Citrus Sinensis ID: 025926

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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-------200-------210-------220-------230-------240------
Protein Sequence
MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAADGPAS
Secondary Structure (PSIPRED)
cEEEEccHHHHHHHcccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccEEcccccccccEEEEEcccccEEEEEEEEEEEEEEEccccHHHHHHHHHHHHHHHHcccccEEEEcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHccHHHHHHHHHHHHHHHHccccccccccccHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccEEEcHHHHHHHHHHccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccEEEEEEcccccccEEEEEcccccEEEEEEEEEEEEEEcccccHHHHHHHHHHHHHHHcccccEEEEEEccccccccccccccccccHHHHccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHccHHHHHHHHHHHHHHHHccccccccEEEcHHHHHccccccc
Coil and Loop (DISEMBL)
mwlmkcpalvsrslkipssdnddddsarpVAKVILSidplqsnedssssssssstRFTMELIStesgnapkrysmdmskdlipmsvfaessngkisvegkiknkfdmrphhenmeNYGKLCRERTnkymtksrqiqvidndngshmrpmpgmmistgftekkkpqpkgsevkrtrrdrgeMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYnnkgsnqgsyelkpeykkaadgpas
Flexible Loop (DISEMBL)
mwlmkcpalvsrslkipssdnddddsaRPVAKVILsidplqsnedssssssssstrfTMELIstesgnapkrYSMDMSKDLIPMSVFaessngkisvegkiknkfdmrphhenmenYGKLCRERTNKYmtksrqiqvidndngshmrpmPGMMistgftekkkpqpkgsevkrtrrdrgemEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKgsnqgsyelkpeykkaadgpas
Low Complexity Region (SEG)
MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDsssssssssTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAADGPAS
Disordered region (IsUnstruct)
***************************************************************************************************************************************************************************************IMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYN************************
Disordered Region (DISOPRED)
MWLMKCPALVSR*******************************************************************DL****VFAESSNGKISVEGKIKNKFDMRPHHENMEN***************************************************************EMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELK************
Disordered Region (DISEMBL)
MWLMKCPALVSRSLKIP*********ARPVAKVILSIDP******************TMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFT****************RDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPE**********
Disordered Region (DISPRO)
MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSID***************STRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMP***********************TRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAADGPAS
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	246	2.2.26 [Sep-21-2011]
Q2T9L9	249	General transcription fac	yes	no	0.601	0.594	0.329	2e-16
Q8R0A0	249	General transcription fac	yes	no	0.601	0.594	0.322	6e-16
P13984	249	General transcription fac	yes	no	0.601	0.594	0.322	9e-16
Q01750	249	General transcription fac	yes	no	0.601	0.594	0.322	1e-15
O94424	307	Transcription initiation	yes	no	0.715	0.573	0.308	2e-15
P41900	277	General transcription fac	yes	no	0.898	0.797	0.256	2e-15
Q03123	264	General transcription fac	N/A	no	0.601	0.560	0.275	3e-14
Q54KT7	241	General transcription fac	yes	no	0.609	0.622	0.314	5e-11
P41896	400	Transcription initiation	yes	no	0.495	0.305	0.320	2e-07

>sp|Q2T9L9|T2FB_BOVIN General transcription factor IIF subunit 2 OS=Bos taurus GN=GTF2F2 PE=2 SV=1

 Score = 85.9 bits (211), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 87/155 (56%), Gaps = 7/155 (4%)

Query: 84  MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
           ++VF ESS+ K+S+EG +  + + RP     ENY +L R +  +     R  Q +D    
Sbjct: 93  LTVFTESSSDKLSLEGIVVQRAECRPAAN--ENYMRLKRLQIEESSKPVRLSQQLDKVVT 150

Query: 144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
           ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct: 151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query: 204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
           T QP  +LKD+LK++ V N KG ++ ++ELKPEY+
Sbjct: 206 TKQPVSYLKDILKEIGVQNVKGIHKNTWELKPEYR 240

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.
Bos taurus (taxid: 9913)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp|Q8R0A0|T2FB_MOUSE General transcription factor IIF subunit 2 OS=Mus musculus GN=Gtf2f2 PE=1 SV=1

 Score = 84.3 bits (207), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 50/155 (32%), Positives = 87/155 (56%), Gaps = 7/155 (4%)

Query: 84  MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
           ++VF ESS+ K+S+EG +  + + RP     ENY KL R +  +     R  Q +D    
Sbjct: 93  LTVFTESSSDKLSLEGIVVQRAECRP--AASENYMKLKRLQIEESSKPVRLSQQLDKVVT 150

Query: 144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
           ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct: 151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query: 204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
           T QP  +LK++LK++ + N KG ++ ++ELKPEY+
Sbjct: 206 TKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 240

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P13984|T2FB_HUMAN General transcription factor IIF subunit 2 OS=Homo sapiens GN=GTF2F2 PE=1 SV=2

 Score = 84.0 bits (206), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 50/155 (32%), Positives = 87/155 (56%), Gaps = 7/155 (4%)

Query: 84  MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
           ++VF ESS+ K+S+EG +  + + RP     ENY +L R +  +     R  Q +D    
Sbjct: 93  LTVFTESSSDKLSLEGIVVQRAECRP--AASENYMRLKRLQIEESSKPVRLSQQLDKVVT 150

Query: 144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
           ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct: 151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query: 204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
           T QP  +LK++LK++ V N KG ++ ++ELKPEY+
Sbjct: 206 TKQPVVYLKEILKEIGVQNVKGIHKNTWELKPEYR 240

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q01750|T2FB_RAT General transcription factor IIF subunit 2 OS=Rattus norvegicus GN=Gtf2f2 PE=2 SV=1

 Score = 83.2 bits (204), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 50/155 (32%), Positives = 86/155 (55%), Gaps = 7/155 (4%)

Query: 84  MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
           ++VF ESS+ K+S+EG +  + + RP     ENY KL R +  +     R  Q  D    
Sbjct: 93  LTVFTESSSDKLSLEGIVVQRAECRP--AASENYMKLKRLQIEESSKPVRLSQQADKVVT 150

Query: 144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
           ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct: 151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query: 204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
           T QP  +LK++LK++ + N KG ++ ++ELKPEY+
Sbjct: 206 TKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 240

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O94424|T2FB_SCHPO Transcription initiation factor IIF subunit beta OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tfg2 PE=1 SV=1

 Score = 83.2 bits (204), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 59/191 (30%), Positives = 97/191 (50%), Gaps = 15/191 (7%)

Query: 63  STESGNAPKRYSMDMSKDLIPMS-VFAES----SNGKISVEGKIKNKFDMRPHHENMENY 117
           S E+ + PK Y++ +    +  S VF ES    S    ++ G + ++ ++ P     ++Y
Sbjct: 73  SPENADVPKIYNLRVMNKFVRNSYVFRESETSSSMKSTALVGTVAHECNVSPVIN--DDY 130

Query: 118 GKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMIS-----TGFTEKKKPQPKGSEVK 172
            ++ ++R        R++Q+ID+  GS +   PG + S     T F    KP+  G  +K
Sbjct: 131 RRVMQKRALAASAPKRKVQMIDDRGGSLL--APGTLGSRSRSTTSFIRNVKPR-TGEGLK 187

Query: 173 RTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYE 232
            +R  R E+ DI+FK FE    WTL+ L +   QPE +LK++L  + + N +G     Y 
Sbjct: 188 NSRIPRNELLDILFKCFEDYEYWTLKGLREYVKQPEVYLKEVLDSIAILNKRGPYALKYS 247

Query: 233 LKPEYKKAADG 243
           LKPEYK   D 
Sbjct: 248 LKPEYKGTMDA 258

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P41900|T2FB_DROME General transcription factor IIF subunit 2 OS=Drosophila melanogaster GN=TfIIFbeta PE=2 SV=2

 Score = 82.8 bits (203), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/250 (25%), Positives = 118/250 (47%), Gaps = 29/250 (11%)

Query: 1   MWLMKCPALVSRS------------LKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSS 48
           +WL+K P  +++             L+I  +       +  +   +L++DP +       
Sbjct: 25  VWLVKVPKYIAQKWEKAPTNMDVGKLRINKTPGQKAQVSLSLTPAVLALDPEEKIPTEHI 84

Query: 49  SSSSSSTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMR 108
              S  T+ T+ + S  + +  K  S   +         A+  N K+ +EG+I  K + R
Sbjct: 85  LDVSQVTKQTLGVFSHMAPSDGKENSTTSA---------AQPDNEKLYMEGRIVQKLECR 135

Query: 109 PHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKG 168
           P  +N   Y KL  E   K     R++Q ID     + +P+     +  + E+KK     
Sbjct: 136 PIADNC--YMKLKLESIRKASEPQRRVQPIDK-IVQNFKPVKDHAHNIEYRERKK----- 187

Query: 169 SEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQ 228
           +E K+ R D+  + D++F  FE+   + ++ L++ T+QP  +LK++LKD+C YN K  ++
Sbjct: 188 AEGKKARDDKNAVMDMLFHAFEKHQYYNIKDLVKITNQPISYLKEILKDVCDYNMKNPHK 247

Query: 229 GSYELKPEYK 238
             +ELK EY+
Sbjct: 248 NMWELKKEYR 257

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q03123|T2FB_XENLA General transcription factor IIF subunit 2 OS=Xenopus laevis GN=gtf2f2 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 46/167 (27%), Positives = 93/167 (55%), Gaps = 19/167 (11%)

Query: 84  MSVFAESSNG------------KISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTK 131
           ++V  ES +G            K+++EG + ++ + RP     +NY ++ R++  +    
Sbjct: 96  LTVLTESLSGQSEDKSENRVIDKLALEGIVVHRAECRP--AASDNYMQMKRKQIEESSKP 153

Query: 132 SRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFER 191
            RQ Q ++    S+ +P+     +  + +KKK      + KR R D+ ++ D++F  FE+
Sbjct: 154 KRQSQQLEKAVTSNYKPVSNHQYNIEYEKKKK-----DDGKRARVDKHQVLDMLFSAFEK 208

Query: 192 QSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
              + ++ L+  T QP  +LK++L+D+ +YN KG+++ ++ELKPEY+
Sbjct: 209 HQYYNIKDLVDITKQPVTYLKEILRDIGIYNMKGTHKNTWELKPEYR 255

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q54KT7|T2FB_DICDI General transcription factor IIF subunit 2 OS=Dictyostelium discoideum GN=gtf2f2 PE=3 SV=2

 Score = 68.6 bits (166), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 84/159 (52%), Gaps = 9/159 (5%)

Query: 83  PMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDN 142
           P+ +F+E  +G +++EG I  + D++   E+ + Y  L + R  KY TK+R  QVID   
Sbjct: 79  PLKIFSEDKDGALALEGNIGLRCDIKIDVESPQ-YRDLMKSRHTKYNTKTRMTQVIDESE 137

Query: 143 --GSHMRPMPGMMIST-GFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQ 199
                +     + +ST G T     Q K S  K+ +    E+ D++F  F  + +  L+ 
Sbjct: 138 LFTPTLFDANKVKVSTVGIT-----QKKKSTDKKEKLPEDEVLDLIFSAFRAEKHLDLKT 192

Query: 200 LIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
           L   T+QP+  LK +L+ +C+ N +G     YELKPE++
Sbjct: 193 LESFTEQPKNHLKTILEKVCILNKRGPYHHLYELKPEFR 231

TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P41896|T2FB_YEAST Transcription initiation factor IIF subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TFG2 PE=1 SV=2

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 41/128 (32%), Positives = 63/128 (49%), Gaps = 6/128 (4%)

Query: 116 NYGKLCRERTNKY-MTKSRQIQVIDNDNGSHMRPMPGMMI---STGFTEKKKPQPKGSEV 171
           NY K+  +R N   +    +I  +D   G  M    GM +   ++ F +  + + K S +
Sbjct: 232 NYHKIVEQRRNIVKLNNKERITTLDETVGVTM-SHTGMSMRSDNSNFLKVGREKAK-SNI 289

Query: 172 KRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSY 231
           K  R  + E+ D +FKLF+    W+L+ L + T QPE  LK+ L  +     KG     Y
Sbjct: 290 KSIRMPKKEILDYLFKLFDEYDYWSLKGLKERTRQPEAHLKECLDKVATLVKKGPYAFKY 349

Query: 232 ELKPEYKK 239
            L+PEYKK
Sbjct: 350 TLRPEYKK 357

TFIIF is a general transcription initiation factor that binds to RNA polymerase II. Its functions include the recruitment of RNA polymerase II to the promoter bound DNA-TBP-TFIIB complex, decreasing the affinity of RNA polymerase II for non-specific DNA, allowing for the subsequent recruitment of TFIIE and TFIIH, and facilitating RNA polymerase II elongation. TFG2 shows ATP-dependent DNA-helicase activity.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	246
255587521	278	Transcription initiation factor IIF subu	0.947	0.838	0.732	2e-98
225449108	257	PREDICTED: general transcription factor	0.947	0.906	0.719	6e-95
296086049	300	unnamed protein product [Vitis vinifera]	0.947	0.776	0.719	1e-94
356511855	252	PREDICTED: general transcription factor	0.939	0.916	0.692	2e-94
297819938	258	hypothetical protein ARALYDRAFT_348323 [	0.930	0.887	0.677	4e-89
334185929	269	Transcription initiation factor IIF, bet	0.947	0.866	0.684	9e-88
449469921	260	PREDICTED: transcription initiation fact	0.930	0.880	0.638	7e-86
449452114	277	PREDICTED: general transcription factor	0.947	0.841	0.650	1e-85
224085774	261	predicted protein [Populus trichocarpa]	0.947	0.892	0.604	1e-84
224062059	265	predicted protein [Populus trichocarpa]	0.943	0.875	0.616	5e-84

>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 =  363 bits (933), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 178/243 (73%), Positives = 205/243 (84%), Gaps = 10/243 (4%)

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 LCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRG 179
           +CRERT KYMTK RQIQ+IDNDNGSHMRPMP +MI++G  +KKKP  K ++VKRTRRDRG
Sbjct: 152 MCRERTKKYMTKGRQIQIIDNDNGSHMRPMP-LMIASGSNDKKKPPAKATDVKRTRRDRG 210

Query: 180 EMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKK 239
           EME IMFKLFERQ NWTLRQLIQETDQPEQFLKD+LK+LCVYNNKG+NQGSYELKPEYK+
Sbjct: 211 EMEAIMFKLFERQPNWTLRQLIQETDQPEQFLKDILKELCVYNNKGTNQGSYELKPEYKR 270

Query: 240 AAD 242
           + +
Sbjct: 271 STE 273

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  352 bits (904), Expect = 6e-95,   Method: Compositional matrix adjust.
 Identities = 174/242 (71%), Positives = 207/242 (85%), Gaps = 9/242 (3%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP +VSRS     S +   DS RPVAKVI+S+DPL +N+D  S       +FTME
Sbjct: 20  VWLMKCPPVVSRS----LSSSSASDSLRPVAKVIVSLDPLLANDDDDSPP-----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 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGE 180
           CRERT+KYMTKSRQIQVIDNDNGSHMRPMPGM+I++  ++KKK   KGS++KRTRRDRGE
Sbjct: 131 CRERTSKYMTKSRQIQVIDNDNGSHMRPMPGMVIASAVSDKKKMPTKGSDMKRTRRDRGE 190

Query: 181 MEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA 240
           ME+I+FKLFERQ NWTLRQLIQETDQPEQFLKD+LKDLCVYNNKG+NQG+YELKPEYK++
Sbjct: 191 MEEILFKLFERQPNWTLRQLIQETDQPEQFLKDLLKDLCVYNNKGTNQGTYELKPEYKRS 250

Query: 241 AD 242
            +
Sbjct: 251 GE 252

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 =  351 bits (901), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 174/242 (71%), Positives = 207/242 (85%), Gaps = 9/242 (3%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP +VSRS     S +   DS RPVAKVI+S+DPL +N+D  S       +FTME
Sbjct: 63  VWLMKCPPVVSRS----LSSSSASDSLRPVAKVIVSLDPLLANDDDDSPP-----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 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGE 180
           CRERT+KYMTKSRQIQVIDNDNGSHMRPMPGM+I++  ++KKK   KGS++KRTRRDRGE
Sbjct: 174 CRERTSKYMTKSRQIQVIDNDNGSHMRPMPGMVIASAVSDKKKMPTKGSDMKRTRRDRGE 233

Query: 181 MEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA 240
           ME+I+FKLFERQ NWTLRQLIQETDQPEQFLKD+LKDLCVYNNKG+NQG+YELKPEYK++
Sbjct: 234 MEEILFKLFERQPNWTLRQLIQETDQPEQFLKDLLKDLCVYNNKGTNQGTYELKPEYKRS 293

Query: 241 AD 242
            +
Sbjct: 294 GE 295

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  351 bits (901), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 169/244 (69%), Positives = 201/244 (82%), Gaps = 13/244 (5%)

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--ISTGFTEKKKPQPKGSEVKRTRRDR 178
           CRERTNKYM KSRQIQVIDND+G+HMRPMPGM+   ++G +EKKK   K ++ KRTRRDR
Sbjct: 129 CRERTNKYMVKSRQIQVIDNDSGAHMRPMPGMISFSTSGPSEKKKSPAKATDTKRTRRDR 188

Query: 179 GEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
           GEME+I+FKLFERQ NW+LR LIQETDQPEQFLKD+LKDLCVYNNKG+NQG+YELKPEY+
Sbjct: 189 GEMEEIVFKLFERQPNWSLRNLIQETDQPEQFLKDILKDLCVYNNKGTNQGTYELKPEYR 248

Query: 239 KAAD 242
           K+ D
Sbjct: 249 KSGD 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  333 bits (854), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 164/242 (67%), Positives = 192/242 (79%), Gaps = 13/242 (5%)

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 LCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRG 179
           LCRERTNKYM K+RQIQVIDN  G HMRPMPGM+I T   EKKK   + SE+KRTRRDR 
Sbjct: 135 LCRERTNKYMGKNRQIQVIDNARGMHMRPMPGMIIPTAAPEKKKLTNRTSEMKRTRRDRR 194

Query: 180 EMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKK 239
           EME++MF LFERQSNWTLR LIQETDQPEQFLKD+L+DLC+YNNKGSNQG+YELKPEYKK
Sbjct: 195 EMEEVMFNLFERQSNWTLRLLIQETDQPEQFLKDLLRDLCIYNNKGSNQGTYELKPEYKK 254

Query: 240 AA 241
           A 
Sbjct: 255 AT 256

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  328 bits (842), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 167/244 (68%), Positives = 194/244 (79%), Gaps = 11/244 (4%)

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 GKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRD 177
           G+LCRERTNKYM K+RQIQVIDN  G HMRPMPGM+I T   EKKK   + SE+KRTRRD
Sbjct: 144 GRLCRERTNKYMGKNRQIQVIDNARGMHMRPMPGMIIPTAAPEKKKLTNRTSEMKRTRRD 203

Query: 178 RGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEY 237
           R EME++MF LFERQSNWTLR LIQETDQPEQFLKD+LKDLC+YNNKGSNQG+YELKPEY
Sbjct: 204 RREMEEVMFNLFERQSNWTLRLLIQETDQPEQFLKDLLKDLCIYNNKGSNQGTYELKPEY 263

Query: 238 KKAA 241
           KKA 
Sbjct: 264 KKAT 267

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  322 bits (826), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 157/246 (63%), Positives = 196/246 (79%), Gaps = 17/246 (6%)

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 LCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGM--MISTGFTEKKKPQP-KGSEVKRTRR 176
           LCRERTNK M K+RQIQVIDND G HMRPMPGM  +IS+   EKKK  P K S+VKRTRR
Sbjct: 130 LCRERTNKSMVKNRQIQVIDNDRGVHMRPMPGMVGLISSTSKEKKKVAPVKQSDVKRTRR 189

Query: 177 DRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPE 236
           DRGE+EDIMFKLFERQ NW L+QL+QETDQP QFLK++L +LCVYN +G+NQG+YELKPE
Sbjct: 190 DRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPE 249

Query: 237 YKKAAD 242
           YKK+ +
Sbjct: 250 YKKSVE 255

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  322 bits (824), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 158/243 (65%), Positives = 195/243 (80%), Gaps = 10/243 (4%)

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-MISTGFTEKKKPQPKGSEVKRTRRDRG 179
           CRERT+K MTKSRQIQVID+  G HMRPMPGM ++S G  EKKK   KGSE KR R++RG
Sbjct: 150 CRERTHKSMTKSRQIQVIDHVTGGHMRPMPGMDVLSFGAAEKKKVVSKGSETKRLRKERG 209

Query: 180 EMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKK 239
           E+E I+FKLFERQ  WT +QLIQETDQPEQ++K++LKDLCVYNNKG +QG+YELKPEY++
Sbjct: 210 ELEKIIFKLFERQPYWTSKQLIQETDQPEQYMKEILKDLCVYNNKGVHQGTYELKPEYRE 269

Query: 240 AAD 242
           +++
Sbjct: 270 SSE 272

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224085774|ref|XP_002307692.1| predicted protein [Populus trichocarpa] gi|118481065|gb|ABK92486.1| unknown [Populus trichocarpa] gi|222857141|gb|EEE94688.1| predicted protein [Populus trichocarpa]

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 148/245 (60%), Positives = 194/245 (79%), Gaps = 12/245 (4%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP +V++S K  +S +  D +  P+AKV+LS+DPLQS++        S+ +FTME
Sbjct: 21  VWLMKCPVVVAKSWKTHTSPSSSDSA--PLAKVVLSLDPLQSDD-------PSALQFTME 71

Query: 61  LISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKL 120
           +  TE+GN PK YS++M KD +PM VF+E+  GK+++EGK+++KFDM+PH +N+E Y KL
Sbjct: 72  MARTEAGNVPKSYSLNMFKDFVPMCVFSETPQGKVAMEGKVEHKFDMKPHEQNIEEYHKL 131

Query: 121 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGM--MISTGFTEKKKPQP-KGSEVKRTRRD 177
           CRERT K M K RQIQVI+ND G HMRPMPGM  +IS+   +KK+PQP K S+VKRTRRD
Sbjct: 132 CRERTKKSMVKIRQIQVINNDRGVHMRPMPGMVGLISSSSKDKKRPQPVKQSDVKRTRRD 191

Query: 178 RGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEY 237
           RGE+EDIMFKLFERQ NW L+QL+QETDQP QFLK++L +LCVYN +G+NQG+YELKPEY
Sbjct: 192 RGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEY 251

Query: 238 KKAAD 242
           KK  +
Sbjct: 252 KKTVE 256

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224062059|ref|XP_002300734.1| predicted protein [Populus trichocarpa] gi|222842460|gb|EEE80007.1| predicted protein [Populus trichocarpa]

 Score =  316 bits (810), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 151/245 (61%), Positives = 194/245 (79%), Gaps = 13/245 (5%)

Query: 1   MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME 60
           +WLMKCP +V++S K  S      DSA P+AKV+LS+DPLQS++        S+ +FTME
Sbjct: 26  VWLMKCPVVVAKSWK--SHHTSSSDSA-PLAKVVLSLDPLQSDD-------PSAIQFTME 75

Query: 61  LISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKL 120
           +  TE+GN PK YS++M KD +PM VF+E+  G++S+EGK+++KFDM+PH EN+E Y KL
Sbjct: 76  MARTETGNVPKSYSLNMFKDFVPMGVFSETPQGRVSMEGKVEHKFDMKPHEENIEEYSKL 135

Query: 121 CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGM--MISTGFTEKKKPQP-KGSEVKRTRRD 177
           CR+RT K M K+RQI+VIDND G HMRPMPGM  +IS+   +KKK QP K S+VKRTRRD
Sbjct: 136 CRDRTKKSMIKNRQIRVIDNDRGVHMRPMPGMVGLISSTSKDKKKTQPVKQSDVKRTRRD 195

Query: 178 RGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEY 237
           RGE+EDIMFKLFERQ NW L+QL+QETDQP QFLK++L +LCVYN +G+NQG+YELKPEY
Sbjct: 196 RGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEY 255

Query: 238 KKAAD 242
           KK A+
Sbjct: 256 KKTAE 260

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	246
TAIR|locus:2005674	261	AT1G75510 [Arabidopsis thalian	0.947	0.892	0.534	1.9e-67
DICTYBASE|DDB_G0287131	241	gtf2f2 "TFIIF subunit" [Dictyo	0.609	0.622	0.320	3.1e-19
UNIPROTKB|E1BXD0	262	GTF2F2 "Uncharacterized protei	0.585	0.549	0.309	1.7e-18
UNIPROTKB|Q2T9L9	249	GTF2F2 "General transcription	0.601	0.594	0.329	3.6e-18
FB|FBgn0010421	277	TfIIFbeta "Transcription facto	0.902	0.801	0.293	4.6e-18
MGI|MGI:1915955	249	Gtf2f2 "general transcription	0.601	0.594	0.322	9.5e-18
UNIPROTKB|Q63489	249	Gtf2f2 "RAP30" [Rattus norvegi	0.601	0.594	0.322	9.5e-18
UNIPROTKB|P13984	249	GTF2F2 "General transcription	0.601	0.594	0.322	1.6e-17
POMBASE|SPBC1198.13c	307	tfg2 "transcription factor TFI	0.719	0.576	0.303	2e-17
RGD|620772	249	Gtf2f2 "general transcription	0.601	0.594	0.322	2e-17

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

 Score = 685 (246.2 bits), Expect = 1.9e-67, P = 1.9e-67
 Identities = 133/249 (53%), Positives = 178/249 (71%)

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--ISTGFTEKKKPQP-KGSEVKR 173
             Y +LCRERT+K M K+RQIQVIDND G HMRPMPGM+  +S+   EK+KP P K +EVKR
Sbjct:   127 YARLCRERTSKAMVKNRQIQVIDNDRGVHMRPMPGMLGLVSSNSKEKRKPPPVKQTEVKR 186

Query:   174 TRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYEL 233
             TRRDRGE+E IMFKLFE Q NWTL+QL+QETDQP QFLK++L +LCVYN +GSNQG+YEL
Sbjct:   187 TRRDRGELEAIMFKLFEGQPNWTLKQLVQETDQPAQFLKEILNELCVYNKRGSNQGTYEL 246

Query:   234 KPEYKKAAD 242
             KPEYKK+A+
Sbjct:   247 KPEYKKSAE 255

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

DICTYBASE|DDB_G0287131 gtf2f2 "TFIIF subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 208 (78.3 bits), Expect = 3.1e-19, Sum P(2) = 3.1e-19
 Identities = 51/159 (32%), Positives = 86/159 (54%)

Query:    83 PMSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDN 142
             P+ +F+E  +G +++EG I  + D++   E+ + Y  L + R  KY TK+R  QVID   
Sbjct:    79 PLKIFSEDKDGALALEGNIGLRCDIKIDVESPQ-YRDLMKSRHTKYNTKTRMTQVIDESE 137

Query:   143 --GSHMRPMPGMMIST-GFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQ 199
                  +     + +ST G T+KKK     S  K+ +    E+ D++F  F  + +  L+ 
Sbjct:   138 LFTPTLFDANKVKVSTVGITQKKK-----STDKKEKLPEDEVLDLIFSAFRAEKHLDLKT 192

Query:   200 LIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
             L   T+QP+  LK +L+ +C+ N +G     YELKPE++
Sbjct:   193 LESFTEQPKNHLKTILEKVCILNKRGPYHHLYELKPEFR 231

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

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1BXD0 GTF2F2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 201 (75.8 bits), Expect = 1.7e-18, Sum P(2) = 1.7e-18
 Identities = 47/152 (30%), Positives = 87/152 (57%)

Query:    88 AES-SNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHM 146
             +ES S  K+S+EG +  + + RP     ENY KL R +  +     R  Q +D    ++ 
Sbjct:   109 SESGSYDKLSLEGIVVQRAECRPAAS--ENYMKLKRFQIEESSKPVRLSQQLDKAVTTNY 166

Query:   147 RPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQ 206
             +P+     +  + +KKK      + KR R D+ ++ D++F  FE+   + ++ L+  T Q
Sbjct:   167 KPVANHQYNIEYEKKKK-----EDGKRARADKQQVLDMLFSAFEKHQYYNIKDLVDITKQ 221

Query:   207 PEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
             P  +LK++L+++ +YN KG+++ ++ELKPEY+
Sbjct:   222 PVIYLKEILREIGIYNVKGTHKNTWELKPEYR 253

GO:0005524 "ATP binding" evidence=IEA

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

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

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA

UNIPROTKB|Q2T9L9 GTF2F2 "General transcription factor IIF subunit 2" [Bos taurus (taxid:9913)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 51/155 (32%), Positives = 87/155 (56%)

Query:    84 MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
             ++VF ESS+ K+S+EG +  + + RP     ENY +L R +  +     R  Q +D    
Sbjct:    93 LTVFTESSSDKLSLEGIVVQRAECRPAAN--ENYMRLKRLQIEESSKPVRLSQQLDKVVT 150

Query:   144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
             ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct:   151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query:   204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
             T QP  +LKD+LK++ V N KG ++ ++ELKPEY+
Sbjct:   206 TKQPVSYLKDILKEIGVQNVKGIHKNTWELKPEYR 240

GO:0015630 "microtubule cytoskeleton" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

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

FB|FBgn0010421 TfIIFbeta "Transcription factor TFIIFbeta" [Drosophila melanogaster (taxid:7227)]

 Score = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 73/249 (29%), Positives = 121/249 (48%)

Query:     1 MWLMKCPALVSRSL-KIPSSDNDDDDSAR----P--VAKVILSIDP----LQSNEDXXXX 49
             +WL+K P  +++   K P+  N D    R    P   A+V LS+ P    L   E     
Sbjct:    25 VWLVKVPKYIAQKWEKAPT--NMDVGKLRINKTPGQKAQVSLSLTPAVLALDPEEKIPTE 82

Query:    50 XXXXXTRFTMELISTESGNAPKRYSMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDMRP 109
                  ++ T + +   S  AP     D  K+    S  A+  N K+ +EG+I  K + RP
Sbjct:    83 HILDVSQVTKQTLGVFSHMAPS----D-GKENSTTSA-AQPDNEKLYMEGRIVQKLECRP 136

Query:   110 HHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGS 169
               +N   Y KL  E   K     R++Q ID     + +P+     +  + E+KK     +
Sbjct:   137 IADNC--YMKLKLESIRKASEPQRRVQPIDKIV-QNFKPVKDHAHNIEYRERKK-----A 188

Query:   170 EVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQG 229
             E K+ R D+  + D++F  FE+   + ++ L++ T+QP  +LK++LKD+C YN K  ++ 
Sbjct:   189 EGKKARDDKNAVMDMLFHAFEKHQYYNIKDLVKITNQPISYLKEILKDVCDYNMKNPHKN 248

Query:   230 SYELKPEYK 238
              +ELK EY+
Sbjct:   249 MWELKKEYR 257

GO:0060261 "positive regulation of transcription initiation from RNA polymerase II promoter" evidence=IDA

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IDA

GO:0001096 "TFIIF-class transcription factor binding" evidence=IPI

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

GO:0005634 "nucleus" evidence=NAS;IDA

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

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

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

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

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

GO:0005524 "ATP binding" evidence=IEA

MGI|MGI:1915955 Gtf2f2 "general transcription factor IIF, polypeptide 2" [Mus musculus (taxid:10090)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 50/155 (32%), Positives = 87/155 (56%)

Query:    84 MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
             ++VF ESS+ K+S+EG +  + + RP     ENY KL R +  +     R  Q +D    
Sbjct:    93 LTVFTESSSDKLSLEGIVVQRAECRPAAS--ENYMKLKRLQIEESSKPVRLSQQLDKVVT 150

Query:   144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
             ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct:   151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query:   204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
             T QP  +LK++LK++ + N KG ++ ++ELKPEY+
Sbjct:   206 TKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 240

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

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

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

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

GO:0016787 "hydrolase activity" evidence=IEA

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

UNIPROTKB|Q63489 Gtf2f2 "RAP30" [Rattus norvegicus (taxid:10116)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 50/155 (32%), Positives = 87/155 (56%)

Query:    84 MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
             ++VF ESS+ K+S+EG +  + + RP     ENY KL R +  +     R  Q +D    
Sbjct:    93 LTVFTESSSDKLSLEGIVVQRAECRPAAS--ENYMKLKRLQIEESSKPVRLSQQLDKVVT 150

Query:   144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
             ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct:   151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query:   204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
             T QP  +LK++LK++ + N KG ++ ++ELKPEY+
Sbjct:   206 TKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 240

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

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

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

UNIPROTKB|P13984 GTF2F2 "General transcription factor IIF subunit 2" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 50/155 (32%), Positives = 87/155 (56%)

Query:    84 MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
             ++VF ESS+ K+S+EG +  + + RP     ENY +L R +  +     R  Q +D    
Sbjct:    93 LTVFTESSSDKLSLEGIVVQRAECRPAAS--ENYMRLKRLQIEESSKPVRLSQQLDKVVT 150

Query:   144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
             ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct:   151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query:   204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
             T QP  +LK++LK++ V N KG ++ ++ELKPEY+
Sbjct:   206 TKQPVVYLKEILKEIGVQNVKGIHKNTWELKPEYR 240

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

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

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

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

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0015630 "microtubule cytoskeleton" evidence=IDA

POMBASE|SPBC1198.13c tfg2 "transcription factor TFIIF complex beta subunit Tfg2 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 57/188 (30%), Positives = 95/188 (50%)

Query:    63 STESGNAPKRYSMDMSKDLIPMS-VFAESSNGK----ISVEGKIKNKFDMRPHHENMENY 117
             S E+ + PK Y++ +    +  S VF ES         ++ G + ++ ++ P     ++Y
Sbjct:    73 SPENADVPKIYNLRVMNKFVRNSYVFRESETSSSMKSTALVGTVAHECNVSPVIN--DDY 130

Query:   118 GKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMP-GMMI--STGFTEKKKPQPKGSEVKRT 174
              ++ ++R        R++Q+ID+  GS + P   G     +T F    KP+  G  +K +
Sbjct:   131 RRVMQKRALAASAPKRKVQMIDDRGGSLLAPGTLGSRSRSTTSFIRNVKPRT-GEGLKNS 189

Query:   175 RRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELK 234
             R  R E+ DI+FK FE    WTL+ L +   QPE +LK++L  + + N +G     Y LK
Sbjct:   190 RIPRNELLDILFKCFEDYEYWTLKGLREYVKQPEVYLKEVLDSIAILNKRGPYALKYSLK 249

Query:   235 PEYKKAAD 242
             PEYK   D
Sbjct:   250 PEYKGTMD 257

GO:0000991 "core RNA polymerase II binding transcription factor activity" evidence=ISS

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

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

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

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

GO:0044732 "mitotic spindle pole body" evidence=IDA

RGD|620772 Gtf2f2 "general transcription factor IIF, polypeptide 2" [Rattus norvegicus (taxid:10116)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 50/155 (32%), Positives = 86/155 (55%)

Query:    84 MSVFAESSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
             ++VF ESS+ K+S+EG +  + + RP     ENY KL R +  +     R  Q  D    
Sbjct:    93 LTVFTESSSDKLSLEGIVVQRAECRPAAS--ENYMKLKRLQIEESSKPVRLSQQADKVVT 150

Query:   144 SHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQE 203
             ++ +P+     +  +  KKK      + KR R D+  + D++F  FE+   + L+ L+  
Sbjct:   151 TNYKPVANHQYNIEYERKKK-----EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDI 205

Query:   204 TDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYK 238
             T QP  +LK++LK++ + N KG ++ ++ELKPEY+
Sbjct:   206 TKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 240

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA;ISO

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

---

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.12	LOW CONFIDENCE prediction!
3rd Layer	3.6.4	LOW CONFIDENCE prediction!

---

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	246
pfam02270	259	pfam02270, TFIIF_beta, Transcription initiation fa	2e-40
COG5090	297	COG5090, TFG2, Transcription initiation factor IIF	3e-23

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

 Score =  139 bits (351), Expect = 2e-40
 Identities = 70/268 (26%), Positives = 112/268 (41%), Gaps = 50/268 (18%)

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  NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPG 151
             K ++EG++ ++ + RP     E Y +L ++R  K     R +QV+D          P 
Sbjct: 117 PKKTALEGRVVHECECRPVEN--EEYMRLKKKRILKASKPKRTVQVLDKI--VTQSYKPP 172

Query: 152 MMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFL 211
              S   +E    + K SE KR R  + E+ D++FK FE+   W+L+ L + T QPE +L
Sbjct: 173 SNHSNN-SEYFIKKKKKSEGKRARMPKNELLDLLFKAFEKHQYWSLKDLKERTRQPEAYL 231

Query: 212 KDMLKDLCVYNNKGSNQGSYELKPEYKK 239
           K++L ++ V N KG    ++ELKPEY+ 
Sbjct: 232 KEILDEIAVLNKKGPYANTWELKPEYRH 259

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

>gnl|CDD|227421 COG5090, TFG2, Transcription initiation factor IIF, small subunit (RAP30) [Transcription]

 Score = 95.0 bits (236), Expect = 3e-23
 Identities = 61/221 (27%), Positives = 102/221 (46%), Gaps = 11/221 (4%)

Query: 30  VAKVILSIDPLQSNEDSSSSSSSSSTRFTMELI-STESGNAPKRYSMDMSKDLIPMS-VF 87
           +A+  LS +        +  +S+     ++ L     +G  P  Y + +    +    VF
Sbjct: 40  LAEKWLSREAEIGELLGTKRTSTDPAVISLLLSNEFCNGGFPSSYDLKIKPKDVNNYYVF 99

Query: 88  AE----SSNGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNG 143
            E    +     +V G + ++  + P  E  + Y +  ++R  K  +K   +QVID   G
Sbjct: 100 RESETSTHEKNTAVVGTVNHECYVTP--EVNDEYLRYKQDRGFKSDSKKSDVQVIDYLKG 157

Query: 144 SHMRPMPGMMIS--TGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLI 201
                  G + S    F  +K+ +    + KR R  + E+ D++FK FE+   WTL+ L 
Sbjct: 158 GKRGEKFGSLRSSTLEFLARKRKK-MLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLA 216

Query: 202 QETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAAD 242
           +   QPE FLK++L D+ V N KG     YEL+PEYK+  D
Sbjct: 217 EFCGQPEAFLKEILDDIAVLNKKGPYANKYELRPEYKQTMD 257

Length = 297

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	246
KOG2905	254	consensus Transcription initiation factor IIF, sma	100.0
PF02270	275	TFIIF_beta: Transcription initiation factor IIF, b	100.0
COG5090	297	TFG2 Transcription initiation factor IIF, small su	100.0
PF09734	310	Tau95: RNA polymerase III transcription factor (TF	95.41
PF12157	457	DUF3591: Protein of unknown function (DUF3591); In	94.96
PF04801	421	Sin_N: Sin-like protein conserved region; InterPro	91.24
KOG0008	1563	consensus Transcription initiation factor TFIID, s	91.14
KOG2473	484	consensus RNA polymerase III transcription factor	88.22
COG5179	968	TAF1 Transcription initiation factor TFIID, subuni	86.75

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

Probab=100.00  E-value=3e-68  Score=464.91  Aligned_cols=219  Identities=40%  Similarity=0.684  Sum_probs=190.1

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEec---------ccCCCCCCc
Q 025926            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELI---------STESGNAPK   71 (246)
Q Consensus         1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l~---------~~~~~~iPk   71 (246)
                      |||||||+||+++|.+++.       ..++|++++...+.+             .++++.|+         ..+.+.+|.
T Consensus        20 vWLvKvP~fLa~kw~~~~~-------~~e~g~l~i~k~~~d-------------aki~l~L~e~~p~~~~~~a~~g~~p~   79 (254)
T KOG2905|consen   20 VWLVKVPKFLAEKWRKIPN-------SHESGKLRINKTPSD-------------AKIVLLLNEAIPEKQEREADVGKFPQ   79 (254)
T ss_pred             EEEEeccHHHHHHHHhccc-------ccccccccccCCCCc-------------ceEEEEeccccccchhhhhhcccCch
Confidence            7999999999999997555       224677766554311             24444444         345889999


Q ss_pred             eeeeccccCCcceeeeeeec-CCceeEEEEEeeeeeEeecCCChHHHHHHHHHHHHHHhcCCcceEEecCCCCCcccCCC
Q 025926           72 RYSMDMSKDLIPMSVFAESS-NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMP  150 (246)
Q Consensus        72 eY~L~~~~~~~~~~VFse~~-~~~~~i~G~V~~~~~~~P~~~~~~~Y~~l~~~R~~~a~~~~r~vq~ld~~~~~~~~p~~  150 (246)
                      .|.+++..++.||||||+++ .|+++++|+|+|+|+|+|+.  |++|++++++|+.+++.|+|+||+||++.|++|+|++
T Consensus        80 ~~~~~~~~~~~~~~~~sd~~~~~k~a~eG~V~~e~~~~P~~--ne~Y~Rl~r~r~~k~~~k~r~vQ~iD~~~g~~~~p~~  157 (254)
T KOG2905|consen   80 QYKLNMKRRFFNMFVESDSSGPKKTAVEGTVVHECDVRPSA--NEEYMRLKRERIVKASKKKRQVQVIDKVVGVHMKPVP  157 (254)
T ss_pred             hhhhccCccccceeeeecCCCCccceeeeeeeeeeeccccc--CHHHHHHHHHHHHHhcCcccccccchhhcccccccCC
Confidence            99999999999999999988 78999999999999999996  5999999999999999999999999999999999999


Q ss_pred             CccccCCc--ccccCCCCCCcccccccCChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCC
Q 025926          151 GMMISTGF--TEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQ  228 (246)
Q Consensus       151 ~~~~~~~~--~~k~k~~~K~~~~K~~R~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~  228 (246)
                      ||.....+  ++++|   +++++|++|+|++||+|+||+|||+|+||+||+|+++|+||++||||||++||+||++|||+
T Consensus       158 ~~~~~~~~~~~~rkK---~k~e~Kr~R~dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~NkKg~~k  234 (254)
T KOG2905|consen  158 GHLRSSSNIAYERKK---AKEEGKRTRRDKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNKKGPYK  234 (254)
T ss_pred             CcccccchhHHHHHh---hhhccccccccHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhccCccc
Confidence            98732221  33331   37899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccchhhhhccCCC
Q 025926          229 GSYELKPEYKKAADGP  244 (246)
Q Consensus       229 ~~weLKpEYk~~~~~~  244 (246)
                      |+||||||||++.++.
T Consensus       235 ~tyeLKPEYK~~~~ee  250 (254)
T KOG2905|consen  235 NTYELKPEYKKYKEEE  250 (254)
T ss_pred             CceecCHHHhhhhhhh
Confidence            9999999999998875

>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=100.00  E-value=3.2e-66  Score=468.30  Aligned_cols=217  Identities=37%  Similarity=0.640  Sum_probs=112.3

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEeccc--CCCCCCceeeeccc
Q 025926            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELIST--ESGNAPKRYSMDMS   78 (246)
Q Consensus         1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l~~~--~~~~iPkeY~L~~~   78 (246)
                      |||||||+|||++|++++.     +++++||+|+++.++.          +  ..++.|.|+..  .+++||++|+|+|+
T Consensus        13 vWLvKVPk~l~e~W~~~~~-----~~~~~iG~lri~~~~~----------~--~~~v~l~L~~~~~~~~~iPkey~L~~~   75 (275)
T PF02270_consen   13 VWLVKVPKFLSEKWSKAPD-----DDEIEIGKLRISKDPN----------G--KPKVSLTLNDSLANHGNIPKEYDLDMS   75 (275)
T ss_dssp             EEEEEEEHHHHHHHTTSBT-----T--TEEEEEEEEEE-T----------T--EEEEEEEE-HHHHT-T-S--EEEEEEE
T ss_pred             ccccccccccccccccccc-----cccccccccccccccc----------c--ccccccccccccccccccccccccccc
Confidence            7999999999999986433     2367899999998731          1  23677777754  35699999999999


Q ss_pred             cCC-cceeeeeeecC-------------------------------------------CceeEEEEEeeeeeEeecCCCh
Q 025926           79 KDL-IPMSVFAESSN-------------------------------------------GKISVEGKIKNKFDMRPHHENM  114 (246)
Q Consensus        79 ~~~-~~~~VFse~~~-------------------------------------------~~~~i~G~V~~~~~~~P~~~~~  114 (246)
                      +.. +|||||||.++                                           ++++|+|+|.|+|+|+|+.  +
T Consensus        76 ~~~~~n~~VFse~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~G~I~~~~~~~P~~--~  153 (275)
T PF02270_consen   76 KDNVQNMYVFSESDQPGFKAKNKERAGAPNAGIPASLLREKKKKDRKRKYQPYVKTIPKKTALEGRIVHECDCRPVL--N  153 (275)
T ss_dssp             --TTEEEEEEEEETT----------------------------------------ETT--EEEEEEEEEEEEE-------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCceEEEEEEEEEEEeEECC--C
Confidence            997 59999999865                                           5889999999999999996  4


Q ss_pred             HHHHHHHHHHHHHHhcCCcceEEecCCCCCcccCCCCccccCCcccccCCCCCCcccccccCChhhHHHHHHHHhhhccC
Q 025926          115 ENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSN  194 (246)
Q Consensus       115 ~~Y~~l~~~R~~~a~~~~r~vq~ld~~~~~~~~p~~~~~~~~~~~~k~k~~~K~~~~K~~R~~~~eLld~LF~~Fek~~y  194 (246)
                      ++|++++++|+.++++|+|++++|+......+.|++.+..+...+.   .+.|+.++|++|||+++|+|+||+|||+|+|
T Consensus       154 ~~Y~~~~~~r~~~a~~~kr~~~~i~~~~~~~~~~~~~~~~~~~~~~---~~~k~~~~K~~R~~~~eL~d~lF~~Fe~~~y  230 (275)
T PF02270_consen  154 DEYRRLKRERIEKANKPKRTVQQIDEDVSQSYKPVSFHSANSKFFI---KKKKKQEEKRARMDKNELLDLLFKLFEKHQY  230 (275)
T ss_dssp             -----------------------------------------------------------THHHHHHHHHHHHHHHHH-S-
T ss_pred             HHHHHHHHHHHHHhcCCCCeeEEeccccccCCCCcccccccchhcc---cccccccccceeCCHHHHHHHHHHHHHhCCC
Confidence            7999999999999999999999999865567777554443322111   1226788999999999999999999999999


Q ss_pred             cchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccccchhhhh
Q 025926          195 WTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKK  239 (246)
Q Consensus       195 WslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~  239 (246)
                      |+||+|+++|+||++||||||+|||+||++|||+|+|+||||||+
T Consensus       231 wslK~L~~~t~QP~~yLKeiL~eIa~~~k~g~~~~~w~LKpeyk~  275 (275)
T PF02270_consen  231 WSLKDLRQRTQQPEAYLKEILEEIAVLNKRGPHKNMWELKPEYKH  275 (275)
T ss_dssp             B-HHHHHHH--S-HHHHHHHHHHH--EE--TT---EE----SS--
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHhccCCcCCcEecchHHcC
Confidence            999999999999999999999999999999999999999999996

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=100.00  E-value=6.2e-57  Score=392.44  Aligned_cols=219  Identities=28%  Similarity=0.433  Sum_probs=183.7

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEe-cccCCCCCCceeeecccc
Q 025926            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMEL-ISTESGNAPKRYSMDMSK   79 (246)
Q Consensus         1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l-~~~~~~~iPkeY~L~~~~   79 (246)
                      |||||||.||+++|...+.   ++  +..+|++|+..+|               ..+++.| +..+++++|++|+|.+.+
T Consensus        31 VWLvkvP~FLaekw~sr~~---~~--g~~lg~~r~~~d~---------------a~isLlL~ne~~n~~~P~~ydl~i~~   90 (297)
T COG5090          31 VWLVKVPLFLAEKWLSREA---EI--GELLGTKRTSTDP---------------AVISLLLSNEFCNGGFPSSYDLKIKP   90 (297)
T ss_pred             EEEEeccHHHHHHHhcchh---hh--hhhhceeeecCCc---------------ceEEEEeccCCccCCCCcceeeeecc
Confidence            7999999999999984222   23  3459999998765               2677777 456899999999999999


Q ss_pred             CCc-ceeeeeeec----CCceeEEEEEeeeeeEeecCCChHHHHHHHHHHHHHHhcCCcceEEecCCCCCcccCCCCccc
Q 025926           80 DLI-PMSVFAESS----NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMI  154 (246)
Q Consensus        80 ~~~-~~~VFse~~----~~~~~i~G~V~~~~~~~P~~~~~~~Y~~l~~~R~~~a~~~~r~vq~ld~~~~~~~~p~~~~~~  154 (246)
                      ..+ +-|||.|+.    .+.|+|+|+|.|+|.+.|..  |++|+++++.|..++..+++.||+||...|+.+.+ .++++
T Consensus        91 k~v~n~yVfre~et~t~~k~tavvGtV~hEC~V~P~v--Nd~Y~r~~q~r~~~~~~~K~~vq~iD~~~g~~~~~-~~~s~  167 (297)
T COG5090          91 KDVNNYYVFRESETSTHEKNTAVVGTVNHECYVTPEV--NDEYLRYKQDRGFKSDSKKSDVQVIDYLKGGKRGE-KFGSL  167 (297)
T ss_pred             ccccceEEEecccccccccccceeeeeccceeecccc--cHHHHHHHHHhhhhhcCccccceeeecccCceecc-Ccccc
Confidence            988 689996653    37999999999999999997  58999999999999999999999999988877766 22222


Q ss_pred             cC--CcccccCCCCCCcccccccCChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccc
Q 025926          155 ST--GFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYE  232 (246)
Q Consensus       155 ~~--~~~~k~k~~~K~~~~K~~R~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~we  232 (246)
                      .+  ..|.+++.+.-+++.|+.|||++||+|+||+|||+|+||+||+|+++++||++||||||++||+|||+|||+++|+
T Consensus       168 Rs~~~~fl~~~r~k~~~~~K~~RlpknEvlD~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~iavLnKkgpya~kY~  247 (297)
T COG5090         168 RSSTLEFLARKRKKMLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYE  247 (297)
T ss_pred             ccchHHHHHhcchhhhcchhhcccchhHHHHHHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHHhhhccCcccceee
Confidence            11  1133322211267789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhhhhccC
Q 025926          233 LKPEYKKAAD  242 (246)
Q Consensus       233 LKpEYk~~~~  242 (246)
                      |+||||...+
T Consensus       248 LrPEYK~~~d  257 (297)
T COG5090         248 LRPEYKQTMD  257 (297)
T ss_pred             cCHHHHhHHH
Confidence            9999998653

>PF09734 Tau95: RNA polymerase III transcription factor (TF)IIIC subunit; InterPro: IPR019136 Transcription factor IIIC (TFIIIC) is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes

Probab=95.41  E-value=0.017  Score=53.23  Aligned_cols=57  Identities=25%  Similarity=0.345  Sum_probs=52.8

Q ss_pred             CChhhHHHHHHHHhhhccCcchHHHHHhhCC--cHHHHHHHHHHHhhHhccCCCCcccc
Q 025926          176 RDRGEMEDIMFKLFERQSNWTLRQLIQETDQ--PEQFLKDMLKDLCVYNNKGSNQGSYE  232 (246)
Q Consensus       176 ~~~~eLld~LF~~Fek~~yWslK~L~~~t~Q--Pe~yLKeiL~eIa~lnk~Gp~~~~we  232 (246)
                      ....+++..|=+|||+.+-|+-++|...+..  -...||.+|--+|=|=+.||+++.|-
T Consensus       231 ~~~~~~~~~l~~lFeeRPIW~r~~L~~~~~~~~~~~~~k~~l~~v~Y~f~~GPwr~~~v  289 (310)
T PF09734_consen  231 PVLQELIQELKKLFEERPIWTRRALLNHLPKSGSQSKLKRALPYVAYYFKNGPWRDCWV  289 (310)
T ss_pred             hhHHHHHHHHHHHHhcCCccCHHHHHHhhhhcccHHHHHHHHHhhEEEEecCcccceeE
Confidence            3447889999999999999999999999999  68899999999999999999999995

This entry represents subunit 5 (also known as the tau 95 subunit) which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable []. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.

>PF12157 DUF3591: Protein of unknown function (DUF3591); InterPro: IPR022591 This functionally uncharacterised domain is found centrally in the eukaryotic transcription initiation factor TFIID subunit 1

Probab=94.96  E-value=0.043  Score=53.64  Aligned_cols=69  Identities=22%  Similarity=0.477  Sum_probs=60.1

Q ss_pred             ccccCChhhHHHHHHHHhh--hccCcchHHHHHhh-CCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhc
Q 025926          172 KRTRRDRGEMEDIMFKLFE--RQSNWTLRQLIQET-DQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA  240 (246)
Q Consensus       172 K~~R~~~~eLld~LF~~Fe--k~~yWslK~L~~~t-~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~  240 (246)
                      |..-.-++-|.-.+|.+|.  ...--.+.+|.... .|.+.=+++-|++.|.|.|.|...|.|.|||.|+--
T Consensus       234 ~~t~~~knrL~~~iyRlf~~~~~~ri~~~di~~~Fp~~se~~iRkrLKe~~~~~R~g~~~~~W~lk~~~~lp  305 (457)
T PF12157_consen  234 KVTNFSKNRLKMIIYRLFNKSQPRRIKVDDIKKHFPDQSESQIRKRLKEFADFQRTGDDSGWWVLKPGFRLP  305 (457)
T ss_pred             hHHHHHHHHHHHHHHHHHhhccCCccCHHHHHHhCCCCcHHHHHHHHHHHHhccCCCCCCCeEEECCCCCCC
Confidence            4555778889999999998  44469999999885 789999999999999999999999999999987743

>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=91.24  E-value=0.29  Score=47.02  Aligned_cols=55  Identities=22%  Similarity=0.401  Sum_probs=48.6

Q ss_pred             hHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccccchhh
Q 025926          180 EMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEY  237 (246)
Q Consensus       180 eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEY  237 (246)
                      -..|.|--+|.++.+=+-++|...|+-|..=++|||++||+++   +....|+||=.+
T Consensus       337 ~aRD~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~---~~~~~W~lk~~~  391 (421)
T PF04801_consen  337 RARDYILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAVLR---PSNRGWKLKLPP  391 (421)
T ss_pred             hhHHHHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhhcc---CCCCceEEccCc
Confidence            3568888999999999999999999999999999999999998   566889997543

RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus

>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=91.14  E-value=0.33  Score=52.72  Aligned_cols=73  Identities=21%  Similarity=0.389  Sum_probs=64.9

Q ss_pred             cccccCChhhHHHHHHHHhhhccC----cchHHHHHhh-CCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhccCC
Q 025926          171 VKRTRRDRGEMEDIMFKLFERQSN----WTLRQLIQET-DQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAADG  243 (246)
Q Consensus       171 ~K~~R~~~~eLld~LF~~Fek~~y----WslK~L~~~t-~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~~~~  243 (246)
                      .|..-+-+|=|.-.||.+|-+..-    -.|.+|.... .|-++=+|.=|++.|.|.|.|+-.|.|.|||.|+--.++
T Consensus       688 Kk~tt~~~nrLkv~IYRlF~~s~~g~r~I~id~lsk~Fp~~se~siRKrLKecad~kR~G~~~~~W~LK~df~lp~ee  765 (1563)
T KOG0008|consen  688 KKLTTFLRNRLKVFIYRLFWKSDSGPRRIRIDDLSKAFPDQSESSIRKRLKECADFKRDGMGKNYWVLKPDFRLPDEE  765 (1563)
T ss_pred             hhHHHHHHHHHHHHHHHHHHhcCCCCcceehhHHHhhCcccchHHHHHHHHHHHHHhhcCCCCCeeEecccccCCCHH
Confidence            356667889999999999998887    8899998876 889999999999999999999999999999999876543

>KOG2473 consensus RNA polymerase III transcription factor (TF)IIIC subunit [Transcription]

Probab=88.22  E-value=0.79  Score=44.94  Aligned_cols=55  Identities=25%  Similarity=0.327  Sum_probs=48.7

Q ss_pred             hhhHHHHHHHHhhhccCcchHHHHH-hhCCcHHHHHHHHHHHhhHhccCCCCcccc
Q 025926          178 RGEMEDIMFKLFERQSNWTLRQLIQ-ETDQPEQFLKDMLKDLCVYNNKGSNQGSYE  232 (246)
Q Consensus       178 ~~eLld~LF~~Fek~~yWslK~L~~-~t~QPe~yLKeiL~eIa~lnk~Gp~~~~we  232 (246)
                      -+|++-.|=.+|++.+-|+-+.|.. .++==.-+||-+|--||-|-.+||++++|-
T Consensus       230 ~~e~~~~l~eLF~~RPIWtR~al~~~~~~~~~h~LK~~Lp~~AYyfssGPwr~~wi  285 (484)
T KOG2473|consen  230 LEEVLRSLRELFEERPIWTRRALLYKELGCTHHKLKRFLPLIAYYFSSGPWRRLWI  285 (484)
T ss_pred             hHHHHHHHHHHHHhCchhhHHhHhhcccCccHHHHHHHHHHHHHHhccCchhceee
Confidence            3567777777999999999999999 666677899999999999999999999994

>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=86.75  E-value=0.76  Score=46.63  Aligned_cols=69  Identities=26%  Similarity=0.354  Sum_probs=57.5

Q ss_pred             cccccCChhhHHHHHHHHhhhccC--cchHHHHHhh-CCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhc
Q 025926          171 VKRTRRDRGEMEDIMFKLFERQSN--WTLRQLIQET-DQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA  240 (246)
Q Consensus       171 ~K~~R~~~~eLld~LF~~Fek~~y--WslK~L~~~t-~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~  240 (246)
                      .|-+-+-++-|..++|.+|...+.  -.|.+|.... .|-+.-.++-|+|-+.|.|.||- |.|.|||.=.-.
T Consensus       592 RKvt~~~knRLKm~~fRl~n~~~~g~l~I~ql~khFpdq~egq~Rq~lKEfm~y~kdGp~-g~W~Lk~~e~ll  663 (968)
T COG5179         592 RKVTVFCKNRLKMAAFRLFNSKEGGSLRISQLDKHFPDQSEGQKRQWLKEFMDYVKDGPD-GVWVLKPSEALL  663 (968)
T ss_pred             hhhHHHHhhhHHHHHHHHhhcCCCCceeeehhhhhCCCcchhHHHHHHHHHHHHhhcCCC-ceEEeccccccC
Confidence            366678888999999999988775  7778887765 78888888888899999999998 999999965433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	246
1bby_A	69	Dna-Binding Domain From Human Rap30, Nmr, Minimized		2e-08

>pdb|1BBY|A Chain A, Dna-Binding Domain From Human Rap30, Nmr, Minimized Average Length = 69

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 25/64 (39%), Positives = 43/64 (67%)
Query: 175 RRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELK 234
           R D+  + D++F  FE+   + L+ L+  T QP  +LK++LK++ V N KG ++ ++ELK
Sbjct: 3   RADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELK 62
Query: 235 PEYK 238
           PEY+
Sbjct: 63  PEYR 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	246
1bby_A	69	RAP30; average structure transcription regulation,	3e-26
1f3u_A	118	Transcription initiation factor IIF, beta subunit;	1e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>1bby_A RAP30; average structure transcription regulation, DNA- binding domain, transcription; NMR {Homo sapiens} SCOP: a.4.5.15 PDB: 2bby_A Length = 69

 Score = 96.4 bits (240), Expect = 3e-26
 Identities = 26/66 (39%), Positives = 44/66 (66%)

Query: 173 RTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYE 232
           R R D+  + D++F  FE+   + L+ L+  T QP  +LK++LK++ V N KG ++ ++E
Sbjct: 1   RARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWE 60

Query: 233 LKPEYK 238
           LKPEY+
Sbjct: 61  LKPEYR 66

>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 = 67.4 bits (164), Expect = 1e-14
 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

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.8 bits (97), Expect = 1e-04
 Identities = 42/263 (15%), Positives = 77/263 (29%), Gaps = 87/263 (33%)

Query: 2   WLMKCPALVSRSLKIP------------SSDNDDDDSARPVAKVILSIDPLQSNEDSSSS 49
           W+      V  S K+              + N  +     + K++  IDP      +S S
Sbjct: 165 WVA---LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP----NWTSRS 217

Query: 50  SSSSSTRFTMELISTESGNAPKRY--SMDMSKDLIPMSVFAESSNGKISVEGKIKNKFDM 107
             SS+ +  +  I  E     +R   S      L+   V     N K        N F++
Sbjct: 218 DHSSNIKLRIHSIQAE----LRRLLKSKPYENCLL---VLLNVQNAKAW------NAFNL 264

Query: 108 RPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKK----- 162
                        C+      +T +R  QV D  + +    +     S   T  +     
Sbjct: 265 S------------CK----ILLT-TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307

Query: 163 ------KPQ--P----KGS--------EVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQ 202
                 +PQ  P      +        E  R            +  ++  +   L  +I+
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT-------WDNWKHVNCDKLTTIIE 360

Query: 203 ---ETDQPEQFLKDMLKDLCVYN 222
                 +P ++ + M   L V+ 
Sbjct: 361 SSLNVLEPAEY-RKMFDRLSVFP 382

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	246
1bby_A	69	RAP30; average structure transcription regulation,	100.0
1f3u_A	118	Transcription initiation factor IIF, beta subunit;	99.93

>1bby_A RAP30; average structure transcription regulation, DNA- binding domain, transcription; NMR {Homo sapiens} SCOP: a.4.5.15 PDB: 2bby_A

Probab=100.00  E-value=2.3e-38  Score=229.81  Aligned_cols=69  Identities=38%  Similarity=0.727  Sum_probs=67.3

Q ss_pred             cccCChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhcc
Q 025926          173 RTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAA  241 (246)
Q Consensus       173 ~~R~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~~  241 (246)
                      ++|||+++|+|+||+|||+|+||+||+|+++|+||++||||||++||+||++|||+|+|+||||||++.
T Consensus         1 r~R~~~~~l~d~lF~~Fek~~yw~lK~L~~~t~QP~~yLKeiL~~Ia~~~k~g~~~~~weLKpEyr~y~   69 (69)
T 1bby_A            1 RARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELKPEYRHYQ   69 (69)
T ss_dssp             CTHHHHHHHHHHHHHHHHHCSCBCHHHHHHHCCSCHHHHHHHHHHHCCCBCCTTCCCBBCCCCSSCCCC
T ss_pred             CCcCCHHHHHHHHHHHHhhcCCCcHHHHHHHHcCcHHHHHHHHHHHHHHHcCCCCCCeeeCcHHHhccC
Confidence            689999999999999999999999999999999999999999999999999999999999999999863

>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=99.93  E-value=3.7e-26  Score=182.27  Aligned_cols=90  Identities=27%  Similarity=0.430  Sum_probs=75.0

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEeccc-----------CCCCC
Q 025926            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELIST-----------ESGNA   69 (246)
Q Consensus         1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l~~~-----------~~~~i   69 (246)
                      |||||||+|||++|+++.+       .+++|+|+++.++           +  ..++.|.|+..           ++.++
T Consensus        17 VWLvKvPk~L~e~W~~~~~-------~~~vGkvri~~~~-----------g--~~~v~l~L~~~~~~~~~~~~~~~~~~i   76 (118)
T 1f3u_A           17 VWLVKVPKYLSQQWAKASG-------RGEVGKLRIAKTQ-----------G--RTEVSFTLNEDLANIHDIGGKPASVSA   76 (118)
T ss_dssp             EEEEEEEHHHHHHHTTCCT-------TCEEEEEEEEEET-----------T--EEEEEEEECHHHHTCCCTTCCCSTTCS
T ss_pred             EEEEECCHHHHHHHHhCCC-------CCceEEEEEecCC-----------C--ceeEEEEeChhHhhhccccccccccCC
Confidence            7999999999999985322       3689999999764           2  13566666522           36889


Q ss_pred             Cceeeecccc-CCcceeeeeeecCCceeEEEEEeeeeeEeec
Q 025926           70 PKRYSMDMSK-DLIPMSVFAESSNGKISVEGKIKNKFDMRPH  110 (246)
Q Consensus        70 PkeY~L~~~~-~~~~~~VFse~~~~~~~i~G~V~~~~~~~P~  110 (246)
                      |++|+|+|++ ..+|||||||+++++++|||+|.|+|+|+|.
T Consensus        77 PkeY~l~~~~~~~~~~~VFSE~~~~~~a~EG~V~~k~d~rP~  118 (118)
T 1f3u_A           77 PREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA  118 (118)
T ss_dssp             CCEEEEEEECCTTSEEEEEEEETTCCEEEEEEEEEEEEECCC
T ss_pred             ChhceEEeeccCCceeEEEeccCCCcEEEEEEEEEEEEeecC
Confidence            9999999999 5679999999999999999999999999994

---

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	246
d2bbya_	69	a.4.5.15 (A:) DNA-binding domain from rap30 {Human	3e-30
d1f3ua_	118	b.65.1.1 (A:) TFIIF beta subunit, Rap30 {Human (Ho	2e-21

>d2bbya_ a.4.5.15 (A:) DNA-binding domain from rap30 {Human (Homo sapiens) [TaxId: 9606]} Length = 69

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding domain from rap30
domain: DNA-binding domain from rap30
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  105 bits (263), Expect = 3e-30
 Identities = 26/67 (38%), Positives = 44/67 (65%)

Query: 173 RTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYE 232
           R R D+  + D++F  FE+   + L+ L+  T QP  +LK++LK++ V N KG ++ ++E
Sbjct: 1   RARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWE 60

Query: 233 LKPEYKK 239
           LKPEY+ 
Sbjct: 61  LKPEYRH 67

>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 = 84.2 bits (208), Expect = 2e-21
 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	246
d2bbya_	69	DNA-binding domain from rap30 {Human (Homo sapiens	100.0
d1f3ua_	118	TFIIF beta subunit, Rap30 {Human (Homo sapiens) [T	99.94
d2doaa1	91	RNA polymerase II elongation factor ELL {Human (Ho	91.0
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	82.68

>d2bbya_ a.4.5.15 (A:) DNA-binding domain from rap30 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding domain from rap30
domain: DNA-binding domain from rap30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.6e-39  Score=231.66  Aligned_cols=69  Identities=38%  Similarity=0.727  Sum_probs=67.4

Q ss_pred             cccCChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhcc
Q 025926          173 RTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAA  241 (246)
Q Consensus       173 ~~R~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~~  241 (246)
                      |+|||+++|+|+||+|||+|+|||||+|+++|+||++||||||++||+||++|||+|+|+||||||++.
T Consensus         1 r~R~~~~~l~d~lF~~Fek~~ywsiK~L~~~t~QP~~yLKeiL~eIa~~~~~g~~~~~weLKpEYr~~k   69 (69)
T d2bbya_           1 RARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELKPEYRHYQ   69 (69)
T ss_dssp             CTHHHHHHHHHHHHHHHHHCSCBCHHHHHHHCCSCHHHHHHHHHHHCCEECCTTCCCEECCCCSSCCCC
T ss_pred             CCccCHHHHHHHHHHHHhhcCCCCHHHHHHHHhChHHHHHHHHHHHHHHHcCCCcCCceeCCHHHhccC
Confidence            689999999999999999999999999999999999999999999999999999999999999999863

>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=99.94  E-value=8.2e-28  Score=189.96  Aligned_cols=90  Identities=27%  Similarity=0.407  Sum_probs=74.5

Q ss_pred             CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEec-----------ccCCCCC
Q 025926            1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELI-----------STESGNA   69 (246)
Q Consensus         1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l~-----------~~~~~~i   69 (246)
                      |||||||+|||++|+++.+       .+++|+||++.++..             .++.+.|+           .+++.+|
T Consensus        17 VWLvKvPkyls~~W~k~~~-------~~~vGklri~~~~~k-------------~ev~l~l~~~~~~~~~~~~~~~~~~i   76 (118)
T d1f3ua_          17 VWLVKVPKYLSQQWAKASG-------RGEVGKLRIAKTQGR-------------TEVSFTLNEDLANIHDIGGKPASVSA   76 (118)
T ss_dssp             EEEEEEEHHHHHHHTTCCT-------TCEEEEEEEEEETTE-------------EEEEEEECHHHHTCCCTTCCCSTTCS
T ss_pred             EEEEECCHHHHHHHhhCCC-------CCcceEEEeccCCCC-------------cceEEecCchHhhhhccccCCCcCCC
Confidence            7999999999999996433       457999999987632             13334333           2357799


Q ss_pred             CceeeeccccCC-cceeeeeeecCCceeEEEEEeeeeeEeec
Q 025926           70 PKRYSMDMSKDL-IPMSVFAESSNGKISVEGKIKNKFDMRPH  110 (246)
Q Consensus        70 PkeY~L~~~~~~-~~~~VFse~~~~~~~i~G~V~~~~~~~P~  110 (246)
                      |++|+|+|++.. +|||||||.+++++++||+|+|+|+|||.
T Consensus        77 Pkey~l~~~~~~~q~~~VFSe~~~~k~~~EG~V~~k~d~RPa  118 (118)
T d1f3ua_          77 PREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA  118 (118)
T ss_dssp             CCEEEEEEECCTTSEEEEEEEETTCCEEEEEEEEEEEEECCC
T ss_pred             ChhhcEecccccCCceEEEEecCCCcEEEEEEEEEEeecCCC
Confidence            999999999986 49999999999999999999999999995

>d2doaa1 a.4.5.81 (A:8-98) RNA polymerase II elongation factor ELL {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ELL N2 domain-like
domain: RNA polymerase II elongation factor ELL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.00  E-value=0.022  Score=40.78  Aligned_cols=30  Identities=20%  Similarity=0.314  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHhhHhccCCCCcccccchhhhhc
Q 025926          208 EQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA  240 (246)
Q Consensus       208 e~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~  240 (246)
                      ..-|.+||++||+++..   .|+|+|||+|-.-
T Consensus        38 ~~~l~~iL~~Va~~~~~---~g~Y~LK~~~~~E   67 (91)
T d2doaa1          38 KDALDGLLQQVANMSAK---DGTCTLQDCMYKD   67 (91)
T ss_dssp             HHHHHHHHHHSSEECSS---SCEEECCSSGGGG
T ss_pred             HHHHHHHHHHHheecCC---CceEeeHHHHHhH
Confidence            34799999999998743   5899999988543

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=82.68  E-value=0.96  Score=29.57  Aligned_cols=43  Identities=7%  Similarity=0.054  Sum_probs=38.1

Q ss_pred             hhhHHHHHHHHhhhccC--cchHHHHHhhCCcHHHHHHHHHHHhh
Q 025926          178 RGEMEDIMFKLFERQSN--WTLRQLIQETDQPEQFLKDMLKDLCV  220 (246)
Q Consensus       178 ~~eLld~LF~~Fek~~y--WslK~L~~~t~QPe~yLKeiL~eIa~  220 (246)
                      ...|...|-.+|.+..+  +++|+|...++.++.=++++|+-.|.
T Consensus         5 q~~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~   49 (64)
T d1lvaa3           5 QKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVR   49 (64)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            46789999999988765  99999999999999999999987764