Citrus Sinensis ID: 046686

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70
Protein Sequence
IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK
Secondary Structure (PSIPRED)
ccEEcccccccccccEEEEcccccHHHHHHHHHHHHHccEEEEEcccccEEEEEcccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccEEcccEEEHcccccHHHHHHHHHHHHHcccEEEccccccEEEEcHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
irlwesdlnkdemtrvhyydefpsrdvFEAACDYardrsglqwedskKMRLVVKAEIHIHIREFLRGQNK
Flexible Loop (DISEMBL)
irlwesdlnkdemtrvhyydefpsrdVFEAACDYARdrsglqwedskkMRLVVKAEIHIHireflrgqnk
Low Complexity Region (SEG)
IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK
Disordered region (IsUnstruct)
*************TRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFL*****
Disordered Region (DISOPRED)
IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQ**
Disordered Region (DISEMBL)
IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK
Disordered Region (DISPRO)
IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQN*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK
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

No hits with e-value below 0.001 by BLAST

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	70
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.971	0.150	0.75	1e-24
224077128	449	predicted protein [Populus trichocarpa]	0.971	0.151	0.75	2e-24
296084734	258	unnamed protein product [Vitis vinifera]	0.942	0.255	0.757	2e-23
147854406	451	hypothetical protein VITISV_005315 [Viti	0.942	0.146	0.757	6e-23
359497087	238	PREDICTED: general transcription factor	0.942	0.277	0.757	6e-23
297800414	452	hypothetical protein ARALYDRAFT_493174 [	1.0	0.154	0.685	8e-23
357461579	452	General transcription factor IIH subunit	0.971	0.150	0.735	1e-22
358346685	451	General transcription factor IIH subunit	0.971	0.150	0.735	1e-22
51969958	452	unnamed protein product [Arabidopsis tha	1.0	0.154	0.671	2e-22
42566894	452	transcription initiation factor TFIIH su	1.0	0.154	0.671	2e-22

>gi|255556021|ref|XP_002519045.1| tfiih, polypeptide, putative [Ricinus communis] gi|223541708|gb|EEF43256.1| tfiih, polypeptide, putative [Ricinus communis]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 51/68 (75%), Positives = 62/68 (91%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWESD+N+ EMT  H YDEFPSRDVFEAAC++ARD +GL WEDSK+MR+VVKAEIH++
Sbjct: 383 IRLWESDMNRVEMTPAHLYDEFPSRDVFEAACNFARDWNGLLWEDSKRMRMVVKAEIHLN 442

Query: 61  IREFLRGQ 68
           +RE+LRGQ
Sbjct: 443 MREYLRGQ 450

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077128|ref|XP_002305144.1| predicted protein [Populus trichocarpa] gi|222848108|gb|EEE85655.1| predicted protein [Populus trichocarpa]

 Score =  115 bits (289), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/68 (75%), Positives = 62/68 (91%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE+DLN+ E+T  H+YDEFPSRD FEAACD+AR+ +GL WEDSKKMR+VVKAEIH++
Sbjct: 381 IRLWEADLNRVEITPSHFYDEFPSRDTFEAACDFAREWNGLLWEDSKKMRVVVKAEIHMN 440

Query: 61  IREFLRGQ 68
           +REFLRGQ
Sbjct: 441 MREFLRGQ 448

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296084734|emb|CBI25875.3| unnamed protein product [Vitis vinifera]

 Score =  113 bits (282), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/66 (75%), Positives = 57/66 (86%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE+DLN+ E    H YDEFPSRDVFEAACD+AR+  GL WEDSKKMRLVVKAEIH+H
Sbjct: 190 IRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAREYGGLLWEDSKKMRLVVKAEIHLH 249

Query: 61  IREFLR 66
           +RE+LR
Sbjct: 250 MREYLR 255

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147854406|emb|CAN81292.1| hypothetical protein VITISV_005315 [Vitis vinifera]

 Score =  111 bits (277), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 50/66 (75%), Positives = 57/66 (86%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE+DLN+ E    H YDEFPSRDVFEAACD+AR+  GL WEDSKKMRLVVKAEIH+H
Sbjct: 383 IRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAREYGGLLWEDSKKMRLVVKAEIHLH 442

Query: 61  IREFLR 66
           +RE+LR
Sbjct: 443 MREYLR 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497087|ref|XP_002267711.2| PREDICTED: general transcription factor IIH subunit 4-like [Vitis vinifera]

 Score =  111 bits (277), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 57/66 (86%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE+DLN+ E    H YDEFPSRDVFEAACD+AR+  GL WEDSKKMRLVVKAEIH+H
Sbjct: 170 IRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAREYGGLLWEDSKKMRLVVKAEIHLH 229

Query: 61  IREFLR 66
           +RE+LR
Sbjct: 230 MREYLR 235

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297800414|ref|XP_002868091.1| hypothetical protein ARALYDRAFT_493174 [Arabidopsis lyrata subsp. lyrata] gi|297313927|gb|EFH44350.1| hypothetical protein ARALYDRAFT_493174 [Arabidopsis lyrata subsp. lyrata]

 Score =  110 bits (276), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 48/70 (68%), Positives = 59/70 (84%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE+DL + EMT+ H+YDEFPS+DVFEAACD+AR+  GL WEDSK+MRLVVK+E+H  
Sbjct: 383 IRLWETDLKRIEMTQAHFYDEFPSKDVFEAACDFAREWGGLLWEDSKRMRLVVKSEVHNQ 442

Query: 61  IREFLRGQNK 70
           +REFL  Q K
Sbjct: 443 MREFLHNQTK 452

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461579|ref|XP_003601071.1| General transcription factor IIH subunit [Medicago truncatula] gi|355490119|gb|AES71322.1| General transcription factor IIH subunit [Medicago truncatula]

 Score =  110 bits (274), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 50/68 (73%), Positives = 58/68 (85%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWESDLN+ EMT  +YYDEFPSRDVFE ACD AR+ SGL WEDSKKM LVVK+E+H +
Sbjct: 384 IRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTY 443

Query: 61  IREFLRGQ 68
           +R+FLR Q
Sbjct: 444 VRDFLRRQ 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358346685|ref|XP_003637396.1| General transcription factor IIH subunit [Medicago truncatula] gi|355503331|gb|AES84534.1| General transcription factor IIH subunit [Medicago truncatula]

 Score =  110 bits (274), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 50/68 (73%), Positives = 58/68 (85%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWESDLN+ EMT  +YYDEFPSRDVFE ACD AR+ SGL WEDSKKM LVVK+E+H +
Sbjct: 383 IRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTY 442

Query: 61  IREFLRGQ 68
           +R+FLR Q
Sbjct: 443 VRDFLRRQ 450

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51969958|dbj|BAD43671.1| unnamed protein product [Arabidopsis thaliana]

 Score =  109 bits (273), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 47/70 (67%), Positives = 60/70 (85%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE+DL + EMT+ H+YDEFPS+DVFEAACD+AR+  GL WEDSK+MRLVVK+E+H  
Sbjct: 383 IRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAREWRGLLWEDSKRMRLVVKSEVHNQ 442

Query: 61  IREFLRGQNK 70
           +REFL  Q++
Sbjct: 443 MREFLHTQSR 452

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42566894|ref|NP_193435.2| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana] gi|51969678|dbj|BAD43531.1| unnamed protein product [Arabidopsis thaliana] gi|115646777|gb|ABJ17114.1| At4g17020 [Arabidopsis thaliana] gi|332658439|gb|AEE83839.1| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana]

 Score =  109 bits (272), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 47/70 (67%), Positives = 60/70 (85%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE+DL + EMT+ H+YDEFPS+DVFEAACD+AR+  GL WEDSK+MRLVVK+E+H  
Sbjct: 383 IRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAREWRGLLWEDSKRMRLVVKSEVHNQ 442

Query: 61  IREFLRGQNK 70
           +REFL  Q++
Sbjct: 443 MREFLHTQSR 452

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	70
WB|WBGene00013529	481	Y73F8A.24 [Caenorhabditis eleg	0.942	0.137	0.303	2.8e-06
DICTYBASE|DDB_G0293228	483	gtf2h4 "TFIIH subunit" [Dictyo	0.942	0.136	0.318	0.00032

WB|WBGene00013529 Y73F8A.24 [Caenorhabditis elegans (taxid:6239)]

 Score = 117 (46.2 bits), Expect = 2.8e-06, P = 2.8e-06
 Identities = 20/66 (30%), Positives = 37/66 (56%)

Query:     1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
             IRLWE +  +  +   + Y  F S D F   C+YAR ++ L W D+++  ++V  + H  
Sbjct:   397 IRLWEDERRRMNLKDAYIYSHFESEDEFHGVCEYARQQNILLWSDNQQKLVIVNEDGHEL 456

Query:    61 IREFLR 66
             +R++ +
Sbjct:   457 VRQWYK 462

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

DICTYBASE|DDB_G0293228 gtf2h4 "TFIIH subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 98 (39.6 bits), Expect = 0.00032, P = 0.00032
 Identities = 21/66 (31%), Positives = 35/66 (53%)

Query:     1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
             I LWE++ N+   T+   Y+ FP+ D + A   +A+++    W       LVVK E +  
Sbjct:   414 ILLWEAERNRITYTKSVLYNSFPTNDCYIATLKFAKEQDYYIWSHDPLKTLVVKEEGNDP 473

Query:    61 IREFLR 66
             IR F++
Sbjct:   474 IRNFIK 479


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.137   0.424    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       70        70   0.00091  102 3  11 22  0.45    28
                                                     29  0.41    29


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  569 (61 KB)
  Total size of DFA:  117 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.48u 0.14s 8.62t   Elapsed:  00:00:01
  Total cpu time:  8.48u 0.14s 8.62t   Elapsed:  00:00:01
  Start:  Mon May 20 21:00:23 2013   End:  Mon May 20 21:00:24 2013

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

GO:0005634 "nucleus" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0005675 "holo TFIIH complex" evidence=ISS

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

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

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

GO:0006281 "DNA repair" evidence=IEA

GO:0044351 "macropinocytosis" 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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pg.C_LG_IV0538	hypothetical protein (449 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_LG_I000900	hypothetical protein (803 aa)				•	•	•	•		0.885
	eugene3.00020503	hypothetical protein (758 aa)				•	•	•	•		0.836
	gw1.V.5266.1	hypothetical protein (289 aa)					•	•	•		0.795
	estExt_fgenesh4_pm.C_1650003	hypothetical protein (413 aa)				•	•	•	•		0.744
	estExt_Genewise1_v1.C_1330021	hypothetical protein (334 aa)						•	•		0.573
	estExt_Genewise1_v1.C_LG_IX3069	SubName- Full=Putative uncharacterized protein; (117 aa)				•		•			0.494
	grail3.0014029901	hypothetical protein (52 aa)						•			0.479
	gw1.70.559.1	hypothetical protein (329 aa)						•	•		0.472
	gw1.IX.2304.1	hypothetical protein (321 aa)						•			0.442
	fgenesh4_pg.C_scaffold_82000017	hypothetical protein (603 aa)						•	•		0.432

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	70
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	2e-07
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	4e-07

>gnl|CDD|233058 TIGR00625, tfb2, Transcription factor tfb2

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 21/70 (30%), Positives = 34/70 (48%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLWE + ++   T    Y++F ++  FE    YAR+   L WE+S K    +    H  
Sbjct: 379 IRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSD 438

Query: 61  IREFLRGQNK 70
           ++ F + Q  
Sbjct: 439 VKRFWKRQKH 448

All proteins in this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 448

>gnl|CDD|227473 COG5144, TFB2, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]

 Score = 44.5 bits (105), Expect = 4e-07
 Identities = 19/66 (28%), Positives = 32/66 (48%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           I LWE + N+  M   + Y +F +   ++   +YA     L W D  K    +K E H  
Sbjct: 377 IVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSL 436

Query: 61  IREFLR 66
           ++EF++
Sbjct: 437 VKEFVK 442

Length = 447

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	70
TIGR00625	448	tfb2 Transcription factor tfb2. This family is bas	99.96
KOG3471	465	consensus RNA polymerase II transcription initiati	99.96
COG5144	447	TFB2 RNA polymerase II transcription initiation/nu	99.91
PF10566	273	Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro:	81.51

>TIGR00625 tfb2 Transcription factor tfb2

Probab=99.96  E-value=3.2e-30  Score=196.89  Aligned_cols=70  Identities=30%  Similarity=0.527  Sum_probs=68.9

Q ss_pred             CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhcC
Q 046686            1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK   70 (70)
Q Consensus         1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~~   70 (70)
                      |||||+||||+++++||||++|+|++||+++++||+++|||+|+|++||+|||+++||++|++|||++++
T Consensus       379 i~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~  448 (448)
T TIGR00625       379 IRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH  448 (448)
T ss_pred             HHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence            7999999999999999999999999999999999999999999999999999999999999999999985

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]

Probab=99.96  E-value=2.9e-30  Score=196.33  Aligned_cols=70  Identities=37%  Similarity=0.574  Sum_probs=68.4

Q ss_pred             CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhcC
Q 046686            1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK   70 (70)
Q Consensus         1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~~   70 (70)
                      |||||+||||+.++|||||++|+|..||+.+++||+++|+|+|+|+.||+|||+++||++|++|||+++|
T Consensus       394 IrLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k  463 (465)
T KOG3471|consen  394 IRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK  463 (465)
T ss_pred             HHHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence            8999999999999999999999999999999999999999999999999999999999999999999764

>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]

Probab=99.91  E-value=3.3e-25  Score=166.47  Aligned_cols=69  Identities=28%  Similarity=0.423  Sum_probs=67.7

Q ss_pred             CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhc
Q 046686            1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQN   69 (70)
Q Consensus         1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~   69 (70)
                      |+|||+||||+.++||+||+||.+.++|+.+++||++.|||+|+|+.||||||+.+||.+|++|+|++-
T Consensus       377 I~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l  445 (447)
T COG5144         377 IVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL  445 (447)
T ss_pred             eeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence            799999999999999999999999999999999999999999999999999999999999999999974

>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro: IPR019563 O-Glycosyl hydrolases 3

Probab=81.51  E-value=3.5  Score=30.31  Aligned_cols=24  Identities=21%  Similarity=0.343  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHcC--eEEeeeCCc
Q 046686           25 RDVFEAACDYARDRS--GLQWEDSKK   48 (70)
Q Consensus        25 ~~~fe~~~~yA~~~g--vLlW~~~~k   48 (70)
                      ..+-..|++||++.|  |+||-+...
T Consensus        72 ~~dl~elv~Ya~~KgVgi~lw~~~~~   97 (273)
T PF10566_consen   72 DFDLPELVDYAKEKGVGIWLWYHSET   97 (273)
T ss_dssp             T--HHHHHHHHHHTT-EEEEEEECCH
T ss_pred             ccCHHHHHHHHHHcCCCEEEEEeCCc
Confidence            567889999999999  899988765

2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands []. ; PDB: 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A 3A24_A.

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	70
3dgp_A	80	RNA polymerase II transcription factor B subunit;	8e-21
3dom_A	108	RNA polymerase II transcription factor B subunit;	4e-20

>3dgp_A RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} Length = 80

 Score = 76.4 bits (188), Expect = 8e-21
 Identities = 18/70 (25%), Positives = 34/70 (48%)

Query: 1  IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
          IRLW+ +L++        Y +F +   +     YA+D   L W+D KK +  +  E +  
Sbjct: 8  IRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQ 67

Query: 61 IREFLRGQNK 70
          + +F + + K
Sbjct: 68 VLDFAKRKLK 77

>3dom_A RNA polymerase II transcription factor B subunit; protein-protein complex, heterodimer, beta-alpha-beta split, strand addition; 2.60A {Saccharomyces cerevisiae} Length = 108

 Score = 75.7 bits (186), Expect = 4e-20
 Identities = 18/70 (25%), Positives = 34/70 (48%)

Query: 1   IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIH 60
           IRLW+ +L++        Y +F +   +     YA+D   L W+D KK +  +  E +  
Sbjct: 36  IRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQ 95

Query: 61  IREFLRGQNK 70
           + +F + + K
Sbjct: 96  VLDFAKRKLK 105

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	70
3dgp_A	80	RNA polymerase II transcription factor B subunit;	100.0
3dom_A	108	RNA polymerase II transcription factor B subunit;	100.0

>3dgp_A RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.9e-41  Score=205.69  Aligned_cols=70  Identities=26%  Similarity=0.516  Sum_probs=61.7

Q ss_pred             CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhcC
Q 046686            1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK   70 (70)
Q Consensus         1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~~   70 (70)
                      |||||+|||||++++||||++|+|+++|+++++||+++|||||+|+.+|+|||+++||++|++|||++++
T Consensus         8 IrLWe~ErnRl~~~~g~Ly~~F~s~~efe~~~~yA~e~gvLlW~~~~kr~~~V~~~gh~~vk~f~k~~~~   77 (80)
T 3dgp_A            8 IRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK   77 (80)
T ss_dssp             ------CGGGCEEEEEEEEECCSCHHHHHHHHHHHHHTTCEEEEETTTTEEEEEGGGHHHHHHHHTTC--
T ss_pred             HHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHHHHHHHHHHh
Confidence            8999999999999999999999999999999999999999999999999999999999999999999874

>3dom_A RNA polymerase II transcription factor B subunit; protein-protein complex, heterodimer, beta-alpha-beta split, strand addition; 2.60A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.1e-38  Score=205.17  Aligned_cols=70  Identities=26%  Similarity=0.516  Sum_probs=68.2

Q ss_pred             CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhcC
Q 046686            1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK   70 (70)
Q Consensus         1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~~   70 (70)
                      |||||+|||||++++||||++|+|+++|+++++||+++|||||+|+.+|+|||+.+||++|++|||++++
T Consensus        36 IrLWE~ErnRl~~~~G~LY~dF~s~~efe~v~~yA~e~gvLlW~d~~kr~~~Vs~egh~~vk~f~Kr~~~  105 (108)
T 3dom_A           36 IRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK  105 (108)
T ss_dssp             HHHHHHHHTTCEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEGGGTEEEEEGGGHHHHHHHHHHHC-
T ss_pred             HHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHHHHHHHHHHh
Confidence            8999999999999999999999999999999999999999999999999999999999999999999874

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	70
d1kwma2	95	Procarboxypeptidase B {Human (Homo sapiens) [TaxId	86.65
d1qbaa3	443	Bacterial chitobiase (beta-N-acetylhexosaminidase)	81.43

>d1kwma2 d.58.3.1 (A:1A-95A) Procarboxypeptidase B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Protease propeptides/inhibitors
family: Pancreatic carboxypeptidase, activation domain
domain: Procarboxypeptidase B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.65  E-value=1.2  Score=24.84  Aligned_cols=47  Identities=15%  Similarity=0.212  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHHHHcCeEEeeeCCc--------ceEEEeccccHHHHHHHHhh
Q 046686           22 FPSRDVFEAACDYARDRSGLQWEDSKK--------MRLVVKAEIHIHIREFLRGQ   68 (70)
Q Consensus        22 F~s~~~fe~~~~yA~~~gvLlW~~~~k--------r~~~V~~~gh~~vr~f~k~~   68 (70)
                      ..|.+..+.+.+.+.+.++-.|..+..        --+.|+++....++++++..
T Consensus        17 ~~~~~q~~~L~~L~~~~~ldfW~~~s~~~~~~g~~vdv~V~p~~~~~~~~~L~~~   71 (95)
T d1kwma2          17 VEDENHINIIRELASTTQIDFWKPDSVTQIKPHSTVDFRVKAEDTVTVENVLKQN   71 (95)
T ss_dssp             ECSHHHHHHHHHHHHHSCEEEEESSSGGGCCSSEEEEEEECGGGHHHHHHHHHHT
T ss_pred             eCCHHHHHHHHHHhccCceEecCCCCccccCCCCeEEEEECHHHHHHHHHHHHHC
Confidence            456788999999999999999987642        14889998888899999874

>d1qbaa3 c.1.8.6 (A:338-780) Bacterial chitobiase (beta-N-acetylhexosaminidase) {Serratia marcescens [TaxId: 615]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: (Trans)glycosidases
family: beta-N-acetylhexosaminidase catalytic domain
domain: Bacterial chitobiase (beta-N-acetylhexosaminidase)
species: Serratia marcescens [TaxId: 615]

Probab=81.43  E-value=0.57  Score=32.08  Aligned_cols=25  Identities=28%  Similarity=0.299  Sum_probs=22.4

Q ss_pred             EecCCCCHHHHHHHHHHHHHcCeEE
Q 046686           18 YYDEFPSRDVFEAACDYARDRSGLQ   42 (70)
Q Consensus        18 Ly~~F~s~~~fe~~~~yA~~~gvLl   42 (70)
                      .++.|-|++|+..+++||++.||-|
T Consensus        82 ~~~~~YT~~ei~eiv~yA~~rgI~v  106 (443)
T d1qbaa3          82 VYGGFFSRQDYIDIIKYAQARQIEV  106 (443)
T ss_dssp             CEECCBCHHHHHHHHHHHHHTTCEE
T ss_pred             CCCCccCHHHHHHHHHHHHHcCCEE
Confidence            4678899999999999999999954