Citrus Sinensis ID: 029410

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190----
Protein Sequence
MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLIL
Secondary Structure (PSIPRED)
cEEEEccHHHHHHHcccccccccccccccccEEEEEEccccccccccccccccccEEEEEEccccccccccEEEccccccccccEEEEEcccccEEEEEEEEEEEEEEcccccHHHHHHHHHHHHHHHccccccEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEEEc
Secondary Structure Prediction (SSPRO)
cccEcccHHHHHHHHHccccccccccccccEEEEEEcccccccccccccccccccEEEEEEccccccccccEEEEccccccccEEEEEEccccEEEEEEEEEEEcccccccccHHHHHHHHHHHHHHHcccccEEEEEEcccccccccccccEEccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEEc
Coil and Loop (DISEMBL)
mwlmkcpalvsrslkipssdnddddsarpVAKVILSidplqsnedssssssssstRFTMELIStesgnapkrysmdmskdlipmsvfaessngkisvegkiknkfdmrphhenmeNYGKLCRERTnkymtksrqiqvidndngshmrpmpgmmisTGFTVLWLTSFLCSVELCFALCyfwenpfsVYIQVRLIL
Flexible Loop (DISEMBL)
mwlmkcpalvsrslkipssdnddddsaRPVAKVILsidplqsnedssssssssstrfTMELIstesgnapkrYSMDMSKDLIPMSVFaessngkisvegkiknkfdmrphhenmenYGKLCRERTNKYmtksrqiqvidndngshmRPMPGMMISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLIL
Low Complexity Region (SEG)
MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDsssssssssTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLIL
Disordered region (IsUnstruct)
********************************************************************************************************************************************************MISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLI*
Disordered Region (DISOPRED)
MWLMKCPALVSR**********************LSI***********************LIS***GNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYG***************************MRPMPGMMISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLIL
Disordered Region (DISEMBL)
MWLMKCPALVSRSLKIP*********ARPVAKVILSIDP******************TMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLIL
Disordered Region (DISPRO)
MWLMKCPALVSRSLKIPS*********RPVAKVILSIDPLQSN*****SSSSSSTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLIL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTVLWLTSFLCSVELCFALCYFWENPFSVYIQVRLIL
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	194
255587521	278	Transcription initiation factor IIF subu	0.762	0.532	0.696	3e-54
356511855	252	PREDICTED: general transcription factor	0.731	0.563	0.673	7e-53
225449108	257	PREDICTED: general transcription factor	0.773	0.583	0.672	7e-51
296086049	300	unnamed protein product [Vitis vinifera]	0.773	0.5	0.672	2e-50
147863867	584	hypothetical protein VITISV_005903 [Viti	0.798	0.265	0.636	8e-50
297819938	258	hypothetical protein ARALYDRAFT_348323 [	0.747	0.562	0.620	1e-47
449452114	277	PREDICTED: general transcription factor	0.737	0.516	0.651	1e-47
255538806	257	Transcription initiation factor IIF subu	0.721	0.544	0.581	2e-47
449469921	260	PREDICTED: transcription initiation fact	0.721	0.538	0.603	2e-46
334185929	269	Transcription initiation factor IIF, bet	0.768	0.553	0.625	1e-45

>gi|255587521|ref|XP_002534300.1| Transcription initiation factor IIF subunit beta, putative [Ricinus communis] gi|223525544|gb|EEF28082.1| Transcription initiation factor IIF subunit beta, putative [Ricinus communis]

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 110/158 (69%), Positives = 128/158 (81%), Gaps = 10/158 (6%)

Query: 1   MWLMKCPALVSRSLKI-PSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTM 59
           +WLMKCPALVS SLK  PSS   D+D +RP+AKVILSI+PL SN+D+SS       +FTM
Sbjct: 40  VWLMKCPALVSNSLKKNPSSP--DNDPSRPIAKVILSINPLNSNDDNSSR------QFTM 91

Query: 60  ELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGK 119
           EL   ESGNAPK YSMDMS+D IPM V +ES+ GK+SVEGKI  KFDMRPH EN+ENY K
Sbjct: 92  ELAGNESGNAPKSYSMDMSEDFIPMFVLSESAQGKVSVEGKILYKFDMRPHTENLENYAK 151

Query: 120 LCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTG 157
           +CRERT KYMTK RQIQ+IDNDNGSHMRPMP +MI++G
Sbjct: 152 MCRERTKKYMTKGRQIQIIDNDNGSHMRPMP-LMIASG 188

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356511855|ref|XP_003524637.1| PREDICTED: general transcription factor IIF subunit 2-like [Glycine max]

 Score =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 103/153 (67%), Positives = 122/153 (79%), Gaps = 11/153 (7%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP LVSRSL+ P SD      +RPVAKV++SIDPL SN+D S        +FTME
Sbjct: 20  VWLMKCPPLVSRSLRAPPSD-----PSRPVAKVVVSIDPLNSNDDDSPP------QFTME 68

Query: 61  LISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKL 120
           L  TE+G+ P+ Y MDMSKD IPMSVF+++  GKISVEGKI NKFDMRPH++ +E YGKL
Sbjct: 69  LAGTEAGHIPRCYVMDMSKDFIPMSVFSDTPQGKISVEGKILNKFDMRPHNQTLELYGKL 128

Query: 121 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMM 153
           CRERTNKYM KSRQIQVIDND+G+HMRPMPGM+
Sbjct: 129 CRERTNKYMVKSRQIQVIDNDSGAHMRPMPGMI 161

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225449108|ref|XP_002274802.1| PREDICTED: general transcription factor IIF subunit 2 [Vitis vinifera]

 Score =  205 bits (522), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 107/159 (67%), Positives = 130/159 (81%), Gaps = 9/159 (5%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP +VSRSL   S+ +    S RPVAKVI+S+DPL +N+D  S       +FTME
Sbjct: 20  VWLMKCPPVVSRSLSSSSASD----SLRPVAKVIVSLDPLLANDDDDSPP-----QFTME 70

Query: 61  LISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKL 120
           L  TESGNAPK YSMDMS+D IPM+VF+ESS G+ +VEGKI NKFDM+PH+EN++NYGKL
Sbjct: 71  LAGTESGNAPKCYSMDMSQDFIPMAVFSESSQGRTAVEGKILNKFDMKPHNENIQNYGKL 130

Query: 121 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFT 159
           CRERT+KYMTKSRQIQVIDNDNGSHMRPMPGM+I++  +
Sbjct: 131 CRERTSKYMTKSRQIQVIDNDNGSHMRPMPGMVIASAVS 169

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086049|emb|CBI31490.3| unnamed protein product [Vitis vinifera]

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 107/159 (67%), Positives = 130/159 (81%), Gaps = 9/159 (5%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP +VSRSL   S+ +    S RPVAKVI+S+DPL +N+D  S       +FTME
Sbjct: 63  VWLMKCPPVVSRSLSSSSASD----SLRPVAKVIVSLDPLLANDDDDSPP-----QFTME 113

Query: 61  LISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKL 120
           L  TESGNAPK YSMDMS+D IPM+VF+ESS G+ +VEGKI NKFDM+PH+EN++NYGKL
Sbjct: 114 LAGTESGNAPKCYSMDMSQDFIPMAVFSESSQGETAVEGKILNKFDMKPHNENIQNYGKL 173

Query: 121 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFT 159
           CRERT+KYMTKSRQIQVIDNDNGSHMRPMPGM+I++  +
Sbjct: 174 CRERTSKYMTKSRQIQVIDNDNGSHMRPMPGMVIASAVS 212

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147863867|emb|CAN81117.1| hypothetical protein VITISV_005903 [Vitis vinifera]

 Score =  202 bits (513), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 107/168 (63%), Positives = 128/168 (76%), Gaps = 13/168 (7%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSS-------- 52
           +WLMKCP +VSRS     S +   DS RPVAKVI+S+DPL +N+D  S            
Sbjct: 20  VWLMKCPPVVSRS----LSSSSASDSLRPVAKVIVSLDPLLANDDDDSPPQGFMIAHEHA 75

Query: 53  -SSTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHH 111
                FTMEL  TESGNAPK YSMDMS+D IPM+VF+ESS G+ +VEGKI NKFDM+PH+
Sbjct: 76  FDYELFTMELAGTESGNAPKCYSMDMSQDFIPMAVFSESSQGRTAVEGKILNKFDMKPHN 135

Query: 112 ENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFT 159
           EN++NYGKLCRERT+KYMTKSRQIQVIDNDNGSHMRPMPGM+I++  +
Sbjct: 136 ENIQNYGKLCRERTSKYMTKSRQIQVIDNDNGSHMRPMPGMVIASAVS 183

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297819938|ref|XP_002877852.1| hypothetical protein ARALYDRAFT_348323 [Arabidopsis lyrata subsp. lyrata] gi|297323690|gb|EFH54111.1| hypothetical protein ARALYDRAFT_348323 [Arabidopsis lyrata subsp. lyrata]

 Score =  195 bits (495), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/158 (62%), Positives = 118/158 (74%), Gaps = 13/158 (8%)

Query: 1   MWLMKCPALVSRSLK-IPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTM 59
           M LMK P+LV+ SL+ +P  D    D  RP AKVIL++D L        +     T+F M
Sbjct: 27  MLLMKAPSLVASSLQSLPFPD----DPYRPDAKVILNVDLL--------APEDEETKFVM 74

Query: 60  ELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGK 119
           EL   ESGN P+RY++DMSKD IPM+VF ESS+GK+SVEGKIKNKFDMRPH+EN+E+YG+
Sbjct: 75  ELARAESGNMPRRYTLDMSKDFIPMNVFCESSDGKMSVEGKIKNKFDMRPHNENIESYGR 134

Query: 120 LCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTG 157
           LCRERTNKYM K+RQIQVIDN  G HMRPMPGM+I T 
Sbjct: 135 LCRERTNKYMGKNRQIQVIDNARGMHMRPMPGMIIPTA 172

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452114|ref|XP_004143805.1| PREDICTED: general transcription factor IIF subunit 2-like [Cucumis sativus]

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 99/152 (65%), Positives = 118/152 (77%), Gaps = 9/152 (5%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           MWL+KCP LV+R+L      N  D  +RPVAKVI+S+DPLQS    +    SSST FTME
Sbjct: 39  MWLLKCPQLVTRAL-----SNSPDAPSRPVAKVIVSVDPLQS----NDDDDSSSTEFTME 89

Query: 61  LISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKL 120
           L ST+SGNA + YS++MS D IPMSVF+ESS GK ++EGKI NKFDM+PH +N+E YGKL
Sbjct: 90  LASTDSGNALRSYSLNMSTDFIPMSVFSESSQGKFTIEGKILNKFDMKPHDQNLERYGKL 149

Query: 121 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGM 152
           CRERT+K MTKSRQIQVID+  G HMRPMPGM
Sbjct: 150 CRERTHKSMTKSRQIQVIDHVTGGHMRPMPGM 181

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538806|ref|XP_002510468.1| Transcription initiation factor IIF subunit beta, putative [Ricinus communis] gi|223551169|gb|EEF52655.1| Transcription initiation factor IIF subunit beta, putative [Ricinus communis]

 Score =  193 bits (491), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 89/153 (58%), Positives = 120/153 (78%), Gaps = 13/153 (8%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP +V+RS K  +S +D    + PVAKV+LS+DPL+S++         S +FTME
Sbjct: 21  VWLMKCPLVVARSWKSHASSSD----SHPVAKVVLSLDPLRSDD---------SLQFTME 67

Query: 61  LISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKL 120
           +  TE+GN PK YS++M KD +PMSVF+E++ G++++EGK+++KFDM+PH ENME YG+L
Sbjct: 68  MAGTENGNVPKSYSLNMFKDFVPMSVFSETTQGRVAIEGKVEHKFDMKPHEENMEEYGRL 127

Query: 121 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMM 153
           CRERTNK M K+RQIQVIDND G HMRPMPGM+
Sbjct: 128 CRERTNKSMIKNRQIQVIDNDRGVHMRPMPGMV 160

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449469921|ref|XP_004152667.1| PREDICTED: transcription initiation factor IIF subunit beta-like [Cucumis sativus] gi|449520699|ref|XP_004167371.1| PREDICTED: transcription initiation factor IIF subunit beta-like [Cucumis sativus]

 Score =  191 bits (484), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 93/154 (60%), Positives = 119/154 (77%), Gaps = 14/154 (9%)

Query: 1   MWLMKCPALVSRSLKI-PSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTM 59
           +WLMKCP LV++S +  P SD      + P+AKVILS+DPLQS+E       SSS +F M
Sbjct: 23  VWLMKCPLLVAKSWQAHPPSD------SLPLAKVILSLDPLQSDE-------SSSLQFKM 69

Query: 60  ELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGK 119
           E+  TE+GN PK +S++M KD +PM VF+E+S GK+S+EGK+++KFDM+PH EN+E YGK
Sbjct: 70  EMAGTETGNVPKSFSLNMFKDFVPMCVFSEASQGKVSMEGKVEHKFDMKPHSENLEMYGK 129

Query: 120 LCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMM 153
           LCRERTNK M K+RQIQVIDND G HMRPMPGM+
Sbjct: 130 LCRERTNKSMVKNRQIQVIDNDRGVHMRPMPGMV 163

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185929|ref|NP_190795.3| Transcription initiation factor IIF, beta subunit [Arabidopsis thaliana] gi|332645403|gb|AEE78924.1| Transcription initiation factor IIF, beta subunit [Arabidopsis thaliana]

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 100/160 (62%), Positives = 120/160 (75%), Gaps = 11/160 (6%)

Query: 1   MWLMKCPALVSRSLKIPS---SDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRF 57
           M LMK P+LV+ SL+  S        DD  RP AKVIL +DPL ++ED         T+F
Sbjct: 32  MLLMKAPSLVASSLQSHSFPDDPYRPDDPYRPDAKVILGVDPL-AHEDEG-------TQF 83

Query: 58  TMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENY 117
            MEL   +SGN P+RY++DMSKD IPM+VF ESS+GK+SVEGKIKNKFDMRPH+EN+E+Y
Sbjct: 84  VMELARADSGNMPRRYTLDMSKDFIPMNVFCESSDGKMSVEGKIKNKFDMRPHNENIESY 143

Query: 118 GKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTG 157
           G+LCRERTNKYM K+RQIQVIDN  G HMRPMPGM+I T 
Sbjct: 144 GRLCRERTNKYMGKNRQIQVIDNARGMHMRPMPGMIIPTA 183

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	194
TAIR|locus:2005674	261	AT1G75510 [Arabidopsis thalian	0.742	0.551	0.439	6e-32

TAIR|locus:2005674 AT1G75510 [Arabidopsis thaliana (taxid:3702)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 69/157 (43%), Positives = 100/157 (63%)

Query:     1 MWLMKCPALVSRSL-KIPSSDNDD---DDSARPVAKVILSIDPLQSNEDXXXXXXXXXTR 56
             +WLMKCP +V ++  KI +S +      DS   +AK++  +DPL+ +             
Sbjct:    16 IWLMKCPVVVDKAWHKIAASSSSSFASSDSPPDMAKIVREVDPLRDDSP---------PE 66

Query:    57 FTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMEN 116
             F M ++  E GN PK Y+++M  D +PM  F++ + G  + EGK+ +KFDM+P+ E +E 
Sbjct:    67 FKMYMVGAEYGNMPKCYALNMFTDFVPMGGFSDVNQGCAAAEGKVDHKFDMKPYGETIEE 126

Query:   117 YGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMM 153
             Y +LCRERT+K M K+RQIQVIDND G HMRPMPGM+
Sbjct:   127 YARLCRERTSKAMVKNRQIQVIDNDRGVHMRPMPGML 163


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        0.320   0.133   0.403    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      194       185   0.00080  110 3  11 22  0.42    32
                                                     31  0.41    35


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:  1
  No. of states in DFA:  597 (63 KB)
  Total size of DFA:  171 KB (2100 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:  17.55u 0.13s 17.68t   Elapsed:  00:00:01
  Total cpu time:  17.55u 0.13s 17.68t   Elapsed:  00:00:01
  Start:  Fri May 10 19:05:09 2013   End:  Fri May 10 19:05:10 2013

GO:0003824 "catalytic activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0005674 "transcription factor TFIIF complex" evidence=IEA;ISS

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

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

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" 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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	194
pfam02270	259	pfam02270, TFIIF_beta, Transcription initiation fa	2e-09

>gnl|CDD|216954 pfam02270, TFIIF_beta, Transcription initiation factor IIF, beta subunit

 Score = 54.7 bits (132), Expect = 2e-09
 Identities = 36/179 (20%), Positives = 60/179 (33%), Gaps = 49/179 (27%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WL+K P  +S       S    D     V K+ +  +            +  S     E
Sbjct: 13  VWLVKVPKYLSEKW----SKAPGDSGGE-VGKLRIKKNNGGK--------AQVSLLLNEE 59

Query: 61  LISTESGNAPKRYSMDMSKDLI-PMSVFAESS---------------------------- 91
           L + +    PK Y +DM    +    VF ES+                            
Sbjct: 60  LENYD---IPKEYDLDMQNVNVQNTYVFTESNLGKYKQKSKEVAGMPEQPQLAYPYVKTI 116

Query: 92  NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMP 150
             K ++EG++ ++ + RP     E Y +L ++R  K     R +QV+D          P
Sbjct: 117 PKKTALEGRVVHECECRPVEN--EEYMRLKKKRILKASKPKRTVQVLDKI--VTQSYKP 171

Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. Length = 259

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	194
KOG2905	254	consensus Transcription initiation factor IIF, sma	100.0
PF02270	275	TFIIF_beta: Transcription initiation factor IIF, b	99.97
COG5090	297	TFG2 Transcription initiation factor IIF, small su	99.8

>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]

Probab=100.00  E-value=8.5e-36  Score=258.87  Aligned_cols=145  Identities=29%  Similarity=0.504  Sum_probs=126.5

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEeeCCCCCCCCCCCCCCCCccEEEEE-----e--cCCCCCCCCcce
Q 029410            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME-----L--ISTESGNAPKRY   73 (194)
Q Consensus         1 VWLVKVPkyvS~~W~ka~~~~~~~d~~~~VgKv~I~~dp~~~~d~~~~~~~~~~v~ftLe-----l--~~~e~~~iPKey   73 (194)
                      |||||||+||+++|.++++       .+.+|+++|++.++.           ++++|.|.     .  ...+.+++|..|
T Consensus        20 vWLvKvP~fLa~kw~~~~~-------~~e~g~l~i~k~~~d-----------aki~l~L~e~~p~~~~~~a~~g~~p~~~   81 (254)
T KOG2905|consen   20 VWLVKVPKFLAEKWRKIPN-------SHESGKLRINKTPSD-----------AKIVLLLNEAIPEKQEREADVGKFPQQY   81 (254)
T ss_pred             EEEEeccHHHHHHHHhccc-------ccccccccccCCCCc-----------ceEEEEeccccccchhhhhhcccCchhh
Confidence            7999999999999998765       134999999998854           56788776     2  334578999999


Q ss_pred             ecccccCCceeEEEeeec-CCceEEEEEeeeeeeeecCCCChHHHHHHHHHHhhhhhccccceEEeccCCCCccccCCCc
Q 029410           74 SMDMSKDLIPMSVFAESS-NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGM  152 (194)
Q Consensus        74 ~L~m~~~~qpm~VFSe~~-~gklalEGkVv~K~dcRP~~~~~~~YmkLkr~ri~kas~ptRqvQ~Ld~~v~~~~kP~pg~  152 (194)
                      .++|+..+.||+|||+++ ++++++||+|+|+|||||+++  ++||||||+||.||+.|.|++|+||+++|++|+|+||+
T Consensus        82 ~~~~~~~~~~~~~~sd~~~~~k~a~eG~V~~e~~~~P~~n--e~Y~Rl~r~r~~k~~~k~r~vQ~iD~~~g~~~~p~~~~  159 (254)
T KOG2905|consen   82 KLNMKRRFFNMFVESDSSGPKKTAVEGTVVHECDVRPSAN--EEYMRLKRERIVKASKKKRQVQVIDKVVGVHMKPVPGH  159 (254)
T ss_pred             hhccCccccceeeeecCCCCccceeeeeeeeeeecccccC--HHHHHHHHHHHHHhcCcccccccchhhcccccccCCCc
Confidence            999999999999999988 689999999999999999988  99999999999999999999999999999999999999


Q ss_pred             eecccccccccccceech
Q 029410          153 MISTGFTVLWLTSFLCSV  170 (194)
Q Consensus       153 ~~~s~~~~~~~~~~~~~~  170 (194)
                      +-+ .|+    ++|.+.+
T Consensus       160 ~~~-~~~----~~~~rkK  172 (254)
T KOG2905|consen  160 LRS-SSN----IAYERKK  172 (254)
T ss_pred             ccc-cch----hHHHHHh
Confidence            832 333    5666665

>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II

Probab=99.97  E-value=3.9e-31  Score=230.73  Aligned_cols=133  Identities=35%  Similarity=0.574  Sum_probs=67.5

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEeeCCCCCCCCCCCCCCCCccEEEEEecCCCCCCCCcceecccccC
Q 029410            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTESGNAPKRYSMDMSKD   80 (194)
Q Consensus         1 VWLVKVPkyvS~~W~ka~~~~~~~d~~~~VgKv~I~~dp~~~~d~~~~~~~~~~v~ftLel~~~e~~~iPKey~L~m~~~   80 (194)
                      |||||||+||+++|+++++    ++ +..||+|+|..+++          +...++|+|+....+.+++|++|.|.|+++
T Consensus        13 vWLvKVPk~l~e~W~~~~~----~~-~~~iG~lri~~~~~----------~~~~v~l~L~~~~~~~~~iPkey~L~~~~~   77 (275)
T PF02270_consen   13 VWLVKVPKFLSEKWSKAPD----DD-EIEIGKLRISKDPN----------GKPKVSLTLNDSLANHGNIPKEYDLDMSKD   77 (275)
T ss_dssp             EEEEEEEHHHHHHHTTSBT----T---TEEEEEEEEEE-T----------TEEEEEEEE-HHHHT-T-S--EEEEEEE--
T ss_pred             ccccccccccccccccccc----cc-cccccccccccccc----------cccccccccccccccccccccccccccccc
Confidence            7999999999999997654    12 23499999999832          235688888744444578999999999999


Q ss_pred             -CceeEEEeeecC-------------------------------------------CceEEEEEeeeeeeeecCCCChHH
Q 029410           81 -LIPMSVFAESSN-------------------------------------------GKISVEGKIKNKFDMRPHHENMEN  116 (194)
Q Consensus        81 -~qpm~VFSe~~~-------------------------------------------gklalEGkVv~K~dcRP~~~~~~~  116 (194)
                       .+||+||||.++                                           ++++|||+|.|+|+|+|..+  +.
T Consensus        78 ~~~n~~VFse~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~G~I~~~~~~~P~~~--~~  155 (275)
T PF02270_consen   78 NVQNMYVFSESDQPGFKAKNKERAGAPNAGIPASLLREKKKKDRKRKYQPYVKTIPKKTALEGRIVHECDCRPVLN--DE  155 (275)
T ss_dssp             TTEEEEEEEEETT----------------------------------------ETT--EEEEEEEEEEEEE---------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCceEEEEEEEEEEEeEECCC--HH
Confidence             599999999765                                           57899999999999999977  79


Q ss_pred             HHHHHHHHhhhhhccccceEEeccCCCCccccCC
Q 029410          117 YGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMP  150 (194)
Q Consensus       117 YmkLkr~ri~kas~ptRqvQ~Ld~~v~~~~kP~p  150 (194)
                      |++++|+|+.++++|+|++|+||+++.+.|+|+.
T Consensus       156 Y~~~~~~r~~~a~~~kr~~~~i~~~~~~~~~~~~  189 (275)
T PF02270_consen  156 YRRLKRERIEKANKPKRTVQQIDEDVSQSYKPVS  189 (275)
T ss_dssp             ----------------------------------
T ss_pred             HHHHHHHHHHHhcCCCCeeEEeccccccCCCCcc
Confidence            9999999999999999999999997766898854

Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.

>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]

Probab=99.80  E-value=1.3e-19  Score=158.70  Aligned_cols=143  Identities=20%  Similarity=0.324  Sum_probs=116.0

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEeeCCCCCCCCCCCCCCCCccEEEEEecCCCCCCCCcceecccccC
Q 029410            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTESGNAPKRYSMDMSKD   80 (194)
Q Consensus         1 VWLVKVPkyvS~~W~ka~~~~~~~d~~~~VgKv~I~~dp~~~~d~~~~~~~~~~v~ftLel~~~e~~~iPKey~L~m~~~   80 (194)
                      |||||||.||+++|..-+     .+.+..+|+++++.||             +.+++.|. +..+++.+|++|.|.+.+-
T Consensus        31 VWLvkvP~FLaekw~sr~-----~~~g~~lg~~r~~~d~-------------a~isLlL~-ne~~n~~~P~~ydl~i~~k   91 (297)
T COG5090          31 VWLVKVPLFLAEKWLSRE-----AEIGELLGTKRTSTDP-------------AVISLLLS-NEFCNGGFPSSYDLKIKPK   91 (297)
T ss_pred             EEEEeccHHHHHHHhcch-----hhhhhhhceeeecCCc-------------ceEEEEec-cCCccCCCCcceeeeeccc
Confidence            799999999999998322     2224459999999877             44677775 4456889999999999988


Q ss_pred             Cc-eeEEEeeecC----CceEEEEEeeeeeeeecCCCChHHHHHHHHHHhhhhhccccceEEeccCCCCccccCCCce-e
Q 029410           81 LI-PMSVFAESSN----GKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMM-I  154 (194)
Q Consensus        81 ~q-pm~VFSe~~~----gklalEGkVv~K~dcRP~~~~~~~YmkLkr~ri~kas~ptRqvQ~Ld~~v~~~~kP~pg~~-~  154 (194)
                      ++ .-.||.|+.+    .+.+++|+|-|.|-+.|..+  ++|+|.++.|--++..|.|.+|+||...+..+-  +|.+ .
T Consensus        92 ~v~n~yVfre~et~t~~k~tavvGtV~hEC~V~P~vN--d~Y~r~~q~r~~~~~~~K~~vq~iD~~~g~~~~--~~~~s~  167 (297)
T COG5090          92 DVNNYYVFRESETSTHEKNTAVVGTVNHECYVTPEVN--DEYLRYKQDRGFKSDSKKSDVQVIDYLKGGKRG--EKFGSL  167 (297)
T ss_pred             cccceEEEecccccccccccceeeeeccceeeccccc--HHHHHHHHHhhhhhcCccccceeeecccCceec--cCcccc
Confidence            66 6699977544    47999999999999999987  899999999999999999999999999997776  4444 4


Q ss_pred             cccccccccccceechh
Q 029410          155 STGFTVLWLTSFLCSVE  171 (194)
Q Consensus       155 ~s~~~~~~~~~~~~~~~  171 (194)
                      +| |+    ++||..+.
T Consensus       168 Rs-~~----~~fl~~~r  179 (297)
T COG5090         168 RS-ST----LEFLARKR  179 (297)
T ss_pred             cc-ch----HHHHHhcc
Confidence            44 55    78988753

---

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	194
1f3u_A	118	Transcription initiation factor IIF, beta subunit;	2e-16

>1f3u_A Transcription initiation factor IIF, beta subunit; general transcription initiation and elongation factor, RNA polymerase II; 1.70A {Homo sapiens} SCOP: b.65.1.1 Length = 118

 Score = 71.2 bits (174), Expect = 2e-16
 Identities = 23/110 (20%), Positives = 48/110 (43%), Gaps = 10/110 (9%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WL+K P  +S+     S   +       V K+ ++    ++  + S + +         
Sbjct: 17  VWLVKVPKYLSQQWAKASGRGE-------VGKLRIAKTQGRT--EVSFTLNEDLANIHDI 67

Query: 61  LISTESGNAPKRYSMDMSKDLI-PMSVFAESSNGKISVEGKIKNKFDMRP 109
                S +AP+ +   +       ++VF ESS+ K+S+EG +  + + RP
Sbjct: 68  GGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRP 117

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	194
1f3u_A	118	Transcription initiation factor IIF, beta subunit;	99.97

>1f3u_A Transcription initiation factor IIF, beta subunit; general transcription initiation and elongation factor, RNA polymerase II; 1.70A {Homo sapiens} SCOP: b.65.1.1

Probab=99.97  E-value=2.5e-31  Score=207.58  Aligned_cols=92  Identities=27%  Similarity=0.430  Sum_probs=79.0

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEeeCCCCCCCCCCCCCCCCccEEEEE--e-c------CCCCCCCCc
Q 029410            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME--L-I------STESGNAPK   71 (194)
Q Consensus         1 VWLVKVPkyvS~~W~ka~~~~~~~d~~~~VgKv~I~~dp~~~~d~~~~~~~~~~v~ftLe--l-~------~~e~~~iPK   71 (194)
                      |||||||+||+++|+++++       +..+|||+|..++++           .+++|+|+  + .      ..++.++||
T Consensus        17 VWLvKvPk~L~e~W~~~~~-------~~~vGkvri~~~~g~-----------~~v~l~L~~~~~~~~~~~~~~~~~~iPk   78 (118)
T 1f3u_A           17 VWLVKVPKYLSQQWAKASG-------RGEVGKLRIAKTQGR-----------TEVSFTLNEDLANIHDIGGKPASVSAPR   78 (118)
T ss_dssp             EEEEEEEHHHHHHHTTCCT-------TCEEEEEEEEEETTE-----------EEEEEEECHHHHTCCCTTCCCSTTCSCC
T ss_pred             EEEEECCHHHHHHHHhCCC-------CCceEEEEEecCCCc-----------eeEEEEeChhHhhhccccccccccCCCh
Confidence            7999999999999986643       235999999998764           45888887  2 2      124689999


Q ss_pred             ceecccccC-CceeEEEeeecCCceEEEEEeeeeeeeecC
Q 029410           72 RYSMDMSKD-LIPMSVFAESSNGKISVEGKIKNKFDMRPH  110 (194)
Q Consensus        72 ey~L~m~~~-~qpm~VFSe~~~gklalEGkVv~K~dcRP~  110 (194)
                      +|+|+|++. +|||+||||+++|+++|||+|+|||||||+
T Consensus        79 eY~l~~~~~~~~~~~VFSE~~~~~~a~EG~V~~k~d~rP~  118 (118)
T 1f3u_A           79 EHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA  118 (118)
T ss_dssp             EEEEEEECCTTSEEEEEEEETTCCEEEEEEEEEEEEECCC
T ss_pred             hceEEeeccCCceeEEEeccCCCcEEEEEEEEEEEEeecC
Confidence            999999995 999999999999999999999999999994

---

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	194
d1f3ua_	118	b.65.1.1 (A:) TFIIF beta subunit, Rap30 {Human (Ho	7e-24

>d1f3ua_ b.65.1.1 (A:) TFIIF beta subunit, Rap30 {Human (Homo sapiens) [TaxId: 9606]} Length = 118

class: All beta proteins
fold: triple barrel
superfamily: Rap30/74 interaction domains
family: Rap30/74 interaction domains
domain: TFIIF beta subunit, Rap30
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 88.8 bits (220), Expect = 7e-24
 Identities = 22/110 (20%), Positives = 46/110 (41%), Gaps = 10/110 (9%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WL+K P  +S+                 V K+ ++    ++  + S + +         
Sbjct: 17  VWLVKVPKYLSQQWA-------KASGRGEVGKLRIAKTQGRT--EVSFTLNEDLANIHDI 67

Query: 61  LISTESGNAPKRYSMDMSKDLI-PMSVFAESSNGKISVEGKIKNKFDMRP 109
                S +AP+ +   +       ++VF ESS+ K+S+EG +  + + RP
Sbjct: 68  GGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRP 117

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	194
d1f3ua_	118	TFIIF beta subunit, Rap30 {Human (Homo sapiens) [T	100.0

>d1f3ua_ b.65.1.1 (A:) TFIIF beta subunit, Rap30 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: triple barrel
superfamily: Rap30/74 interaction domains
family: Rap30/74 interaction domains
domain: TFIIF beta subunit, Rap30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.3e-34  Score=221.83  Aligned_cols=92  Identities=27%  Similarity=0.424  Sum_probs=80.6

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEeeCCCCCCCCCCCCCCCCccEEEEE--e-------cCCCCCCCCc
Q 029410            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME--L-------ISTESGNAPK   71 (194)
Q Consensus         1 VWLVKVPkyvS~~W~ka~~~~~~~d~~~~VgKv~I~~dp~~~~d~~~~~~~~~~v~ftLe--l-------~~~e~~~iPK   71 (194)
                      ||||||||||+++|+++++       +..||||+|.++|++           .+++|+|+  +       ..+++++|||
T Consensus        17 VWLvKvPkyls~~W~k~~~-------~~~vGklri~~~~~k-----------~ev~l~l~~~~~~~~~~~~~~~~~~iPk   78 (118)
T d1f3ua_          17 VWLVKVPKYLSQQWAKASG-------RGEVGKLRIAKTQGR-----------TEVSFTLNEDLANIHDIGGKPASVSAPR   78 (118)
T ss_dssp             EEEEEEEHHHHHHHTTCCT-------TCEEEEEEEEEETTE-----------EEEEEEECHHHHTCCCTTCCCSTTCSCC
T ss_pred             EEEEECCHHHHHHHhhCCC-------CCcceEEEeccCCCC-----------cceEEecCchHhhhhccccCCCcCCCCh
Confidence            7999999999999998744       234999999999987           45888886  1       1345789999


Q ss_pred             ceecccccC-CceeEEEeeecCCceEEEEEeeeeeeeecC
Q 029410           72 RYSMDMSKD-LIPMSVFAESSNGKISVEGKIKNKFDMRPH  110 (194)
Q Consensus        72 ey~L~m~~~-~qpm~VFSe~~~gklalEGkVv~K~dcRP~  110 (194)
                      +|+|+|+++ .|||+||||+++|+++|||+|+|||||||+
T Consensus        79 ey~l~~~~~~~q~~~VFSe~~~~k~~~EG~V~~k~d~RPa  118 (118)
T d1f3ua_          79 EHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA  118 (118)
T ss_dssp             EEEEEEECCTTSEEEEEEEETTCCEEEEEEEEEEEEECCC
T ss_pred             hhcEecccccCCceEEEEecCCCcEEEEEEEEEEeecCCC
Confidence            999999999 789999999999999999999999999995