Psyllid ID: psy2291

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
MEIYCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDRD
Secondary Structure (PSIPRED)
cEEEEEccccccccccccccccccccccEEEEEEcccHHHHHHHHHHHccccccccEEEEEccccEEEEEHHHHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEccccccccccccccccccccccEEEEEEcccHHHHHHHHHcccccccccEEEEEEccccEEEEcHHHHHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
meiycnyvddkpmKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQdldethlfISSDVIELLMTRVDDLLdqisfpindrd
Flexible Loop (DISEMBL)
meiycnyvddkpmkQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLldqisfpindrd
Low Complexity Region (SEG)
MEIYCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDRD
Disordered region (IsUnstruct)
**IYCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF******
Disordered Region (DISOPRED)
*EIYC**VDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLD**********
Disordered Region (DISEMBL)
MEIYCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDRD
Disordered Region (DISPRO)
MEIYCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPI****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEIYCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDRD
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	96	2.2.26 [Sep-21-2011]
Q5ZKH0	71	General transcription fac	yes	N/A	0.687	0.929	0.529	7e-15
Q6ZYL4	71	General transcription fac	yes	N/A	0.687	0.929	0.455	9e-13
Q2T9Z5	71	General transcription fac	yes	N/A	0.687	0.929	0.455	9e-13
Q8K2X8	71	General transcription fac	yes	N/A	0.687	0.929	0.455	1e-12
Q4P985	62	RNA polymerase II transcr	N/A	N/A	0.437	0.677	0.521	0.0006

>sp|Q5ZKH0|TF2H5_CHICK General transcription factor IIH subunit 5 OS=Gallus gallus GN=GTF2H5 PE=3 SV=1

 Score = 79.3 bits (194), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 36/68 (52%), Positives = 51/68 (75%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  +I C  D  MKQFLL+LDE+N LG++FIIQDLDETH+F+ ++++  L  RV +L+DQ
Sbjct: 6  KGVLIEC--DPAMKQFLLYLDESNALGKKFIIQDLDETHVFVLAELVNFLQERVGELMDQ 63

Query: 88 ISFPINDR 95
           SFPI  +
Sbjct: 64 NSFPITQK 71

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.
Gallus gallus (taxid: 9031)

>sp|Q6ZYL4|TF2H5_HUMAN General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 51/68 (75%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ
Sbjct: 6  KGVLIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQ 63

Query: 88 ISFPINDR 95
           +F +  +
Sbjct: 64 NAFSLTQK 71

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.

Homo sapiens (taxid: 9606)

>sp|Q2T9Z5|TF2H5_BOVIN General transcription factor IIH subunit 5 OS=Bos taurus GN=GTF2H5 PE=3 SV=1

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 51/68 (75%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ
Sbjct: 6  KGVLIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQ 63

Query: 88 ISFPINDR 95
           +F +  +
Sbjct: 64 NAFSLTQK 71

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.

Bos taurus (taxid: 9913)

>sp|Q8K2X8|TF2H5_MOUSE General transcription factor IIH subunit 5 OS=Mus musculus GN=Gtf2h5 PE=1 SV=1

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 50/68 (73%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  +I C  D  MKQFLL+LDE N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ
Sbjct: 6  KGVLIEC--DPAMKQFLLYLDEANALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQ 63

Query: 88 ISFPINDR 95
           +F +  +
Sbjct: 64 NAFSLTQK 71

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.

Mus musculus (taxid: 10090)

>sp|Q4P985|TFB5_USTMA RNA polymerase II transcription factor B subunit 5 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=TFB5 PE=3 SV=2

 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 29/46 (63%), Gaps = 4/46 (8%)

Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVD 82
          D  +KQ +L LDE N    RFII DLDETHL IS D I+ L   ++
Sbjct: 12 DAAVKQLILSLDERN----RFIIMDLDETHLLISPDRIDWLRAELE 53

Component of the general transcription and DNA repair factor IIH (TFIIH), which is essential for both basal and activated transcription, as well as for nucleotide excision repair (NER) of DNA. TFB5 is required for stable recruitment of TFIIH to a promoter, but not for stability of TFIIH subunits.

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

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	96
332022217	73	General transcription factor IIH subunit	0.729	0.958	0.642	8e-19
357617748	73	hypothetical protein KGM_16313 [Danaus p	0.687	0.904	0.632	4e-17
195161284	73	GL26481 [Drosophila persimilis] gi|19847	0.697	0.917	0.623	4e-17
281364435	73	Tfb5 [Drosophila melanogaster] gi|194856	0.697	0.917	0.623	8e-17
289743363	73	putative BBOX Zn-finger protein [Glossin	0.697	0.917	0.608	3e-16
242011976	71	TFIIH basal transcription factor complex	0.687	0.929	0.602	4e-16
194761538	73	GF15714 [Drosophila ananassae] gi|190616	0.697	0.917	0.608	5e-16
195114636	73	GI14600 [Drosophila mojavensis] gi|19391	0.697	0.917	0.594	6e-16
427785875	71	Putative proteinral transcription factor	0.687	0.929	0.544	9e-16
241646745	71	general transcription factor IIE (TFIIE)	0.687	0.929	0.558	1e-15

>gi|332022217|gb|EGI62532.1| General transcription factor IIH subunit 5 [Acromyrmex echinatior]

 Score = 97.8 bits (242), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/70 (64%), Positives = 57/70 (81%)

Query: 26 LGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLL 85
          L  R  ++ FSD  MKQFLLHLDET+ LGR+FIIQDLDE HLFIS+D++E L  +VDDL+
Sbjct: 2  LNIRTKLYVFSDAAMKQFLLHLDETSALGRKFIIQDLDEKHLFISADILETLQAKVDDLM 61

Query: 86 DQISFPINDR 95
          DQISFP+ ++
Sbjct: 62 DQISFPLAEK 71

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357617748|gb|EHJ70975.1| hypothetical protein KGM_16313 [Danaus plexippus]

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 43/68 (63%), Positives = 55/68 (80%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLDET  LGR+FI+QDLDETH+FISSD++E L  RVDDL+DQ
Sbjct: 6  KGVLVEC--DPAMKQFLLHLDETLALGRKFILQDLDETHVFISSDIVETLQARVDDLMDQ 63

Query: 88 ISFPINDR 95
           SFP++D+
Sbjct: 64 FSFPVHDK 71

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195161284|ref|XP_002021498.1| GL26481 [Drosophila persimilis] gi|198472498|ref|XP_002133059.1| GA28879 [Drosophila pseudoobscura pseudoobscura] gi|194103298|gb|EDW25341.1| GL26481 [Drosophila persimilis] gi|198139040|gb|EDY70461.1| GA28879 [Drosophila pseudoobscura pseudoobscura]

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 43/69 (62%), Positives = 57/69 (82%), Gaps = 2/69 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLDE   LGR+FIIQDLDE+HLFIS+D++E+L  RVDDL+D+
Sbjct: 6  KGVLVEC--DPAMKQFLLHLDEKLALGRKFIIQDLDESHLFISTDIVEVLQARVDDLMDR 63

Query: 88 ISFPINDRD 96
          ISFP++D+D
Sbjct: 64 ISFPLHDKD 72

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|281364435|ref|NP_001137791.2| Tfb5 [Drosophila melanogaster] gi|194856448|ref|XP_001968752.1| GG24326 [Drosophila erecta] gi|195342622|ref|XP_002037899.1| GM18045 [Drosophila sechellia] gi|195472803|ref|XP_002088688.1| GE18705 [Drosophila yakuba] gi|195550871|ref|XP_002076121.1| GD11985 [Drosophila simulans] gi|190660619|gb|EDV57811.1| GG24326 [Drosophila erecta] gi|194132749|gb|EDW54317.1| GM18045 [Drosophila sechellia] gi|194174789|gb|EDW88400.1| GE18705 [Drosophila yakuba] gi|194201770|gb|EDX15346.1| GD11985 [Drosophila simulans] gi|272406899|gb|ACL82997.2| Tfb5 [Drosophila melanogaster]

 Score = 91.3 bits (225), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 43/69 (62%), Positives = 56/69 (81%), Gaps = 2/69 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLDE   LGR+FIIQDLDE HLFIS+D++E+L  RVDDL+D+
Sbjct: 6  KGVLVEC--DPAMKQFLLHLDEKLALGRKFIIQDLDENHLFISTDIVEVLQARVDDLMDR 63

Query: 88 ISFPINDRD 96
          ISFP++D+D
Sbjct: 64 ISFPLHDKD 72

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289743363|gb|ADD20429.1| putative BBOX Zn-finger protein [Glossina morsitans morsitans]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 42/69 (60%), Positives = 56/69 (81%), Gaps = 2/69 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLDET  LGR+FIIQDLDE HLFIS+D+++ L  RVDDL+D+
Sbjct: 6  KGVLVEC--DPAMKQFLLHLDETLALGRKFIIQDLDEKHLFISTDIVDALQARVDDLMDR 63

Query: 88 ISFPINDRD 96
          ISFP++++D
Sbjct: 64 ISFPLHEKD 72

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242011976|ref|XP_002426719.1| TFIIH basal transcription factor complex TTD-A subunit, putative [Pediculus humanus corporis] gi|212510890|gb|EEB13981.1| TFIIH basal transcription factor complex TTD-A subunit, putative [Pediculus humanus corporis]

 Score = 88.6 bits (218), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 41/68 (60%), Positives = 56/68 (82%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D+ MKQFLLHLDET  LG++FIIQDLD+THLFISSD++ +L T+VDDL+DQ
Sbjct: 6  KGVLVEC--DQAMKQFLLHLDETLALGKKFIIQDLDDTHLFISSDILYILQTKVDDLIDQ 63

Query: 88 ISFPINDR 95
          IS P+ ++
Sbjct: 64 ISAPVTEK 71

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194761538|ref|XP_001962986.1| GF15714 [Drosophila ananassae] gi|190616683|gb|EDV32207.1| GF15714 [Drosophila ananassae]

 Score = 88.2 bits (217), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 42/69 (60%), Positives = 56/69 (81%), Gaps = 2/69 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLDE   LGR+FIIQDLDE HLFIS+D++++L  RVDDL+D+
Sbjct: 6  KGVLVEC--DPAMKQFLLHLDEKLALGRKFIIQDLDEHHLFISTDIVDVLQARVDDLMDR 63

Query: 88 ISFPINDRD 96
          ISFP++D+D
Sbjct: 64 ISFPLHDKD 72

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195114636|ref|XP_002001873.1| GI14600 [Drosophila mojavensis] gi|193912448|gb|EDW11315.1| GI14600 [Drosophila mojavensis]

 Score = 88.2 bits (217), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 41/69 (59%), Positives = 56/69 (81%), Gaps = 2/69 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLDE   LGR+FIIQDLDE HLFIS+D++E+L  RVD+L+D+
Sbjct: 6  KGVLVEC--DPAMKQFLLHLDEKLALGRKFIIQDLDENHLFISTDIVEVLQARVDELMDR 63

Query: 88 ISFPINDRD 96
          ISFP++++D
Sbjct: 64 ISFPLHEKD 72

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427785875|gb|JAA58389.1| Putative proteinral transcription factor iie tfiie subunit [Rhipicephalus pulchellus]

 Score = 87.4 bits (215), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 37/68 (54%), Positives = 57/68 (83%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLD+TN LG++FIIQDLDETH+FI+++++E L  ++DD++DQ
Sbjct: 6  KGILVEC--DPAMKQFLLHLDDTNALGKKFIIQDLDETHVFITAEILETLQNKIDDIMDQ 63

Query: 88 ISFPINDR 95
          ISFP++++
Sbjct: 64 ISFPLSEK 71

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241646745|ref|XP_002411111.1| general transcription factor IIE (TFIIE) subunit, putative [Ixodes scapularis] gi|215503741|gb|EEC13235.1| general transcription factor IIE (TFIIE) subunit, putative [Ixodes scapularis] gi|442749503|gb|JAA66911.1| Putative proteinral transcription factor iie tfiie subunit [Ixodes ricinus]

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 38/68 (55%), Positives = 56/68 (82%), Gaps = 2/68 (2%)

Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  ++ C  D  MKQFLLHLD+TN LGR+FIIQDLDETH+FI++D+++ L  ++DD++DQ
Sbjct: 6  KGILVEC--DPAMKQFLLHLDDTNALGRKFIIQDLDETHVFITADILDTLQNKIDDIMDQ 63

Query: 88 ISFPINDR 95
          ISFP+ ++
Sbjct: 64 ISFPLAEK 71

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

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	96
FB|FBgn0259719	73	Tfb5 [Drosophila melanogaster	0.666	0.876	0.651	1.5e-19
ZFIN|ZDB-GENE-041001-144	71	gtf2h5 "general transcription	0.656	0.887	0.553	1.3e-15
UNIPROTKB|Q5ZKH0	71	GTF2H5 "General transcription	0.656	0.887	0.553	2.6e-15
UNIPROTKB|Q2T9Z5	71	GTF2H5 "General transcription	0.656	0.887	0.476	1.6e-13
UNIPROTKB|E2RRJ1	71	GTF2H5 "Uncharacterized protei	0.656	0.887	0.476	1.6e-13
UNIPROTKB|Q6ZYL4	71	GTF2H5 "General transcription	0.656	0.887	0.476	1.6e-13
UNIPROTKB|F2Z5A9	71	GTF2H5 "Uncharacterized protei	0.656	0.887	0.476	1.6e-13
RGD|1560991	71	Gtf2h5 "general transcription	0.656	0.887	0.476	1.6e-13
MGI|MGI:107227	71	Gtf2h5 "general transcription	0.656	0.887	0.476	2.1e-13
RGD|2319072	71	LOC100365408 "general transcri	0.635	0.859	0.437	9.4e-11

FB|FBgn0259719 Tfb5 [Drosophila melanogaster (taxid:7227)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 43/66 (65%), Positives = 55/66 (83%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             ++ C  D  MKQFLLHLDE   LGR+FIIQDLDE HLFIS+D++E+L  RVDDL+D+ISF
Sbjct:     9 LVEC--DPAMKQFLLHLDEKLALGRKFIIQDLDENHLFISTDIVEVLQARVDDLMDRISF 66

Query:    91 PINDRD 96
             P++D+D
Sbjct:    67 PLHDKD 72

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

GO:0000439 "core TFIIH complex" evidence=IDA

GO:0005675 "holo TFIIH complex" evidence=IDA

GO:0001111 "promoter clearance from RNA polymerase II promoter" evidence=ISS

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

GO:0005634 "nucleus" evidence=IDA

GO:0001113 "transcriptional open complex formation at RNA polymerase II promoter" evidence=ISS

GO:0006289 "nucleotide-excision repair" evidence=IDA

GO:0009411 "response to UV" evidence=IDA

ZFIN|ZDB-GENE-041001-144 gtf2h5 "general transcription factor IIH, polypeptide 5" [Danio rerio (taxid:7955)]

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 36/65 (55%), Positives = 52/65 (80%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             ++ C  D  MKQFLL+LDET+ LG++FIIQDLD+TH+FI ++V+++L  RV +L+DQ SF
Sbjct:     9 LVEC--DPAMKQFLLYLDETSALGKKFIIQDLDDTHVFILAEVVQILQERVGELMDQNSF 66

Query:    91 PINDR 95
             PI  +
Sbjct:    67 PITQK 71

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

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

UNIPROTKB|Q5ZKH0 GTF2H5 "General transcription factor IIH subunit 5" [Gallus gallus (taxid:9031)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 36/65 (55%), Positives = 50/65 (76%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             +I C  D  MKQFLL+LDE+N LG++FIIQDLDETH+F+ ++++  L  RV +L+DQ SF
Sbjct:     9 LIEC--DPAMKQFLLYLDESNALGKKFIIQDLDETHVFVLAELVNFLQERVGELMDQNSF 66

Query:    91 PINDR 95
             PI  +
Sbjct:    67 PITQK 71

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

UNIPROTKB|Q2T9Z5 GTF2H5 "General transcription factor IIH subunit 5" [Bos taurus (taxid:9913)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 31/65 (47%), Positives = 50/65 (76%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F
Sbjct:     9 LIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAF 66

Query:    91 PINDR 95
              +  +
Sbjct:    67 SLTQK 71

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

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

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|E2RRJ1 GTF2H5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 31/65 (47%), Positives = 50/65 (76%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F
Sbjct:     9 LIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAF 66

Query:    91 PINDR 95
              +  +
Sbjct:    67 SLTQK 71

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

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|Q6ZYL4 GTF2H5 "General transcription factor IIH subunit 5" [Homo sapiens (taxid:9606)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 31/65 (47%), Positives = 50/65 (76%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F
Sbjct:     9 LIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAF 66

Query:    91 PINDR 95
              +  +
Sbjct:    67 SLTQK 71

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

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

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

UNIPROTKB|F2Z5A9 GTF2H5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 31/65 (47%), Positives = 50/65 (76%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F
Sbjct:     9 LIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAF 66

Query:    91 PINDR 95
              +  +
Sbjct:    67 SLTQK 71

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

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

RGD|1560991 Gtf2h5 "general transcription factor IIH, polypeptide 5" [Rattus norvegicus (taxid:10116)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 31/65 (47%), Positives = 50/65 (76%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F
Sbjct:     9 LIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAF 66

Query:    91 PINDR 95
              +  +
Sbjct:    67 SLTQK 71

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

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

MGI|MGI:107227 Gtf2h5 "general transcription factor IIH, polypeptide 5" [Mus musculus (taxid:10090)]

 Score = 175 (66.7 bits), Expect = 2.1e-13, P = 2.1e-13
 Identities = 31/65 (47%), Positives = 49/65 (75%)

Query:    31 IIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
             +I C  D  MKQFLL+LDE N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F
Sbjct:     9 LIEC--DPAMKQFLLYLDEANALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAF 66

Query:    91 PINDR 95
              +  +
Sbjct:    67 SLTQK 71

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

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

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

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

RGD|2319072 LOC100365408 "general transcription factor IIH, polypeptide 5-like" [Rattus norvegicus (taxid:10116)]

 Score = 150 (57.9 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 28/64 (43%), Positives = 46/64 (71%)

Query:    24 NTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDD 83
             NTL +  +I C  D   KQF L+L+E+N LG++F+IQD+D+TH F+  +++ +L  +V +
Sbjct:     3 NTL-KGVLIEC--DSATKQFFLYLNESNALGKKFVIQDIDDTHAFVIVELVNVLQEQVGE 59

Query:    84 LLDQ 87
             L+DQ
Sbjct:    60 LMDQ 63

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6ZYL4	TF2H5_HUMAN	No assigned EC number	0.4558	0.6875	0.9295	yes	N/A
Q2T9Z5	TF2H5_BOVIN	No assigned EC number	0.4558	0.6875	0.9295	yes	N/A
Q8K2X8	TF2H5_MOUSE	No assigned EC number	0.4558	0.6875	0.9295	yes	N/A
Q5ZKH0	TF2H5_CHICK	No assigned EC number	0.5294	0.6875	0.9295	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	96
pfam06331	68	pfam06331, Tbf5, Transcription factor TFIIH comple	2e-16

>gnl|CDD|218993 pfam06331, Tbf5, Transcription factor TFIIH complex subunit Tfb5

 Score = 66.8 bits (164), Expect = 2e-16
 Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPIND 94
          D  +KQ +LH+DE    G  FII+DLD+THL +   V+E L   ++ LL++  +   +
Sbjct: 13 DPSIKQIILHIDEQEHHG--FIIEDLDDTHLLVKESVVEFLKEELERLLEENIYNPTE 68

This family is a component of the general transcription and DNA repair factor IIH. TFB5 has been shown to be required for efficient recruitment of TFIIH to a promoter. Length = 68

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	96
PF06331	68	Tbf5: Transcription factor TFIIH complex subunit T	100.0
KOG3451|consensus	71		99.97

>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1

Probab=100.00  E-value=1.4e-33  Score=183.89  Aligned_cols=68  Identities=47%  Similarity=0.854  Sum_probs=60.4

Q ss_pred             cccccceeEEeecCCHHHHHHHHHhhccCCCCCCeEEEecCCceEEEccchHHHHHHHHHHHHhhcCCCCCC
Q psy2291          23 TNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPIND   94 (96)
Q Consensus        23 ~~~~~kGvLI~C~~DpaiKq~Il~Lde~~~~~~kFIIeDLDdtHLfVk~~~v~~Lk~~l~~~ld~nsy~~~~   94 (96)
                      |++|.|||||+|  ||||||||++||+++++|  |||+|||||||||+++++++||+||+++|++|+|+++|
T Consensus         1 Mv~a~kGvLv~C--Dpa~Kq~il~ld~~~~~~--FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~~   68 (68)
T PF06331_consen    1 MVNAIKGVLVEC--DPAIKQFILHLDESMPHG--FIIEDLDDTHLFVKPDVVEMLKEELDELLDQNSYPPTE   68 (68)
T ss_dssp             --EEEEEEEEES---HHHHHHHHHHHHHCCTS--SEEEEECTTEEEE-CCCHHHHHHHHHHCCCC-TTTTS-
T ss_pred             CCceeeeEEEEc--CHHHHHHHHHHhcCCCCC--eEEEEcCCCeEEEcHhHHHHHHHHHHHHHHhcCCCCCC
Confidence            678999999999  999999999999988876  99999999999999999999999999999999999875

These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.

>KOG3451|consensus

Probab=99.97  E-value=1.2e-30  Score=171.50  Aligned_cols=71  Identities=28%  Similarity=0.691  Sum_probs=68.3

Q ss_pred             cccccceeEEeecCCHHHHHHHHHhhccCCCCCCeEEEecCCceEEEccchHHHHHHHHHHHHhhcCCCCCCC
Q psy2291          23 TNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDR   95 (96)
Q Consensus        23 ~~~~~kGvLI~C~~DpaiKq~Il~Lde~~~~~~kFIIeDLDdtHLfVk~~~v~~Lk~~l~~~ld~nsy~~~~~   95 (96)
                      |++|.|||||+|  |||+||+|+++|+++++|.+|||++||||||||+|++++++|.+|+++|++|+|++.++
T Consensus         1 Mvna~KGvlV~c--Dp~~kqlilnmd~sm~~~skfii~eLDdthLfV~p~~vemvk~~le~~le~n~ye~~~e   71 (71)
T KOG3451|consen    1 MVNAKKGVLVTC--DPAFKQLILNMDDSMQLGSKFIIEELDDTHLFVNPSIVEMVKNELERILENNNYEAVDE   71 (71)
T ss_pred             CCccccceEEec--ChhHHHHhhhccccCCCCCCeeEEEeccceeeecHHHHHHHHHHHHHHHHhcCCCcCCC
Confidence            578999999999  99999999999999999999999999999999999999999999999999999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	96
2jnj_A	74	Solution Structure Of The P8 Tfiih Subunit Length =		8e-14
1ydl_A	79	Crystal Structure Of The Human Tfiih, Northeast Str		1e-12

>pdb|2JNJ|A Chain A, Solution Structure Of The P8 Tfiih Subunit Length = 74

Iteration: 1
 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 51/68 (75%), Gaps = 2/68 (2%)
Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  +I C  D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ
Sbjct: 9  KGVLIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQ 66
Query: 88 ISFPINDR 95
           +F +  +
Sbjct: 67 NAFSLTQK 74

>pdb|1YDL|A Chain A, Crystal Structure Of The Human Tfiih, Northeast Structural Genomics Target Hr2045 Length = 79

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 30/68 (44%), Positives = 49/68 (72%), Gaps = 2/68 (2%)
Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
          +  +I C  D   KQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L DQ
Sbjct: 14 KGXLIEC--DPAXKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELXDQ 71
Query: 88 ISFPINDR 95
           +F +  +
Sbjct: 72 NAFSLTQK 79

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
1ydl_A	79	TFIIH, general transcription factor IIH, polypepti	3e-20
3dgp_B	71	RNA polymerase II transcription factor B subunit;	3e-15

>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A Length = 79

 Score = 76.4 bits (188), Expect = 3e-20
 Identities = 29/59 (49%), Positives = 47/59 (79%)

Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDR 95
          D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F +  +
Sbjct: 21 DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK 79

>3dgp_B RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} PDB: 3dom_B Length = 71

 Score = 63.2 bits (154), Expect = 3e-15
 Identities = 13/60 (21%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDRD 96
          D  +K  +L +D         ++++LD+THL ++   +E +   ++ LL +  +   D +
Sbjct: 12 DPSIKALILQIDAKM---SDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPMDEE 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
1ydl_A	79	TFIIH, general transcription factor IIH, polypepti	100.0
3dgp_B	71	RNA polymerase II transcription factor B subunit;	99.98
1ydl_A	79	TFIIH, general transcription factor IIH, polypepti	88.98

>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A

Probab=100.00  E-value=3.1e-34  Score=191.04  Aligned_cols=70  Identities=44%  Similarity=0.879  Sum_probs=68.2

Q ss_pred             ccccceeEEeecCCHHHHHHHHHhhccCCCCCCeEEEecCCceEEEccchHHHHHHHHHHHHhhcCCCCCCC
Q psy2291          24 NTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDR   95 (96)
Q Consensus        24 ~~~~kGvLI~C~~DpaiKq~Il~Lde~~~~~~kFIIeDLDdtHLfVk~~~v~~Lk~~l~~~ld~nsy~~~~~   95 (96)
                      -++.|||||+|  ||||||||++||+++|+|++|||+|||||||||+|+++++||+||+++|++|+|++.||
T Consensus        10 ~~~~kGvLI~C--Dpa~Kq~Il~lde~~~~~~kFIIedLDdtHLfV~~~~v~~lk~~l~~~ld~ns~~~~~k   79 (79)
T 1ydl_A           10 HGTRKGMLIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK   79 (79)
T ss_dssp             CCCCCCEEEEC--CHHHHHHHHHHHHTTTTSSCCEEEECSSSEEEECTTHHHHHHHHHHHTSCCCTTTTTTC
T ss_pred             cccccceEEEe--CHHHHHHHHHHhccCCcCCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCcccC
Confidence            57899999999  99999999999999999999999999999999999999999999999999999999986

>3dgp_B RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} SCOP: d.295.1.0 PDB: 3dom_B

Probab=99.98  E-value=5.2e-33  Score=181.92  Aligned_cols=67  Identities=21%  Similarity=0.509  Sum_probs=60.5

Q ss_pred             ccccceeEEeecCCHHHHHHHHHhhccCCCCCCeEEEecCCceEEEccchHHHHHHHHHHHHhhcCCCCCCC
Q psy2291          24 NTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDR   95 (96)
Q Consensus        24 ~~~~kGvLI~C~~DpaiKq~Il~Lde~~~~~~kFIIeDLDdtHLfVk~~~v~~Lk~~l~~~ld~nsy~~~~~   95 (96)
                      ++|+|||||+|  ||||||||++||++   +++|||+|||||||||+++++++||+||+++|++|+|++++.
T Consensus         1 ~~A~kGvLi~C--Dpa~Kq~il~lde~---~~~FIIedLDdtHl~V~~~~v~~lk~~l~~~l~~n~~~~~~~   67 (71)
T 3dgp_B            1 ARARKGALVQC--DPSIKALILQIDAK---MSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPMDE   67 (71)
T ss_dssp             CEEEEEEEEEC--CHHHHHHHHHHHHH---HCSSEEEEEETTEEEECGGGHHHHHHHHHHHHHSCSCC----
T ss_pred             CCceeEEEEEc--CHHHHHHHHHHcCC---CCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCCccc
Confidence            47899999999  99999999999998   349999999999999999999999999999999999999875

>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A

Probab=88.98  E-value=0.088  Score=34.51  Aligned_cols=25  Identities=64%  Similarity=0.994  Sum_probs=22.0

Q ss_pred             CcchhhhheeccccccccceeEEee
Q psy2291          10 DKPMKQFLLHLDETNTLGRRFIIHC   34 (96)
Q Consensus        10 ~~~~~~~~~~l~~~~~~~kGvLI~C   34 (96)
                      +-+||||++||++..++.+..+|+=
T Consensus        21 Dpa~Kq~Il~lde~~~~~~kFIIed   45 (79)
T 1ydl_A           21 DPAMKQFLLYLDESNALGKKFIIQD   45 (79)
T ss_dssp             CHHHHHHHHHHHHTTTTSSCCEEEE
T ss_pred             CHHHHHHHHHHhccCCcCCCEEEEE
Confidence            5789999999999999988888763

---

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	96
d1ydla1	66	d.295.1.1 (A:6-71) General transcription factor II	1e-20

>d1ydla1 d.295.1.1 (A:6-71) General transcription factor IIH polypeptide 5, TFB5 {Human (Homo sapiens) [TaxId: 9606]} Length = 66

class: Alpha and beta proteins (a+b)
fold: TFB5-like
superfamily: TFB5-like
family: TFB5-like
domain: General transcription factor IIH polypeptide 5, TFB5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.8 bits (187), Expect = 1e-20
 Identities = 29/59 (49%), Positives = 47/59 (79%)

Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDR 95
          D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F +  +
Sbjct: 8  DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	96
d1ydla1	66	General transcription factor IIH polypeptide 5, TF	100.0
d1ydla1	66	General transcription factor IIH polypeptide 5, TF	91.72

>d1ydla1 d.295.1.1 (A:6-71) General transcription factor IIH polypeptide 5, TFB5 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: TFB5-like
superfamily: TFB5-like
family: TFB5-like
domain: General transcription factor IIH polypeptide 5, TFB5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3e-35  Score=188.70  Aligned_cols=66  Identities=47%  Similarity=0.943  Sum_probs=65.0

Q ss_pred             ceeEEeecCCHHHHHHHHHhhccCCCCCCeEEEecCCceEEEccchHHHHHHHHHHHHhhcCCCCCCC
Q psy2291          28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDR   95 (96)
Q Consensus        28 kGvLI~C~~DpaiKq~Il~Lde~~~~~~kFIIeDLDdtHLfVk~~~v~~Lk~~l~~~ld~nsy~~~~~   95 (96)
                      |||||+|  ||||||||+|||+++|+|++|||+|||||||||+|+++++||+||+++|++|+|++.||
T Consensus         1 KGvLv~C--Dp~~Kq~il~ld~~~~~~~kFII~dLDdtHl~V~~~~~~~lk~~l~~l~d~nsy~~~~k   66 (66)
T d1ydla1           1 KGMLIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK   66 (66)
T ss_dssp             CCEEEEC--CHHHHHHHHHHHHTTTTSSCCEEEECSSSEEEECTTHHHHHHHHHHHTSCCCTTTTTTC
T ss_pred             CcEEEEc--CHHHHHHHHHhccCCccCCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCcccC
Confidence            7999999  99999999999999999999999999999999999999999999999999999999986

>d1ydla1 d.295.1.1 (A:6-71) General transcription factor IIH polypeptide 5, TFB5 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: TFB5-like
superfamily: TFB5-like
family: TFB5-like
domain: General transcription factor IIH polypeptide 5, TFB5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.72  E-value=0.017  Score=35.16  Aligned_cols=25  Identities=64%  Similarity=0.994  Sum_probs=22.2

Q ss_pred             CcchhhhheeccccccccceeEEee
Q psy2291          10 DKPMKQFLLHLDETNTLGRRFIIHC   34 (96)
Q Consensus        10 ~~~~~~~~~~l~~~~~~~kGvLI~C   34 (96)
                      +-+||||++|+++..++.+..+|+=
T Consensus         8 Dp~~Kq~il~ld~~~~~~~kFII~d   32 (66)
T d1ydla1           8 DPAMKQFLLYLDESNALGKKFIIQD   32 (66)
T ss_dssp             CHHHHHHHHHHHHTTTTSSCCEEEE
T ss_pred             CHHHHHHHHHhccCCccCCCEEEEE
Confidence            5789999999999999988888874