 HLHTYRFCDNVWTFILQDAMFKSDDRQENVSRVKIVACDSK 102

GO:0005634 "nucleus" evidence=ISM

GO:0005672 "transcription factor TFIIA complex" evidence=IEA;ISS

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

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

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

---

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)
P0CR84	T2AG_CRYNJ	No assigned EC number	0.4553	0.9722	0.8267	yes	N/A
P52656	T2AG_DROME	No assigned EC number	0.8095	0.9722	0.9905	yes	N/A
Q80ZM7	T2AG_MOUSE	No assigned EC number	0.7211	0.9537	0.9449	yes	N/A
A2XZI2	T2AG_ORYSI	No assigned EC number	0.5247	0.9259	0.9433	N/A	N/A
O74948	T2AG_SCHPO	No assigned EC number	0.5392	0.9351	0.9266	yes	N/A
Q90YG6	T2AG_ONCMY	No assigned EC number	0.7211	0.9537	0.9537	N/A	N/A
O08950	T2AG_RAT	No assigned EC number	0.7211	0.9537	0.9449	yes	N/A
Q39236	T2AG_ARATH	No assigned EC number	0.5247	0.9259	0.9433	yes	N/A
Q9IA78	T2AG_PAROL	No assigned EC number	0.7378	0.9444	0.9189	N/A	N/A
P32774	T2AG_YEAST	No assigned EC number	0.4102	0.9444	0.8360	yes	N/A
Q9NEX2	T2AG_CAEEL	No assigned EC number	0.4901	0.9444	0.9026	yes	N/A
B7Q1Q9	T2AG_IXOSC	No assigned EC number	0.7941	0.9444	0.8644	N/A	N/A
Q9W5B9	T2AH_DROME	No assigned EC number	0.5148	0.9351	0.9439	no	N/A
Q54ND1	T2AG_DICDI	No assigned EC number	0.5	0.9444	0.8869	yes	N/A
Q5BB99	T2AG_EMENI	No assigned EC number	0.5049	0.9166	0.8918	yes	N/A
P52657	T2AG_HUMAN	No assigned EC number	0.7211	0.9537	0.9449	yes	N/A
Q0DLD3	T2AG_ORYSJ	No assigned EC number	0.5247	0.9259	0.9433	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	108
COG5123	113	COG5123, TOA2, Transcription initiation factor IIA	2e-28
pfam02268	49	pfam02268, TFIIA_gamma_N, Transcription initiation	2e-24
cd10145	49	cd10145, TFIIA_gamma_N, Gamma subunit of transcrip	6e-24
pfam02751	51	pfam02751, TFIIA_gamma_C, Transcription initiation	1e-22
cd10014	47	cd10014, TFIIA_gamma_C, Gamma subunit of transcrip	3e-21

>gnl|CDD|227452 COG5123, TOA2, Transcription initiation factor IIA, gamma subunit [Transcription]

 Score = 99.3 bits (247), Expect = 2e-28
 Identities = 51/109 (46%), Positives = 66/109 (60%), Gaps = 8/109 (7%)

Query: 3   YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGK 62
           Y+LYR + +G  L+++LDELI  G I+P LAM VL  FDKS+   L   V S LTFK GK
Sbjct: 5   YELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFK-GK 63

Query: 63  LNTYRFCDNVWTFVLT------DVEFREVAEIA-RVNKLKIVACDGKSS 104
           L+TY FCD VWTF+        + E+    E+     K +IVAC G+ S
Sbjct: 64  LDTYNFCDGVWTFITKNFVMSLNNEYFNAGEVNIVACKARIVACAGRRS 112

Length = 113

>gnl|CDD|145428 pfam02268, TFIIA_gamma_N, Transcription initiation factor IIA, gamma subunit, helical domain

 Score = 86.9 bits (216), Expect = 2e-24
 Identities = 34/49 (69%), Positives = 38/49 (77%)

Query: 1  MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP 49
          M Y+LYR +TLG  L ++LDELI  G ITP LAMKVLLQFDKSIN AL 
Sbjct: 1  MYYELYRRSTLGMALTDALDELISDGRITPQLAMKVLLQFDKSINEALA 49

Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle. Length = 49

>gnl|CDD|199901 cd10145, TFIIA_gamma_N, Gamma subunit of transcription initiation factor IIA, N-terminal helical domain

 Score = 85.7 bits (213), Expect = 6e-24
 Identities = 37/48 (77%), Positives = 40/48 (83%)

Query: 2  SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP 49
           Y+LYRNTTLG  LQ++LDELIQ G ITP LAMKVLLQFDKSIN AL 
Sbjct: 1  YYELYRNTTLGIALQDALDELIQDGQITPQLAMKVLLQFDKSINEALA 48

Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The N-terminal domain of the gamma subunit forms a 4-helix bundle together with the alpha subunit. Length = 49

>gnl|CDD|190407 pfam02751, TFIIA_gamma_C, Transcription initiation factor IIA, gamma subunit

 Score = 82.3 bits (204), Expect = 1e-22
 Identities = 31/52 (59%), Positives = 40/52 (76%), Gaps = 2/52 (3%)

Query: 51  KVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFRE-VAEIARVNKLKIVACDG 101
           KVKS+LTFK G L+TYRFCDNVWTF++ + +F+    E   V+K+KIVACD 
Sbjct: 1   KVKSKLTFK-GHLDTYRFCDNVWTFIVKNAQFKLDDQETVTVDKVKIVACDS 51

Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel. Length = 51

>gnl|CDD|199900 cd10014, TFIIA_gamma_C, Gamma subunit of transcription initiation factor IIA, C-terminal domain

 Score = 78.8 bits (195), Expect = 3e-21
 Identities = 34/48 (70%), Positives = 39/48 (81%), Gaps = 2/48 (4%)

Query: 56  LTFKSGKLNTYRFCDNVWTFVLTDVEFREV-AEIARVNKLKIVACDGK 102
           LTFK G L TYRFCDNVWTF+L DVEF+E   E+  V+K+KIVACDGK
Sbjct: 1   LTFK-GHLKTYRFCDNVWTFILNDVEFKESNTEVVTVDKVKIVACDGK 47

Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The C-terminal domain of the gamma (TFIIA_gamma_C) subunit forms a beta-barrel structure together with TFIIA beta. Length = 47

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	108
KOG3463|consensus	109		100.0
COG5123	113	TOA2 Transcription initiation factor IIA, gamma su	100.0
PF02751	52	TFIIA_gamma_C: Transcription initiation factor IIA	99.95
PF02268	49	TFIIA_gamma_N: Transcription initiation factor IIA	99.93
PF10925	59	DUF2680: Protein of unknown function (DUF2680); In	92.74
cd01709	346	RT_like_1 RT_like_1: A subfamily of reverse transc	88.6
PF09925	145	DUF2157: Predicted membrane protein (DUF2157); Int	87.17
cd03487	214	RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr	87.07
cd01646	158	RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip	86.89
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	85.97

>KOG3463|consensus

Probab=100.00  E-value=8.7e-54  Score=297.74  Aligned_cols=105  Identities=70%  Similarity=1.094  Sum_probs=101.7

Q ss_pred             Ch-hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcC
Q psy7895           1 MS-YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTD   79 (108)
Q Consensus         1 m~-y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd   79 (108)
                      |+ |||||+||||.+|++|||||+++|.|||+||++||++||+||+++|+++|+++++|| |+|.|||||||||||+++|
T Consensus         1 m~~YelYR~ttlG~~L~~tLDe~v~~g~itp~la~~VL~~FDKSi~~al~~~vk~kmsfk-g~L~tYr~CDnVWTFil~~   79 (109)
T KOG3463|consen    1 MSYYELYRRTTLGNALQKTLDELVSDGVITPSLAKKVLEQFDKSINEALNDKVKNKMSFK-GKLDTYRFCDNVWTFILKD   79 (109)
T ss_pred             CcHHHHHHHhhHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcccceeee-eccceeeeccceeeEEEcC
Confidence            66 999999999999999999999999999999999999999999999999999999999 9999999999999999999


Q ss_pred             eEEEecceEee-cCcEEEEEecCCCCCC
Q psy7895          80 VEFREVAEIAR-VNKLKIVACDGKSSDD  106 (108)
Q Consensus        80 ~~f~~~~~~~~-~~~lKIVAcd~~~~~~  106 (108)
                      ++|+.+++..+ +|+||||||||+.++.
T Consensus        80 ~~~r~~~e~~~~vdkvkIVACdg~~~~~  107 (109)
T KOG3463|consen   80 VEFREDNESFKTVDKVKIVACDGKDSGA  107 (109)
T ss_pred             eEEecccccccccceEEEEEecCccccc
Confidence            99999999986 9999999999987653

>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]

Probab=100.00  E-value=3.5e-42  Score=238.72  Aligned_cols=101  Identities=50%  Similarity=0.859  Sum_probs=96.5

Q ss_pred             hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeEE
Q psy7895           3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEF   82 (108)
Q Consensus         3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f   82 (108)
                      |||||+|+||..|.|+|||+|++|.|+|+||++||+.||+++.++|++.|+|+++|| |+|++|+|||+||||+++|+.|
T Consensus         5 YElYRrs~ig~~L~dalD~lis~g~isp~lam~vLetFDksv~e~l~~~v~s~ltfK-G~lDtY~fcD~VWtFi~kn~~~   83 (113)
T COG5123           5 YELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFK-GKLDTYNFCDGVWTFITKNFVM   83 (113)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHhhhHHHHHHHhhhheeeEEe-ecccccccccceeEEEecCeEE
Confidence            999999999999999999999999999999999999999999999999999999999 9999999999999999999999


Q ss_pred             Eecc------eE-eecCcEEEEEecCCCC
Q psy7895          83 REVA------EI-ARVNKLKIVACDGKSS  104 (108)
Q Consensus        83 ~~~~------~~-~~~~~lKIVAcd~~~~  104 (108)
                      ++++      +. |.+++++||||.++..
T Consensus        84 s~~n~~~~a~e~~i~~~k~rIvaca~r~s  112 (113)
T COG5123          84 SLNNEYFNAGEVNIVACKARIVACAGRRS  112 (113)
T ss_pred             EeccccccccccceEeeeeeEEeeccccC
Confidence            9986      43 7889999999998764

>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site

Probab=99.95  E-value=9e-29  Score=153.55  Aligned_cols=50  Identities=64%  Similarity=1.193  Sum_probs=45.1

Q ss_pred             hccCceeEeccccceeeeeCcEEEEEEcCeEEEe--cceEeecCcEEEEEecC
Q psy7895          51 KVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFRE--VAEIARVNKLKIVACDG  101 (108)
Q Consensus        51 ~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f~~--~~~~~~~~~lKIVAcd~  101 (108)
                      +|++|++|| |||+|||||||||||+++|++|++  +++.+++|+||||||||
T Consensus         1 ~vk~k~~fK-G~L~tYrfcDnVWTFi~kn~~fk~~~~~~~~~~dkvKIVACd~   52 (52)
T PF02751_consen    1 KVKNKLSFK-GHLDTYRFCDNVWTFILKNVEFKMEDNNETVKVDKVKIVACDS   52 (52)
T ss_dssp             T---EEEEE-EEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEEEEEEEEEES
T ss_pred             CcceeEEEE-EeeeEEEeeCcEEEEEEcCEEEEEecCCcEEEcCeEEEEEcCC
Confidence            489999999 999999999999999999999999  58899999999999996

After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.

>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site

Probab=99.93  E-value=1.3e-26  Score=142.31  Aligned_cols=49  Identities=69%  Similarity=0.969  Sum_probs=44.3

Q ss_pred             ChhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy7895           1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP   49 (108)
Q Consensus         1 m~y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~   49 (108)
                      |+|||||+||||.||+|||||||++|.|+|+||++||++||++|+++|+
T Consensus         1 ~~yelYR~stlG~aL~dtLDeli~~~~I~p~La~kVL~~FDksi~~~L~   49 (49)
T PF02268_consen    1 MYYELYRRSTLGIALTDTLDELIQEGKITPQLAMKVLEQFDKSINEALS   49 (49)
T ss_dssp             ---CGGGCSHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHcchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            8999999999999999999999999999999999999999999999985

After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.

>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known

Probab=92.74  E-value=0.37  Score=30.36  Aligned_cols=32  Identities=19%  Similarity=0.255  Sum_probs=28.4

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHh
Q psy7895          16 QESLDELIQYGTITPTLAMKVLLQFDKSINGA   47 (108)
Q Consensus        16 ~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~   47 (108)
                      ...+|..++.|.||+++|..+.+.+|.-....
T Consensus        21 K~~idk~Ve~G~iTqeqAd~ik~~id~~~~~~   52 (59)
T PF10925_consen   21 KQIIDKYVEAGVITQEQADAIKKHIDQRQEYM   52 (59)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999877654

>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs)

Probab=88.60  E-value=0.7  Score=38.39  Aligned_cols=65  Identities=18%  Similarity=0.163  Sum_probs=46.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeE-E----Eec------ceEeecCc
Q psy7895          25 YGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVE-F----REV------AEIARVNK   93 (108)
Q Consensus        25 ~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~-f----~~~------~~~~~~~~   93 (108)
                      .|.|||=+|+-+|..||..|++...           | ..-||+.|++|-+ -..-+ .    .+.      +=.++.+|
T Consensus        87 GgviSplLaNiyL~~lD~~v~~~~~-----------g-~~l~RYaDD~vi~-~~~~~a~~aw~~i~~fl~~lGLelN~eK  153 (346)
T cd01709          87 SHALSDVFGELVLFCLDFAVNQATD-----------G-GLLYRLHDDLWFW-GQPETCAKAWKAIQEFAKVMGLELNKEK  153 (346)
T ss_pred             CchhhHHHHHHHHHHHHHHHHhcCC-----------C-ceEEEEcCeEEEE-cCHHHHHHHHHHHHHHHHHcCceecccc
Confidence            4689999999999999999998642           3 4789999999988 32100 0    000      22466688


Q ss_pred             EEEEEecCC
Q psy7895          94 LKIVACDGK  102 (108)
Q Consensus        94 lKIVAcd~~  102 (108)
                      =+||-|...
T Consensus       154 T~iV~~~~~  162 (346)
T cd01709         154 TGSVYLSDD  162 (346)
T ss_pred             ceEEEeccC
Confidence            888887654

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.

>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function

Probab=87.17  E-value=0.6  Score=33.24  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=22.0

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHH
Q psy7895          19 LDELIQYGTITPTLAMKVLLQFD   41 (108)
Q Consensus        19 Ldeli~~~~Is~~la~kVl~~FD   41 (108)
                      |++++++|.|+|+++.++++.++
T Consensus         1 l~~w~~~GlI~~~q~~~i~~~~~   23 (145)
T PF09925_consen    1 LDRWVEQGLITPEQAEAILAFYG   23 (145)
T ss_pred             CHhHHHCCCCCHHHHHHHHHHhh
Confidence            68999999999999999999998

>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=87.07  E-value=1.9  Score=32.08  Aligned_cols=46  Identities=22%  Similarity=0.322  Sum_probs=35.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeE
Q psy7895          25 YGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVE   81 (108)
Q Consensus        25 ~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~   81 (108)
                      ...+||-|++-+|..||..+.+....        .  .+..+||+||+ +|..++..
T Consensus       107 G~~lSp~Lanl~l~~~d~~l~~~~~~--------~--~~~~~RYaDD~-~i~~~~~~  152 (214)
T cd03487         107 GAPTSPALSNLVFRKLDERLSKLAKS--------N--GLTYTRYADDI-TFSSNKKL  152 (214)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHHHHH--------c--CCeEEEEeccE-EEEccccc
Confidence            35899999999999999999876432        1  24567999996 67777765

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=86.89  E-value=1.4  Score=31.34  Aligned_cols=40  Identities=18%  Similarity=0.205  Sum_probs=34.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEE
Q psy7895          25 YGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFV   76 (108)
Q Consensus        25 ~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~   76 (108)
                      ...+||=+++.+|..||..+.+.           . +.+...||+||++-+.
T Consensus        57 G~~lS~~L~~~~l~~~d~~i~~~-----------~-~~~~~~RY~DD~~i~~   96 (158)
T cd01646          57 GPLTSRFLANIYLNDVDHELKSK-----------L-KGVDYVRYVDDIRIFA   96 (158)
T ss_pred             CcchHHHHHHHHHHHHHHHHHhc-----------c-CCceEEEecCcEEEEc
Confidence            34899999999999999999876           4 5678999999999877

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=85.97  E-value=2.3  Score=25.23  Aligned_cols=35  Identities=29%  Similarity=0.397  Sum_probs=28.2

Q ss_pred             HHHHhhhHHHHHHHHHHHHHHCC-CCCHHHHHHHHHH
Q psy7895           4 QLYRNTTLGNTLQESLDELIQYG-TITPTLAMKVLLQ   39 (108)
Q Consensus         4 ~lYR~stlG~aL~dtLdeli~~~-~Is~~la~kVl~~   39 (108)
                      +.+|+.-|- .....|++|.+.| .|+|++..++|+.
T Consensus        11 ~Ak~~GlI~-~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen   11 LAKRRGLIS-EVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHcCChh-hHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            345555565 7888999999988 8999999999874

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	108
1nvp_D	108	Human TfiiaTBPDNA COMPLEX Length = 108		3e-40
1rm1_B	122	Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex L		4e-19
1ytf_D	121	Yeast TfiiaTBPDNA COMPLEX Length = 121		4e-19

>pdb|1NVP|D Chain D, Human TfiiaTBPDNA COMPLEX Length = 108

Iteration: 1
 Score =  159 bits (403), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 74/103 (71%), Positives = 90/103 (87%), Gaps = 1/103 (0%)
Query: 2   SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSG 61
           +YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ G
Sbjct: 1   AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFR-G 59
Query: 62  KLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
            LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct: 60  SLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 102

>pdb|1RM1|B Chain B, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex Length = 122

Iteration: 1
 Score = 89.7 bits (221), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/117 (41%), Positives = 73/117 (62%), Gaps = 15/117 (12%)
Query: 3   YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGK 62
           Y+LYR +T+GN+L ++LD LI  G I  +LAM+VL  FDK +   L    +S+LT K G 
Sbjct: 7   YELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVK-GN 65
Query: 63  LNTYRFCDNVWTFVLTDVE------FREVAE--------IARVNKLKIVACDGKSSD 105
           L+TY FCD+VWTF++ + +       R+ ++        +  V+KL+IVAC+ K S+
Sbjct: 66  LDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE 122

>pdb|1YTF|D Chain D, Yeast TfiiaTBPDNA COMPLEX Length = 121

Iteration: 1
 Score = 89.4 bits (220), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/117 (41%), Positives = 73/117 (62%), Gaps = 15/117 (12%)
Query: 3   YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGK 62
           Y+LYR +T+GN+L ++LD LI  G I  +LAM+VL  FDK +   L    +S+LT K G 
Sbjct: 6   YELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVK-GN 64
Query: 63  LNTYRFCDNVWTFVLTDVE------FREVAE--------IARVNKLKIVACDGKSSD 105
           L+TY FCD+VWTF++ + +       R+ ++        +  V+KL+IVAC+ K S+
Sbjct: 65  LDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE 121

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	108
1nvp_D	108	Transcription initiation factor IIA gamma chain; t	5e-52
1nh2_D	121	Transcription initiation factor IIA small chain; t	1e-46

>1nvp_D Transcription initiation factor IIA gamma chain; transcription regulation, DNA, complex, transcription/DNA complex; 2.10A {Homo sapiens} SCOP: a.32.1.1 b.56.1.1 Length = 108

 Score =  158 bits (400), Expect = 5e-52
 Identities = 74/106 (69%), Positives = 90/106 (84%), Gaps = 1/106 (0%)

Query: 2   SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSG 61
           +YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ G
Sbjct: 1   AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFR-G 59

Query: 62  KLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSSDDR 107
            LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++   
Sbjct: 60  SLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSN 105

>1nh2_D Transcription initiation factor IIA small chain; transcription/DNA; HET: 5IU; 1.90A {Saccharomyces cerevisiae} SCOP: a.32.1.1 b.56.1.1 PDB: 1ytf_D* 1rm1_B Length = 121

 Score =  145 bits (366), Expect = 1e-46
 Identities = 47/117 (40%), Positives = 70/117 (59%), Gaps = 15/117 (12%)

Query: 3   YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGK 62
           Y+LYR +T+GN+L ++LD LI  G I  +LAM+VL  FDK +   L    +S+LT K G 
Sbjct: 6   YELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVK-GN 64

Query: 63  LNTYRFCDNVWTFVLTDVEFR--------------EVAEIARVNKLKIVACDGKSSD 105
           L+TY FCD+VWTF++ + +                +   +  V+KL+IVAC+ K S+
Sbjct: 65  LDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE 121

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	108
1nvp_D	108	Transcription initiation factor IIA gamma chain; t	100.0
1nh2_D	121	Transcription initiation factor IIA small chain; t	100.0

>1nvp_D Transcription initiation factor IIA gamma chain; transcription regulation, DNA, complex, transcription/DNA complex; 2.10A {Homo sapiens} SCOP: a.32.1.1 b.56.1.1

Probab=100.00  E-value=9.8e-55  Score=303.26  Aligned_cols=104  Identities=71%  Similarity=1.169  Sum_probs=96.5

Q ss_pred             hhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeE
Q psy7895           2 SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVE   81 (108)
Q Consensus         2 ~y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~   81 (108)
                      ||||||+|+||.||+||||||+++|.|+|+||++||++||++|+++|+++|++|++|| |+|++||||||||||+++||+
T Consensus         1 ~y~lYR~stiG~aL~dtLdEli~~~~Isp~la~kVL~~FDksi~~aL~~~vksk~sfK-G~L~tYrfcDnVWTf~lkd~~   79 (108)
T 1nvp_D            1 AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFR-GSLNTYRFCDNVWTFVLNDVE   79 (108)
T ss_dssp             -CGGGGSSHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHTCCCEEEEE-EEEEEEEEETTEEEEEEEEEE
T ss_pred             ChhHHhhChHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEe-eccCCccccCcEEEEEEeceE
Confidence            6999999999999999999999999999999999999999999999999999999999 999999999999999999999


Q ss_pred             EEecceEeecCcEEEEEecCCCCCC
Q psy7895          82 FREVAEIARVNKLKIVACDGKSSDD  106 (108)
Q Consensus        82 f~~~~~~~~~~~lKIVAcd~~~~~~  106 (108)
                      |+++++.+++|+|||||||++.+++
T Consensus        80 fk~~~~~~~~d~vKIVAC~~~~~~~  104 (108)
T 1nvp_D           80 FREVTELIKVDKVKIVACDGKNTGS  104 (108)
T ss_dssp             EECSSCEEEEEEEEEEEEC------
T ss_pred             EEeccceeecCeEEEEEeCCCCCCC
Confidence            9999999999999999999998765

>1nh2_D Transcription initiation factor IIA small chain; transcription/DNA; HET: 5IU; 1.90A {Saccharomyces cerevisiae} SCOP: a.32.1.1 b.56.1.1 PDB: 1ytf_D* 1rm1_B

Probab=100.00  E-value=4.7e-53  Score=299.67  Aligned_cols=103  Identities=46%  Similarity=0.824  Sum_probs=100.2

Q ss_pred             ChhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCe
Q psy7895           1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDV   80 (108)
Q Consensus         1 m~y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~   80 (108)
                      |+|+|||+|+||.||++|||||+++|.|+|+||++||++||++|+++|+++|++|++|| |+|++||||||||||+++||
T Consensus         4 ~~y~lYR~StiG~aL~dtLdEli~~~~Isp~la~kVL~~FDksi~~aL~~~vksk~sfK-G~L~tYrfcDnVWtfilkd~   82 (121)
T 1nh2_D            4 GYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVK-GNLDTYGFCDDVWTFIVKNC   82 (121)
T ss_dssp             CCCCGGGGSHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHSCCCEEEEE-EEEEEEEEETTEEEEEEEEE
T ss_pred             chHHHHHhchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEE-eeeccccccCcEEEEEEece
Confidence            78999999999999999999999999999999999999999999999999999999999 99999999999999999999


Q ss_pred             EEEec--------------ceEeecCcEEEEEecCCCC
Q psy7895          81 EFREV--------------AEIARVNKLKIVACDGKSS  104 (108)
Q Consensus        81 ~f~~~--------------~~~~~~~~lKIVAcd~~~~  104 (108)
                      +|+++              ++.+++|+|||||||++.+
T Consensus        83 ~fk~~~~~~~~~~~~~~~~~~~~~vdkvKIVAC~~k~~  120 (121)
T 1nh2_D           83 QVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKS  120 (121)
T ss_dssp             EEEEEC-------------CEEEEEEEEEEEEEESSCC
T ss_pred             EEEeccccccccccccccCCceeecceEEEEEeCCCCC
Confidence            99988              4689999999999999975

---

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	108
d1nvpd1	51	a.32.1.1 (D:3-53) Small chain TOA2, N-terminal dom	5e-27
d1nh2d1	50	a.32.1.1 (D:5-54) Small chain TOA2, N-terminal dom	6e-24
d1nvpd2	46	b.56.1.1 (D:54-99) Small chain TOA2, C-terminal do	1e-23
d1nh2d2	67	b.56.1.1 (D:55-121) Small chain TOA2, C-terminal d	5e-20

>d1nvpd1 a.32.1.1 (D:3-53) Small chain TOA2, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 51

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Small chain TOA2, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.0 bits (229), Expect = 5e-27
 Identities = 38/51 (74%), Positives = 44/51 (86%)

Query: 3  YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVK 53
          YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V+
Sbjct: 1  YQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVR 51

>d1nh2d1 a.32.1.1 (D:5-54) Small chain TOA2, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 50

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Small chain TOA2, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 84.3 bits (209), Expect = 6e-24
 Identities = 23/46 (50%), Positives = 32/46 (69%)

Query: 3  YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGAL 48
          Y+LYR +T+GN+L ++LD LI  G I  +LAM+VL  FDK +   L
Sbjct: 3  YELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETL 48

>d1nvpd2 b.56.1.1 (D:54-99) Small chain TOA2, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 46

class: All beta proteins
fold: Transcription factor IIA (TFIIA), beta-barrel domain
superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
family: Transcription factor IIA (TFIIA), beta-barrel domain
domain: Small chain TOA2, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.6 bits (207), Expect = 1e-23
 Identities = 34/47 (72%), Positives = 41/47 (87%), Gaps = 1/47 (2%)

Query: 54  SRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACD 100
           +R+ F+ G LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACD
Sbjct: 1   NRVNFR-GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACD 46

>d1nh2d2 b.56.1.1 (D:55-121) Small chain TOA2, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 67

class: All beta proteins
fold: Transcription factor IIA (TFIIA), beta-barrel domain
superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
family: Transcription factor IIA (TFIIA), beta-barrel domain
domain: Small chain TOA2, C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 74.7 bits (183), Expect = 5e-20
 Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 15/67 (22%)

Query: 52  VKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFR--------------EVAEIARVNKLKIV 97
            +S+LT K G L+TY FCD+VWTF++ + +                +   +  V+KL+IV
Sbjct: 2   TQSKLTVK-GNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIV 60

Query: 98  ACDGKSS 104
           AC+ K S
Sbjct: 61  ACNSKKS 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	108
d1nh2d2	67	Small chain TOA2, C-terminal domain {Baker's yeast	99.95
d1nvpd2	46	Small chain TOA2, C-terminal domain {Human (Homo s	99.95
d1nvpd1	51	Small chain TOA2, N-terminal domain {Human (Homo s	99.94
d1nh2d1	50	Small chain TOA2, N-terminal domain {Baker's yeast	99.93

>d1nh2d2 b.56.1.1 (D:55-121) Small chain TOA2, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Transcription factor IIA (TFIIA), beta-barrel domain
superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
family: Transcription factor IIA (TFIIA), beta-barrel domain
domain: Small chain TOA2, C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.95  E-value=4.7e-29  Score=159.00  Aligned_cols=52  Identities=46%  Similarity=0.920  Sum_probs=47.6

Q ss_pred             ccCceeEeccccceeeeeCcEEEEEEcCeEEEec--------------ceEeecCcEEEEEecCCCC
Q psy7895          52 VKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREV--------------AEIARVNKLKIVACDGKSS  104 (108)
Q Consensus        52 vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f~~~--------------~~~~~~~~lKIVAcd~~~~  104 (108)
                      +++|++|| |+|+|||||||||||+|+|++|+++              ++++++|++||||||++.+
T Consensus         2 ~KsKltfK-G~L~TYRFCDnVWTFiiknv~fk~~~~~~~~~~~g~~~~~~~~~vDkvKIVACd~K~a   67 (67)
T d1nh2d2           2 TQSKLTVK-GNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKS   67 (67)
T ss_dssp             CCCEEEEE-EEEEEEEEETTEEEEEEEEEEEEEEC-------------CEEEEEEEEEEEEEESSCC
T ss_pred             CceeEEEE-eeecceeccccEEEEEEeeeEEEeccccccccccccCCcceeEecceEEEEEecCccC
Confidence            68999999 9999999999999999999999973              3468999999999999864

>d1nvpd2 b.56.1.1 (D:54-99) Small chain TOA2, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Transcription factor IIA (TFIIA), beta-barrel domain
superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
family: Transcription factor IIA (TFIIA), beta-barrel domain
domain: Small chain TOA2, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=4.8e-29  Score=148.57  Aligned_cols=46  Identities=74%  Similarity=1.362  Sum_probs=44.7

Q ss_pred             CceeEeccccceeeeeCcEEEEEEcCeEEEecceEeecCcEEEEEec
Q psy7895          54 SRLTFKSGKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACD  100 (108)
Q Consensus        54 sk~~~K~G~L~tYr~cDnVWtF~lkd~~f~~~~~~~~~~~lKIVAcd  100 (108)
                      ||++|| |||+|||||||||||+++|++|+.+++.+++|++||||||
T Consensus         1 nk~tfK-G~L~tYRfCDnVWTFilkdv~fk~~~~~~~vdkvKIVACd   46 (46)
T d1nvpd2           1 NRVNFR-GSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACD   46 (46)
T ss_dssp             CEEEEE-EEEEEEEEETTEEEEEEEEEEEECSSCEEEEEEEEEEEEC
T ss_pred             CceEEE-EEeeeeccCCcEEEEEEeceEEecCCeEEecCeEEEEECC
Confidence            689999 9999999999999999999999998999999999999997

>d1nvpd1 a.32.1.1 (D:3-53) Small chain TOA2, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Small chain TOA2, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=7.6e-28  Score=146.16  Aligned_cols=51  Identities=75%  Similarity=1.066  Sum_probs=50.1

Q ss_pred             hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhcc
Q psy7895           3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVK   53 (108)
Q Consensus         3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vk   53 (108)
                      |||||+||||.+|+|||||||++|.|+|+||++||.+||++|+++|+++||
T Consensus         1 YelYR~sTlG~tL~dtLDeli~~~~I~p~LA~kVL~qFDk~i~~aL~~~Vk   51 (51)
T d1nvpd1           1 YQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVR   51 (51)
T ss_dssp             CGGGGSSHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CcchhcchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            899999999999999999999999999999999999999999999999986

>d1nh2d1 a.32.1.1 (D:5-54) Small chain TOA2, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Small chain TOA2, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.93  E-value=1.8e-26  Score=139.51  Aligned_cols=48  Identities=48%  Similarity=0.804  Sum_probs=47.0

Q ss_pred             hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895           3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPS   50 (108)
Q Consensus         3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~   50 (108)
                      |||||+||||.+|+|||||||++|.|+|+||++||.+|||+|+++|++
T Consensus         3 YelYR~stlG~~L~dtLDeli~~~~I~p~LA~kVL~qFDk~i~~aL~~   50 (50)
T d1nh2d1           3 YELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKD   50 (50)
T ss_dssp             CCGGGGSHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            899999999999999999999999999999999999999999999975