Citrus Sinensis ID: 024896

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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-------250-------260-
Protein Sequence
MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSVEDGGAD
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEEccHHHHHHHHccccccccccEEEEEEEccccccccEEEEEEEccccccccccccccccccccccccEEEEEEcccccEEEEEEEEEEEEEEcccccHHHHHHHHHHHHHHHccccccEEEEcccccccccccccccccccccccccccccccccHHHHcccccHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHHHccccccccccccHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHccccccccccccccccEEEEEccHHHHHHHHHccccccccEEEEEEEEcccccccccEEEEcccccccccccccccccccccccccccEEEEEcccccEEEEEEEEEEEEEEcccccHHHHHHHHHHHHHHHcccccEEEEEEcccccccccccccccccccccHHcccccccccHccccccccHHHHHHHHHHHHHHcccccHHHHHHHHccHHHHHHHHHHHHHHHHccccccccEEccHHHHHcccccccc
Coil and Loop (DISEMBL)
meddqsnhgngkgnldtakadRSVWLMKCPLVVAKSwqnqassqdsqpVAKVILsldplqsdsmqftMETTAVsndslnrpksyslnmfkdfvpmsvfsesnqgkvamegkvehkfdmkpheknMEEYGRLCRERTNKSMIKNRQiqvidndhgvhmrpmpgmvglissnskdkkkaqpvkqtevkrtrrdrgeLEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYnkrgtnqgtyelkpeykksvedggad
Flexible Loop (DISEMBL)
meddqsnhgngkgnldtakadrSVWLMKCPLVVAKSWQnqassqdsqPVAKVILSLDPLQSDSMQFTMETTavsndslnrpKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVehkfdmkpheknmeEYGRLCRERtnksmiknrqiqvidndhgvhMRPMPGMVGLIssnskdkkkaqpvkqtevkrtrrdrgelEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNkrgtnqgtyelkpeykksvedggad
Low Complexity Region (SEG)
MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSVEDGGAD
Disordered region (IsUnstruct)
*********************RSVWLMKCPLVVAKSW**************************************************MFKDFV******************************************************VI**********************************************EDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGT*********************
Disordered Region (DISOPRED)
******N***GKGNLDTAKADRSVWLMKCPLVVAKSWQ****************************************************DF****VFSESNQGKVAMEGKVEHKFDMKPHEKNMEE**********************DND*****************************************ELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELK*************
Disordered Region (DISEMBL)
************GNLDTAKADRSVWLMKCPLVVAKSW***********VAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISS********************RDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYK*********
Disordered Region (DISPRO)
***********KGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVH******************************RTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKS*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSVEDGGAD
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	261	2.2.26 [Sep-21-2011]
O94424	307	Transcription initiation	yes	no	0.919	0.781	0.306	2e-22
P13984	249	General transcription fac	yes	no	0.873	0.915	0.3	5e-19
Q2T9L9	249	General transcription fac	yes	no	0.873	0.915	0.296	8e-19
Q8R0A0	249	General transcription fac	yes	no	0.873	0.915	0.292	9e-19
Q01750	249	General transcription fac	yes	no	0.873	0.915	0.292	3e-18
P41900	277	General transcription fac	yes	no	0.869	0.819	0.270	5e-18
Q03123	264	General transcription fac	N/A	no	0.873	0.863	0.272	2e-17
Q54KT7	241	General transcription fac	yes	no	0.812	0.879	0.301	1e-16
P41896	400	Transcription initiation	yes	no	0.574	0.375	0.331	1e-10

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

 Score =  106 bits (264), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 80/261 (30%), Positives = 130/261 (49%), Gaps = 21/261 (8%)

Query: 2   EDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQS 61
           EDD+  + +  G+LD  +    VWL+K P  +   W N     D+  +  V      +++
Sbjct: 12  EDDR--YEDDAGDLDLGQIGSRVWLVKIPKFLMDKW-NSIPEDDAANLGCV-----RVKN 63

Query: 62  DSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMS-VFSESNQGK----VAMEGKVEHKF 116
           D +Q  ++ +  + D    PK Y+L +   FV  S VF ES         A+ G V H+ 
Sbjct: 64  DEIQLLLQNSPENADV---PKIYNLRVMNKFVRNSYVFRESETSSSMKSTALVGTVAHEC 120

Query: 117 DMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLIS-SNSKDKK 175
           ++ P     ++Y R+ ++R   +    R++Q+ID+  G  +   PG +G  S S +   +
Sbjct: 121 NVSPVIN--DDYRRVMQKRALAASAPKRKVQMIDDRGGSLL--APGTLGSRSRSTTSFIR 176

Query: 176 KAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVY 235
             +P     +K +R  R EL DI+FK FE    W LK L +   QP  +LKE+L+ + + 
Sbjct: 177 NVKPRTGEGLKNSRIPRNELLDILFKCFEDYEYWTLKGLREYVKQPEVYLKEVLDSIAIL 236

Query: 236 NKRGTNQGTYELKPEYKKSVE 256
           NKRG     Y LKPEYK +++
Sbjct: 237 NKRGPYALKYSLKPEYKGTMD 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.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

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

 Score = 94.7 bits (234), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 128/250 (51%), Gaps = 22/250 (8%)

Query: 11  GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM-E 69
           G+ +L  AK +  VWL+K P  +++ W   A +     V K+ ++    +++ + FT+ E
Sbjct: 5   GELDLTGAKQNTGVWLVKVPKYLSQQW---AKASGRGEVGKLRIAKTQGRTE-VSFTLNE 60

Query: 70  TTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPHE 122
             A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P  
Sbjct: 61  DLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAA 120

Query: 123 KNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQ 182
              E Y RL R +  +S    R  Q +D     + +P+        +N +   + +  K+
Sbjct: 121 S--ENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPV--------ANHQYNIEYERKKK 170

Query: 183 TEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQ 242
            + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ V N +G ++
Sbjct: 171 EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHK 230

Query: 243 GTYELKPEYK 252
            T+ELKPEY+
Sbjct: 231 NTWELKPEYR 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|Q2T9L9|T2FB_BOVIN General transcription factor IIF subunit 2 OS=Bos taurus GN=GTF2F2 PE=2 SV=1

 Score = 94.4 bits (233), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 129/250 (51%), Gaps = 22/250 (8%)

Query: 11  GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM-E 69
           G+ +L  AK +  VWL+K P  +++ W   A +     V K+ ++ +  +++ + FT+ E
Sbjct: 5   GELDLTGAKQNTGVWLVKVPKYLSQQW---AKAPGRGEVGKLRIAKNQGRTE-VSFTLNE 60

Query: 70  TTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPHE 122
             A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P  
Sbjct: 61  DLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAA 120

Query: 123 KNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQ 182
              E Y RL R +  +S    R  Q +D     + +P+        +N +   + +  K+
Sbjct: 121 N--ENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPV--------ANHQYNIEYERKKK 170

Query: 183 TEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQ 242
            + KR R D+  + D++F  FE+   + LK LV  T QP  +LK+IL E+ V N +G ++
Sbjct: 171 EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVSYLKDILKEIGVQNVKGIHK 230

Query: 243 GTYELKPEYK 252
            T+ELKPEY+
Sbjct: 231 NTWELKPEYR 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: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 94.0 bits (232), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 129/250 (51%), Gaps = 22/250 (8%)

Query: 11  GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM-E 69
           G+ +L  AK +  VWL+K P  +++ W   A +     V K+ ++ +  +++ + FT+ E
Sbjct: 5   GELDLTGAKQNTGVWLVKVPKYLSQQW---AKASGRGEVGKLRIAKNQGRTE-VSFTLNE 60

Query: 70  TTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPHE 122
             A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P  
Sbjct: 61  DLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAA 120

Query: 123 KNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQ 182
              E Y +L R +  +S    R  Q +D     + +P+        +N +   + +  K+
Sbjct: 121 S--ENYMKLKRLQIEESSKPVRLSQQLDKVVTTNYKPV--------ANHQYNIEYERKKK 170

Query: 183 TEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQ 242
            + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ + N +G ++
Sbjct: 171 EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIHK 230

Query: 243 GTYELKPEYK 252
            T+ELKPEY+
Sbjct: 231 NTWELKPEYR 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|Q01750|T2FB_RAT General transcription factor IIF subunit 2 OS=Rattus norvegicus GN=Gtf2f2 PE=2 SV=1

 Score = 92.0 bits (227), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 128/250 (51%), Gaps = 22/250 (8%)

Query: 11  GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM-E 69
           G+ +L  AK +  VWL+K P  +++ W   A +     V K+ ++ +  +++ + FT+ E
Sbjct: 5   GELDLTGAKQNTGVWLVKVPKYLSQQW---AKAPGRGEVGKLRIAKNQGRTE-VSFTLNE 60

Query: 70  TTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPHE 122
             A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P  
Sbjct: 61  DLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAA 120

Query: 123 KNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQ 182
              E Y +L R +  +S    R  Q  D     + +P+        +N +   + +  K+
Sbjct: 121 S--ENYMKLKRLQIEESSKPVRLSQQADKVVTTNYKPV--------ANHQYNIEYERKKK 170

Query: 183 TEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQ 242
            + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ + N +G ++
Sbjct: 171 EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIHK 230

Query: 243 GTYELKPEYK 252
            T+ELKPEY+
Sbjct: 231 NTWELKPEYR 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|P41900|T2FB_DROME General transcription factor IIF subunit 2 OS=Drosophila melanogaster GN=TfIIFbeta PE=2 SV=2

 Score = 91.7 bits (226), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 69/255 (27%), Positives = 124/255 (48%), Gaps = 28/255 (10%)

Query: 14  NLDTAKADRSVWLMKCPLVVAKSWQNQASSQD----------------SQPVAKVILSLD 57
           +LD + A R VWL+K P  +A+ W+   ++ D                S  +   +L+LD
Sbjct: 15  DLDLSNAGRGVWLVKVPKYIAQKWEKAPTNMDVGKLRINKTPGQKAQVSLSLTPAVLALD 74

Query: 58  PLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFD 117
           P +    +  ++ + V+  +L      + +  K+    S     N+ K+ MEG++  K +
Sbjct: 75  PEEKIPTEHILDVSQVTKQTLGVFSHMAPSDGKENSTTSAAQPDNE-KLYMEGRIVQKLE 133

Query: 118 MKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKA 177
            +P   N   Y +L  E   K+    R++Q ID     + +P+      I    +++KKA
Sbjct: 134 CRPIADNC--YMKLKLESIRKASEPQRRVQPIDKIVQ-NFKPVKDHAHNIEY--RERKKA 188

Query: 178 QPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK 237
                 E K+ R D+  + D++F  FE+   + +K LV+ T+QP  +LKEIL ++C YN 
Sbjct: 189 ------EGKKARDDKNAVMDMLFHAFEKHQYYNIKDLVKITNQPISYLKEILKDVCDYNM 242

Query: 238 RGTNQGTYELKPEYK 252
           +  ++  +ELK EY+
Sbjct: 243 KNPHKNMWELKKEYR 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 = 89.7 bits (221), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/264 (27%), Positives = 136/264 (51%), Gaps = 36/264 (13%)

Query: 11  GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM-E 69
           G+ +L+ AK +  +WL+K P  +A+ W   A +     V K+ +  +  +++ + FT+ E
Sbjct: 6   GELDLNGAKQNTGMWLVKLPKYLAQQW---AKATGRGEVGKLRIVKNQGKTE-VSFTLNE 61

Query: 70  TTAVSNDSLNRPKSYSLNMFKD--FV-------PMSVFSESNQG------------KVAM 108
             A   D   +P S  ++  ++  F+        ++V +ES  G            K+A+
Sbjct: 62  ELASIQDIGGKPASSLVSTPREHPFLLQSVGGQTLTVLTESLSGQSEDKSENRVIDKLAL 121

Query: 109 EGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLIS 168
           EG V H+ + +P   +   Y ++ R++  +S    RQ Q ++     + +P+        
Sbjct: 122 EGIVVHRAECRPAASD--NYMQMKRKQIEESSKPKRQSQQLEKAVTSNYKPV-------- 171

Query: 169 SNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEI 228
           SN +   + +  K+ + KR R D+ ++ D++F  FE+   + +K LV  T QP  +LKEI
Sbjct: 172 SNHQYNIEYEKKKKDDGKRARVDKHQVLDMLFSAFEKHQYYNIKDLVDITKQPVTYLKEI 231

Query: 229 LNELCVYNKRGTNQGTYELKPEYK 252
           L ++ +YN +GT++ T+ELKPEY+
Sbjct: 232 LRDIGIYNMKGTHKNTWELKPEYR 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 = 87.0 bits (214), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 113/249 (45%), Gaps = 37/249 (14%)

Query: 13  GNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAK----VILSLDPLQSDSMQFTM 68
           G ++T  AD  VWL+K P  +++SWQ     +  Q   K    + LS  P      +F +
Sbjct: 11  GEVNTDNADNQVWLIKVPKFLSESWQKIGQGEIGQIHIKGGDNISLSYGP--DVGQEFQL 68

Query: 69  ETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEY 128
            TTA + D+                P+ +FSE   G +A+EG +  + D+K   ++  +Y
Sbjct: 69  ITTANTLDN---------------QPLKIFSEDKDGALALEGNIGLRCDIKIDVES-PQY 112

Query: 129 GRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKRT 188
             L + R  K   K R  QVID        P      L  +N   K K   V  T+ K++
Sbjct: 113 RDLMKSRHTKYNTKTRMTQVIDESE--LFTPT-----LFDAN---KVKVSTVGITQKKKS 162

Query: 189 RRD-----RGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQG 243
                     E+ D++F  F  + +  LK L   T+QP   LK IL ++C+ NKRG    
Sbjct: 163 TDKKEKLPEDEVLDLIFSAFRAEKHLDLKTLESFTEQPKNHLKTILEKVCILNKRGPYHH 222

Query: 244 TYELKPEYK 252
            YELKPE++
Sbjct: 223 LYELKPEFR 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 = 67.4 bits (163), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/154 (33%), Positives = 78/154 (50%), Gaps = 4/154 (2%)

Query: 105 KVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQ-IQVIDNDHGVHMRPMPGM 163
           K A+ G V H+  + P   N   Y ++  +R N   + N++ I  +D   GV M    GM
Sbjct: 211 KTAIVGTVCHECQVMPS-MNDPNYHKIVEQRRNIVKLNNKERITTLDETVGVTM-SHTGM 268

Query: 164 VGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQ 223
             + S NS   K  +   ++ +K  R  + E+ D +FKLF+    W+LK L + T QP  
Sbjct: 269 -SMRSDNSNFLKVGREKAKSNIKSIRMPKKEILDYLFKLFDEYDYWSLKGLKERTRQPEA 327

Query: 224 FLKEILNELCVYNKRGTNQGTYELKPEYKKSVED 257
            LKE L+++    K+G     Y L+PEYKK  E+
Sbjct: 328 HLKECLDKVATLVKKGPYAFKYTLRPEYKKLKEE 361

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	261
317106673	262	JHL18I08.10 [Jatropha curcas]	0.992	0.988	0.818	1e-120
255538806	257	Transcription initiation factor IIF subu	0.969	0.984	0.843	1e-120
449469921	260	PREDICTED: transcription initiation fact	0.980	0.984	0.793	1e-118
224085774	261	predicted protein [Populus trichocarpa]	0.980	0.980	0.785	1e-117
224062059	265	predicted protein [Populus trichocarpa]	0.938	0.924	0.804	1e-116
302142579	259	unnamed protein product [Vitis vinifera]	0.980	0.988	0.784	1e-113
356518378	262	PREDICTED: transcription initiation fact	0.980	0.977	0.756	1e-113
359492177	260	PREDICTED: transcription initiation fact	0.980	0.984	0.784	1e-113
359807121	262	uncharacterized protein LOC100788473 [Gl	0.931	0.927	0.791	1e-113
388521215	258	unknown [Lotus japonicus]	0.927	0.937	0.792	1e-112

>gi|317106673|dbj|BAJ53176.1| JHL18I08.10 [Jatropha curcas]

 Score =  437 bits (1125), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 216/264 (81%), Positives = 239/264 (90%), Gaps = 5/264 (1%)

Query: 1   MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQ 60
           M++D  N+G+  G L+TAKADRSVWLMKCPLVVAKSWQ+ ASS DS PVAKV+LSLDPL+
Sbjct: 1   MDEDHGNNGSNSGVLETAKADRSVWLMKCPLVVAKSWQSHASSSDSHPVAKVVLSLDPLR 60

Query: 61  SD---SMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFD 117
           SD   ++QFTME     N+  N PKSYSLNMFKDFVPM VFSE++QG+VAMEGKVEHKFD
Sbjct: 61  SDDPSALQFTMEMAG--NEIGNIPKSYSLNMFKDFVPMCVFSETSQGRVAMEGKVEHKFD 118

Query: 118 MKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKA 177
           MKPHE+N+EEYGRLCRERTNKSM+KNRQIQVIDND GVHMRPMPGM+GL+SS+SKDKKK 
Sbjct: 119 MKPHEENIEEYGRLCRERTNKSMVKNRQIQVIDNDRGVHMRPMPGMIGLMSSSSKDKKKT 178

Query: 178 QPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK 237
            PVKQ+++KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK
Sbjct: 179 APVKQSDMKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK 238

Query: 238 RGTNQGTYELKPEYKKSVEDGGAD 261
           RGTNQGTYELKPEYKKS ED GAD
Sbjct: 239 RGTNQGTYELKPEYKKSAEDAGAD 262

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

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 =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 216/256 (84%), Positives = 233/256 (91%), Gaps = 3/256 (1%)

Query: 7   NHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSD-SMQ 65
           +HG+  G L+TAKADRSVWLMKCPLVVA+SW++ ASS DS PVAKV+LSLDPL+SD S+Q
Sbjct: 4   DHGSSSGILETAKADRSVWLMKCPLVVARSWKSHASSSDSHPVAKVVLSLDPLRSDDSLQ 63

Query: 66  FTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNM 125
           FTME     N   N PKSYSLNMFKDFVPMSVFSE+ QG+VA+EGKVEHKFDMKPHE+NM
Sbjct: 64  FTMEMAGTENG--NVPKSYSLNMFKDFVPMSVFSETTQGRVAIEGKVEHKFDMKPHEENM 121

Query: 126 EEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEV 185
           EEYGRLCRERTNKSMIKNRQIQVIDND GVHMRPMPGMVGLISS+SKDKKK  PVKQ+++
Sbjct: 122 EEYGRLCRERTNKSMIKNRQIQVIDNDRGVHMRPMPGMVGLISSSSKDKKKTAPVKQSDM 181

Query: 186 KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTY 245
           KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTY
Sbjct: 182 KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTY 241

Query: 246 ELKPEYKKSVEDGGAD 261
           ELKPEYKKS ED G D
Sbjct: 242 ELKPEYKKSAEDTGGD 257

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 =  429 bits (1103), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 208/262 (79%), Positives = 227/262 (86%), Gaps = 6/262 (2%)

Query: 3   DDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSD 62
           +D+   G    NLDT KADRSVWLMKCPL+VAKSWQ    S DS P+AKVILSLDPLQSD
Sbjct: 2   EDEHGSGGSSSNLDTGKADRSVWLMKCPLLVAKSWQAHPPS-DSLPLAKVILSLDPLQSD 60

Query: 63  ---SMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMK 119
              S+QF ME      ++ N PKS+SLNMFKDFVPM VFSE++QGKV+MEGKVEHKFDMK
Sbjct: 61  ESSSLQFKMEMAGT--ETGNVPKSFSLNMFKDFVPMCVFSEASQGKVSMEGKVEHKFDMK 118

Query: 120 PHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQP 179
           PH +N+E YG+LCRERTNKSM+KNRQIQVIDND GVHMRPMPGMVGLISS SK+KKK  P
Sbjct: 119 PHSENLEMYGKLCRERTNKSMVKNRQIQVIDNDRGVHMRPMPGMVGLISSTSKEKKKVAP 178

Query: 180 VKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRG 239
           VKQ++VKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRG
Sbjct: 179 VKQSDVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRG 238

Query: 240 TNQGTYELKPEYKKSVEDGGAD 261
           TNQGTYELKPEYKKSVED G +
Sbjct: 239 TNQGTYELKPEYKKSVEDTGGE 260

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 =  428 bits (1100), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 209/266 (78%), Positives = 233/266 (87%), Gaps = 10/266 (3%)

Query: 1   MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQAS--SQDSQPVAKVILSLDP 58
           ME+D S+      NL+T+KAD+SVWLMKCP+VVAKSW+   S  S DS P+AKV+LSLDP
Sbjct: 1   MEEDNSS---SSANLETSKADKSVWLMKCPVVVAKSWKTHTSPSSSDSAPLAKVVLSLDP 57

Query: 59  LQSD---SMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHK 115
           LQSD   ++QFTME      ++ N PKSYSLNMFKDFVPM VFSE+ QGKVAMEGKVEHK
Sbjct: 58  LQSDDPSALQFTMEM--ARTEAGNVPKSYSLNMFKDFVPMCVFSETPQGKVAMEGKVEHK 115

Query: 116 FDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKK 175
           FDMKPHE+N+EEY +LCRERT KSM+K RQIQVI+ND GVHMRPMPGMVGLISS+SKDKK
Sbjct: 116 FDMKPHEQNIEEYHKLCRERTKKSMVKIRQIQVINNDRGVHMRPMPGMVGLISSSSKDKK 175

Query: 176 KAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVY 235
           + QPVKQ++VKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVY
Sbjct: 176 RPQPVKQSDVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVY 235

Query: 236 NKRGTNQGTYELKPEYKKSVEDGGAD 261
           NKRGTNQGTYELKPEYKK+VED GAD
Sbjct: 236 NKRGTNQGTYELKPEYKKTVEDTGAD 261

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 =  422 bits (1086), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 202/251 (80%), Positives = 226/251 (90%), Gaps = 6/251 (2%)

Query: 15  LDTAKADRSVWLMKCPLVVAKSWQ-NQASSQDSQPVAKVILSLDPLQSD---SMQFTMET 70
           L+T+KAD++VWLMKCP+VVAKSW+ +  SS DS P+AKV+LSLDPLQSD   ++QFTME 
Sbjct: 17  LETSKADKAVWLMKCPVVVAKSWKSHHTSSSDSAPLAKVVLSLDPLQSDDPSAIQFTME- 75

Query: 71  TAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGR 130
                ++ N PKSYSLNMFKDFVPM VFSE+ QG+V+MEGKVEHKFDMKPHE+N+EEY +
Sbjct: 76  -MARTETGNVPKSYSLNMFKDFVPMGVFSETPQGRVSMEGKVEHKFDMKPHEENIEEYSK 134

Query: 131 LCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKRTRR 190
           LCR+RT KSMIKNRQI+VIDND GVHMRPMPGMVGLISS SKDKKK QPVKQ++VKRTRR
Sbjct: 135 LCRDRTKKSMIKNRQIRVIDNDRGVHMRPMPGMVGLISSTSKDKKKTQPVKQSDVKRTRR 194

Query: 191 DRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPE 250
           DRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPE
Sbjct: 195 DRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPE 254

Query: 251 YKKSVEDGGAD 261
           YKK+ ED GAD
Sbjct: 255 YKKTAEDTGAD 265

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142579|emb|CBI19782.3| unnamed protein product [Vitis vinifera]

 Score =  414 bits (1064), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 207/264 (78%), Positives = 231/264 (87%), Gaps = 8/264 (3%)

Query: 1   MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQ 60
           ME++Q N  +   NL+T KA+RSVWLMKCPL V+KS     SS +SQPVAKV+LSLDPL+
Sbjct: 1   MEEEQGNSSSS--NLETGKAERSVWLMKCPLAVSKS-WQSHSSSESQPVAKVVLSLDPLR 57

Query: 61  SD---SMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFD 117
           S+   +++FTME T     + N PKSYSLNMFKDFVPM VFSE+NQG+VAMEGKVEHKFD
Sbjct: 58  SEDPSALEFTMEMTGTG--APNMPKSYSLNMFKDFVPMCVFSETNQGRVAMEGKVEHKFD 115

Query: 118 MKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKA 177
           MKPH +N+EEYG+LCRERTNKSMIKNRQIQVIDND GVHMRPMPGMVGLI+SNSKDKKK 
Sbjct: 116 MKPHNENIEEYGKLCRERTNKSMIKNRQIQVIDNDRGVHMRPMPGMVGLIASNSKDKKKT 175

Query: 178 QPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK 237
            PVK +++KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK
Sbjct: 176 APVKGSDMKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK 235

Query: 238 RGTNQGTYELKPEYKKSVEDGGAD 261
           RGTNQGTYELKPEYKKS ED GA+
Sbjct: 236 RGTNQGTYELKPEYKKSAEDTGAE 259

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518378|ref|XP_003527856.1| PREDICTED: transcription initiation factor IIF subunit beta-like [Glycine max]

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 202/267 (75%), Positives = 227/267 (85%), Gaps = 11/267 (4%)

Query: 1   MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQ 60
           M+++    G+   NL+T KA+RSVWLMKCPLVVAKSWQ    SQ   P+AKV+LSLDPL 
Sbjct: 1   MDEENGYSGSISSNLETTKAERSVWLMKCPLVVAKSWQTHPPSQ---PLAKVVLSLDPLH 57

Query: 61  SD-----SMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQG-KVAMEGKVEH 114
            +     ++QFTME      +++N  K+YSLNMFKDFVPM VFSE++QG KVAMEGKVEH
Sbjct: 58  PEEDDPSAVQFTMEMAGT--EAVNMSKTYSLNMFKDFVPMCVFSETSQGGKVAMEGKVEH 115

Query: 115 KFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDK 174
           KFDMKPH +N+EEYG+LCRERTNKSMIKNRQIQVIDND GV MRPMPGM+GL+SSNSKDK
Sbjct: 116 KFDMKPHGENIEEYGKLCRERTNKSMIKNRQIQVIDNDRGVLMRPMPGMIGLVSSNSKDK 175

Query: 175 KKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCV 234
           KK QPVKQ++ KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCV
Sbjct: 176 KKTQPVKQSDTKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCV 235

Query: 235 YNKRGTNQGTYELKPEYKKSVEDGGAD 261
           YNKRG NQGTYELKPEYKKSVED  A+
Sbjct: 236 YNKRGANQGTYELKPEYKKSVEDTSAE 262

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359492177|ref|XP_002279990.2| PREDICTED: transcription initiation factor IIF subunit beta [Vitis vinifera]

 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 208/265 (78%), Positives = 229/265 (86%), Gaps = 9/265 (3%)

Query: 1   MEDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQ 60
           ME++Q N  +   NL+T KA+RSVWLMKCPL V+KS     SS +SQPVAKV+LSLDPL+
Sbjct: 1   MEEEQGNSSSS--NLETGKAERSVWLMKCPLAVSKS-WQSHSSSESQPVAKVVLSLDPLR 57

Query: 61  SDS----MQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKF 116
           S+      QFTME T     + N PKSYSLNMFKDFVPM VFSE+NQG+VAMEGKVEHKF
Sbjct: 58  SEDPSALEQFTMEMTGTG--APNMPKSYSLNMFKDFVPMCVFSETNQGRVAMEGKVEHKF 115

Query: 117 DMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKK 176
           DMKPH +N+EEYG+LCRERTNKSMIKNRQIQVIDND GVHMRPMPGMVGLI+SNSKDKKK
Sbjct: 116 DMKPHNENIEEYGKLCRERTNKSMIKNRQIQVIDNDRGVHMRPMPGMVGLIASNSKDKKK 175

Query: 177 AQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYN 236
             PVK +++KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYN
Sbjct: 176 TAPVKGSDMKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYN 235

Query: 237 KRGTNQGTYELKPEYKKSVEDGGAD 261
           KRGTNQGTYELKPEYKKS ED GA+
Sbjct: 236 KRGTNQGTYELKPEYKKSAEDTGAE 260

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359807121|ref|NP_001241605.1| uncharacterized protein LOC100788473 [Glycine max] gi|255646380|gb|ACU23669.1| unknown [Glycine max]

 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 201/254 (79%), Positives = 223/254 (87%), Gaps = 11/254 (4%)

Query: 14  NLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSD-----SMQFTM 68
           NL+T KA+RSVWLMKCPLVVAKSWQ    SQ   P+AKV+LSLDPL  +     ++QFTM
Sbjct: 14  NLETTKAERSVWLMKCPLVVAKSWQAHPPSQ---PLAKVVLSLDPLHPEEDDPSAVQFTM 70

Query: 69  ETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQG-KVAMEGKVEHKFDMKPHEKNMEE 127
           E     ++++N PK+YSLNMFKDFVPM VFSE++QG KVAMEGKVEHKFDMKPH +N+EE
Sbjct: 71  EMAG--SEAVNMPKTYSLNMFKDFVPMCVFSETSQGGKVAMEGKVEHKFDMKPHGENIEE 128

Query: 128 YGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKR 187
           YG+LCRERTNKSMIKNRQIQVIDND GV MRPMPGM+GL+SSNSKDKKK QPVKQ++ KR
Sbjct: 129 YGKLCRERTNKSMIKNRQIQVIDNDRGVLMRPMPGMIGLVSSNSKDKKKTQPVKQSDTKR 188

Query: 188 TRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYEL 247
           TRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRG NQGTYEL
Sbjct: 189 TRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGANQGTYEL 248

Query: 248 KPEYKKSVEDGGAD 261
           KPEYKKSVED  A+
Sbjct: 249 KPEYKKSVEDTSAE 262

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388521215|gb|AFK48669.1| unknown [Lotus japonicus]

 Score =  410 bits (1054), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 198/250 (79%), Positives = 224/250 (89%), Gaps = 8/250 (3%)

Query: 13  GNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDS----MQFTM 68
            N++T+KA+RSVWLMKCP+VVAKSWQN   S  SQP++KV+LSLDPL  +     +QFTM
Sbjct: 8   SNVETSKAERSVWLMKCPVVVAKSWQNHHPS-PSQPLSKVVLSLDPLLPEDDPSHLQFTM 66

Query: 69  ETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQG-KVAMEGKVEHKFDMKPHEKNMEE 127
           E T   ++++N PK+Y+LNMFKDFVPM VFSE++QG KVAMEGKVEHKFDMKPH +N+EE
Sbjct: 67  EMTG--SEAVNMPKTYALNMFKDFVPMCVFSETSQGGKVAMEGKVEHKFDMKPHGENIEE 124

Query: 128 YGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKR 187
           YG+LCRERTNKSMIKNRQIQVIDND GV MRPMPGM+GL+SSNSKDKK+ QPVKQ++ KR
Sbjct: 125 YGKLCRERTNKSMIKNRQIQVIDNDRGVLMRPMPGMIGLVSSNSKDKKRTQPVKQSDTKR 184

Query: 188 TRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYEL 247
           TRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRG NQGTYEL
Sbjct: 185 TRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGANQGTYEL 244

Query: 248 KPEYKKSVED 257
           KPEYKKSVED
Sbjct: 245 KPEYKKSVED 254

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

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	261
TAIR|locus:2005674	261	AT1G75510 [Arabidopsis thalian	0.934	0.934	0.700	5.7e-91
POMBASE|SPBC1198.13c	307	tfg2 "transcription factor TFI	0.919	0.781	0.310	3.3e-24
UNIPROTKB|Q2T9L9	249	GTF2F2 "General transcription	0.888	0.931	0.303	8e-21
UNIPROTKB|P13984	249	GTF2F2 "General transcription	0.869	0.911	0.310	8e-21
MGI|MGI:1915955	249	Gtf2f2 "general transcription	0.869	0.911	0.302	1.3e-20
UNIPROTKB|Q63489	249	Gtf2f2 "RAP30" [Rattus norvegi	0.869	0.911	0.298	2.1e-20
RGD|620772	249	Gtf2f2 "general transcription	0.869	0.911	0.298	4.4e-20
FB|FBgn0010421	277	TfIIFbeta "Transcription facto	0.869	0.819	0.274	5.7e-20
UNIPROTKB|E2RGQ0	245	GTF2F2 "Uncharacterized protei	0.865	0.922	0.302	2.5e-19
ZFIN|ZDB-GENE-050417-374	256	gtf2f2b "general transcription	0.854	0.871	0.302	3.1e-19

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

 Score = 907 (324.3 bits), Expect = 5.7e-91, P = 5.7e-91
 Identities = 180/257 (70%), Positives = 206/257 (80%)

Query:    14 NLDTAKADRSVWLMKCPLVVAKSWQNQASSQ-------DSQP-VAKVILSLDPLQSDSM- 64
             NLD  K+DRS+WLMKCP+VV K+W   A+S        DS P +AK++  +DPL+ DS  
Sbjct:     6 NLDIEKSDRSIWLMKCPVVVDKAWHKIAASSSSSFASSDSPPDMAKIVREVDPLRDDSPP 65

Query:    65 QFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKN 124
             +F M    V  +  N PK Y+LNMF DFVPM  FS+ NQG  A EGKV+HKFDMKP+ + 
Sbjct:    66 EFKMYM--VGAEYGNMPKCYALNMFTDFVPMGGFSDVNQGCAAAEGKVDHKFDMKPYGET 123

Query:   125 MEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTE 184
             +EEY RLCRERT+K+M+KNRQIQVIDND GVHMRPMPGM+GL+SSNSK+K+K  PVKQTE
Sbjct:   124 IEEYARLCRERTSKAMVKNRQIQVIDNDRGVHMRPMPGMLGLVSSNSKEKRKPPPVKQTE 183

Query:   185 VKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGT 244
             VKRTRRDRGELE IMFKLFE QPNW LKQLVQETDQPAQFLKEILNELCVYNKRG+NQGT
Sbjct:   184 VKRTRRDRGELEAIMFKLFEGQPNWTLKQLVQETDQPAQFLKEILNELCVYNKRGSNQGT 243

Query:   245 YELKPEYKKSVED--GG 259
             YELKPEYKKS ED  GG
Sbjct:   244 YELKPEYKKSAEDDTGG 260

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

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

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 81/261 (31%), Positives = 131/261 (50%)

Query:     2 EDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQS 61
             EDD+  + +  G+LD  +    VWL+K P  +   W N     D+  +  V      +++
Sbjct:    12 EDDR--YEDDAGDLDLGQIGSRVWLVKIPKFLMDKW-NSIPEDDAANLGCV-----RVKN 63

Query:    62 DSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMS-VFSESNQGK----VAMEGKVEHKF 116
             D +Q  ++    S ++ + PK Y+L +   FV  S VF ES         A+ G V H+ 
Sbjct:    64 DEIQLLLQN---SPENADVPKIYNLRVMNKFVRNSYVFRESETSSSMKSTALVGTVAHEC 120

Query:   117 DMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLIS-SNSKDKK 175
             ++ P     ++Y R+ ++R   +    R++Q+ID D G  +   PG +G  S S +   +
Sbjct:   121 NVSPVIN--DDYRRVMQKRALAASAPKRKVQMID-DRGGSLLA-PGTLGSRSRSTTSFIR 176

Query:   176 KAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVY 235
               +P     +K +R  R EL DI+FK FE    W LK L +   QP  +LKE+L+ + + 
Sbjct:   177 NVKPRTGEGLKNSRIPRNELLDILFKCFEDYEYWTLKGLREYVKQPEVYLKEVLDSIAIL 236

Query:   236 NKRGTNQGTYELKPEYKKSVE 256
             NKRG     Y LKPEYK +++
Sbjct:   237 NKRGPYALKYSLKPEYKGTMD 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

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

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 78/257 (30%), Positives = 132/257 (51%)

Query:    12 KGNLDT--AKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM- 68
             +G LD   AK +  VWL+K P  +++ W   A +     V K+ ++ +  +++ + FT+ 
Sbjct:     4 RGELDLTGAKQNTGVWLVKVPKYLSQQW---AKAPGRGEVGKLRIAKNQGRTE-VSFTLN 59

Query:    69 ETTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPH 121
             E  A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P 
Sbjct:    60 EDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA 119

Query:   122 EKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVK 181
                 E Y RL R +  +S    R  Q +D     + +P+         N + ++K    K
Sbjct:   120 AN--ENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANH----QYNIEYERK----K 169

Query:   182 QTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTN 241
             + + KR R D+  + D++F  FE+   + LK LV  T QP  +LK+IL E+ V N +G +
Sbjct:   170 KEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVSYLKDILKEIGVQNVKGIH 229

Query:   242 QGTYELKPEYKK-SVED 257
             + T+ELKPEY+   VE+
Sbjct:   230 KNTWELKPEYRHYQVEE 246

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

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

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 78/251 (31%), Positives = 130/251 (51%)

Query:    12 KGNLDT--AKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM- 68
             +G LD   AK +  VWL+K P  +++ W  +AS +    V K+ ++    +++ + FT+ 
Sbjct:     4 RGELDLTGAKQNTGVWLVKVPKYLSQQWA-KASGRGE--VGKLRIAKTQGRTE-VSFTLN 59

Query:    69 ETTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPH 121
             E  A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P 
Sbjct:    60 EDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA 119

Query:   122 EKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVK 181
                 E Y RL R +  +S    R  Q +D     + +P+         N + ++K    K
Sbjct:   120 AS--ENYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANH----QYNIEYERK----K 169

Query:   182 QTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTN 241
             + + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ V N +G +
Sbjct:   170 KEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIH 229

Query:   242 QGTYELKPEYK 252
             + T+ELKPEY+
Sbjct:   230 KNTWELKPEYR 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

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

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 76/251 (30%), Positives = 131/251 (52%)

Query:    12 KGNLDT--AKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM- 68
             +G LD   AK +  VWL+K P  +++ W  +AS +    V K+ ++ +  +++ + FT+ 
Sbjct:     4 RGELDLTGAKQNTGVWLVKVPKYLSQQWA-KASGRGE--VGKLRIAKNQGRTE-VSFTLN 59

Query:    69 ETTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPH 121
             E  A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P 
Sbjct:    60 EDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA 119

Query:   122 EKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVK 181
                 E Y +L R +  +S    R  Q +D     + +P+         N + ++K    K
Sbjct:   120 AS--ENYMKLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANH----QYNIEYERK----K 169

Query:   182 QTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTN 241
             + + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ + N +G +
Sbjct:   170 KEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIH 229

Query:   242 QGTYELKPEYK 252
             + T+ELKPEY+
Sbjct:   230 KNTWELKPEYR 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 = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 75/251 (29%), Positives = 129/251 (51%)

Query:    12 KGNLDT--AKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM- 68
             +G LD   AK +  VWL+K P  +++ W   A +     V K+ ++ +  +++ + FT+ 
Sbjct:     4 RGELDLTGAKQNTGVWLVKVPKYLSQQW---AKAPGRGEVGKLRIAKNQGRTE-VSFTLN 59

Query:    69 ETTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPH 121
             E  A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P 
Sbjct:    60 EDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA 119

Query:   122 EKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVK 181
                 E Y +L R +  +S    R  Q +D     + +P+         N + ++K    K
Sbjct:   120 AS--ENYMKLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANH----QYNIEYERK----K 169

Query:   182 QTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTN 241
             + + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ + N +G +
Sbjct:   170 KEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIH 229

Query:   242 QGTYELKPEYK 252
             + T+ELKPEY+
Sbjct:   230 KNTWELKPEYR 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

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

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 75/251 (29%), Positives = 128/251 (50%)

Query:    12 KGNLDT--AKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM- 68
             +G LD   AK +  VWL+K P  +++ W   A +     V K+ ++ +  +++ + FT+ 
Sbjct:     4 RGELDLTGAKQNTGVWLVKVPKYLSQQW---AKAPGRGEVGKLRIAKNQGRTE-VSFTLN 59

Query:    69 ETTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPH 121
             E  A  +D   +P S S      FV        ++VF+ES+  K+++EG V  + + +P 
Sbjct:    60 EDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA 119

Query:   122 EKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVK 181
                 E Y +L R +  +S    R  Q  D     + +P+         N + ++K    K
Sbjct:   120 AS--ENYMKLKRLQIEESSKPVRLSQQADKVVTTNYKPVANH----QYNIEYERK----K 169

Query:   182 QTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTN 241
             + + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ + N +G +
Sbjct:   170 KEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIH 229

Query:   242 QGTYELKPEYK 252
             + T+ELKPEY+
Sbjct:   230 KNTWELKPEYR 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

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

 Score = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 70/255 (27%), Positives = 125/255 (49%)

Query:    14 NLDTAKADRSVWLMKCPLVVAKSWQ-------------NQASSQDSQ---PVAKVILSLD 57
             +LD + A R VWL+K P  +A+ W+             N+   Q +Q    +   +L+LD
Sbjct:    15 DLDLSNAGRGVWLVKVPKYIAQKWEKAPTNMDVGKLRINKTPGQKAQVSLSLTPAVLALD 74

Query:    58 PLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFD 117
             P +    +  ++ + V+  +L      + +  K+    S     N+ K+ MEG++  K +
Sbjct:    75 PEEKIPTEHILDVSQVTKQTLGVFSHMAPSDGKENSTTSAAQPDNE-KLYMEGRIVQKLE 133

Query:   118 MKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKA 177
              +P   N   Y +L  E   K+    R++Q ID     + +P+      I    +++KKA
Sbjct:   134 CRPIADNC--YMKLKLESIRKASEPQRRVQPIDKIVQ-NFKPVKDHAHNIEY--RERKKA 188

Query:   178 QPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNK 237
                   E K+ R D+  + D++F  FE+   + +K LV+ T+QP  +LKEIL ++C YN 
Sbjct:   189 ------EGKKARDDKNAVMDMLFHAFEKHQYYNIKDLVKITNQPISYLKEILKDVCDYNM 242

Query:   238 RGTNQGTYELKPEYK 252
             +  ++  +ELK EY+
Sbjct:   243 KNPHKNMWELKKEYR 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

UNIPROTKB|E2RGQ0 GTF2F2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 231 (86.4 bits), Expect = 2.5e-19, P = 2.5e-19
 Identities = 76/251 (30%), Positives = 129/251 (51%)

Query:    12 KGNLD--TAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM- 68
             +G LD  + K +  VWL+K P  +++ W   A       V K+ ++ +  +++ + FT+ 
Sbjct:     4 RGELDLTSTKQNTGVWLVKVPKYLSQQW---AKDPGRGEVGKLRIAKNQGRTE-VSFTLN 59

Query:    69 ETTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKPH 121
             E  A  +D   +  S S      FV        ++VF+ES+  K+++EG V  + + +P 
Sbjct:    60 EDLANIHDIGGKLASVSTPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRP- 118

Query:   122 EKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVK 181
                 E+Y RL R +  +S    R  Q +D     + +P+         N + ++K    K
Sbjct:   119 -ATSEKYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANH----QYNIEYERK----K 169

Query:   182 QTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTN 241
             + + KR R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ V N +GT+
Sbjct:   170 KEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGVQNVKGTH 229

Query:   242 QGTYELKPEYK 252
             + T+ELKPEY+
Sbjct:   230 K-TWELKPEYR 239

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

GO:0005524 "ATP binding" evidence=IEA

ZFIN|ZDB-GENE-050417-374 gtf2f2b "general transcription factor IIF, polypeptide 2b" [Danio rerio (taxid:7955)]

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 75/248 (30%), Positives = 129/248 (52%)

Query:    14 NLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSM-QFTM--ET 70
             +L  AK +  VWL+K P  +++ W  +AS +    V K  L +   Q  ++  F +  E 
Sbjct:     9 DLTRAKQNTGVWLVKVPKYLSQQWA-KASGRGE--VGK--LKIGKAQGKTVVSFNLNEEL 63

Query:    71 TAV--SND---SLNRPKSYSLNMFK-DFVPMSVFSESNQGKVAMEGKVEHKFDMKPHEKN 124
             T V  S +   S+  P+ +   M       ++VF+ES+  K+A+EG V  + + +P    
Sbjct:    64 TVVDCSGEKISSVRSPREHPFTMQTVGGQTLAVFTESSD-KIALEGMVVQRAECRPAVS- 121

Query:   125 MEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTE 184
              E Y +L + +  +S    R  Q ++     + +P+       S N + +K+    K+ E
Sbjct:   122 -ESYMKLKKLQIEESTKPLRFSQRLEKAITTNYKPVSNH----SHNLEYEKR----KKEE 172

Query:   185 VKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGT 244
              KR R D+ ++ +++F  FE+   + ++ LV  T QP  +LKEIL E+ VYN RG ++ T
Sbjct:   173 GKRARADKQKVLEMLFSAFEKHQFYNIRDLVDITKQPVIYLKEILREIGVYNSRGPHKST 232

Query:   245 YELKPEYK 252
             +ELKPEY+
Sbjct:   233 WELKPEYR 240

GO:0005634 "nucleus" evidence=IEA

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

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q54KT7	T2FB_DICDI	3, ., 6, ., 4, ., 1, 2	0.3012	0.8122	0.8796	yes	no

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	0.737
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

Your Input: grail3.0002061701 SubName- Full=Putative uncharacterized protein; (262 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	261
pfam02270	259	pfam02270, TFIIF_beta, Transcription initiation fa	4e-64
COG5090	297	COG5090, TFG2, Transcription initiation factor IIF	2e-32

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

 Score =  200 bits (511), Expect = 4e-64
 Identities = 86/271 (31%), Positives = 130/271 (47%), Gaps = 41/271 (15%)

Query: 12  KGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETT 71
            G+LD + A +SVWL+K P  +++ W         + V K+ +  +      +   +   
Sbjct: 1   SGDLDLSNAKQSVWLVKVPKYLSEKWSKAPGDSGGE-VGKLRIKKNNGGKAQVSLLL--- 56

Query: 72  AVSNDSLNRPKSYSLNMFKDFV-PMSVFSESNQG-------------------------- 104
               ++ + PK Y L+M    V    VF+ESN G                          
Sbjct: 57  NEELENYDIPKEYDLDMQNVNVQNTYVFTESNLGKYKQKSKEVAGMPEQPQLAYPYVKTI 116

Query: 105 --KVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPG 162
             K A+EG+V H+ + +P E   EEY RL ++R  K+    R +QV+D    V     P 
Sbjct: 117 PKKTALEGRVVHECECRPVEN--EEYMRLKKKRILKASKPKRTVQVLDKI--VTQSYKP- 171

Query: 163 MVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPA 222
                S+NS+   K    K++E KR R  + EL D++FK FE+   W+LK L + T QP 
Sbjct: 172 -PSNHSNNSEYFIKK--KKKSEGKRARMPKNELLDLLFKAFEKHQYWSLKDLKERTRQPE 228

Query: 223 QFLKEILNELCVYNKRGTNQGTYELKPEYKK 253
            +LKEIL+E+ V NK+G    T+ELKPEY+ 
Sbjct: 229 AYLKEILDEIAVLNKKGPYANTWELKPEYRH 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 =  120 bits (301), Expect = 2e-32
 Identities = 77/249 (30%), Positives = 116/249 (46%), Gaps = 16/249 (6%)

Query: 14  NLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAV 73
           +LD       VWL+K PL +A+ W     ++  + +     S DP     +   +     
Sbjct: 21  DLDLNNRHTKVWLVKVPLFLAEKW-LSREAEIGELLGTKRTSTDPAV---ISLLLSN--- 73

Query: 74  SNDSLNRPKSYSLNMFKDFVPMS-VFSESNQG----KVAMEGKVEHKFDMKPHEKNMEEY 128
              +   P SY L +    V    VF ES         A+ G V H+  + P E N +EY
Sbjct: 74  EFCNGGFPSSYDLKIKPKDVNNYYVFRESETSTHEKNTAVVGTVNHECYVTP-EVN-DEY 131

Query: 129 GRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKRT 188
            R  ++R  KS  K   +QVID   G           L SS  +   + +     + KR 
Sbjct: 132 LRYKQDRGFKSDSKKSDVQVIDYLKGGKRGE--KFGSLRSSTLEFLARKRKKMLMDKKRE 189

Query: 189 RRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELK 248
           R  + E+ D++FK FE+ P W LK L +   QP  FLKEIL+++ V NK+G     YEL+
Sbjct: 190 RLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYELR 249

Query: 249 PEYKKSVED 257
           PEYK+++++
Sbjct: 250 PEYKQTMDE 258

Length = 297

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	261
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	95.24
PF12157	457	DUF3591: Protein of unknown function (DUF3591); In	94.95
KOG0008	1563	consensus Transcription initiation factor TFIID, s	92.48
PF04801	421	Sin_N: Sin-like protein conserved region; InterPro	90.82
PF04004	171	Leo1: Leo1-like protein; InterPro: IPR007149 Membe	90.57
KOG2473	484	consensus RNA polymerase III transcription factor	87.89
COG5179	968	TAF1 Transcription initiation factor TFIID, subuni	87.7

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

Probab=100.00  E-value=2.9e-71  Score=484.85  Aligned_cols=240  Identities=42%  Similarity=0.661  Sum_probs=207.6

Q ss_pred             CCCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEE-----ecccCCCCCCCCccee
Q 024896           11 GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTME-----TTAVSNDSLNRPKSYS   85 (261)
Q Consensus        11 ~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~-----l~~~~~~~~~iPkey~   85 (261)
                      +.++||.++++.+|||||||+||+++|..++.+.   ++|++++.+.++. .++.|.+.     .....++.+.+|..|.
T Consensus         7 ~~~dl~l~~~~~~vWLvKvP~fLa~kw~~~~~~~---e~g~l~i~k~~~d-aki~l~L~e~~p~~~~~~a~~g~~p~~~~   82 (254)
T KOG2905|consen    7 ESLDLDLENSGRGVWLVKVPKFLAEKWRKIPNSH---ESGKLRINKTPSD-AKIVLLLNEAIPEKQEREADVGKFPQQYK   82 (254)
T ss_pred             hhhhhccccccceEEEEeccHHHHHHHHhccccc---ccccccccCCCCc-ceEEEEeccccccchhhhhhcccCchhhh
Confidence            6789999999999999999999999999866432   7999999876543 44444443     0011134578999999


Q ss_pred             eccccCCceeeeeeecC-CcceeEEEEeeeeeEEeeCCCChHHHHHHHHHHhHHhhccccceEEeecCCCcccccCCCcc
Q 024896           86 LNMFKDFVPMSVFSESN-QGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMV  164 (261)
Q Consensus        86 l~~~~~~~~~~VFse~~-~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~~~R~~~a~~pkr~v~~ld~~~~~~~~p~~~~~  164 (261)
                      +++..++.|+||||+++ +++++++|+|+|+|+|+|+.  |++|++++++|+.+++.|+|+||+||++.|++|+|++||.
T Consensus        83 ~~~~~~~~~~~~~sd~~~~~k~a~eG~V~~e~~~~P~~--ne~Y~Rl~r~r~~k~~~k~r~vQ~iD~~~g~~~~p~~~~~  160 (254)
T KOG2905|consen   83 LNMKRRFFNMFVESDSSGPKKTAVEGTVVHECDVRPSA--NEEYMRLKRERIVKASKKKRQVQVIDKVVGVHMKPVPGHL  160 (254)
T ss_pred             hccCccccceeeeecCCCCccceeeeeeeeeeeccccc--CHHHHHHHHHHHHHhcCcccccccchhhcccccccCCCcc
Confidence            99998999999999987 78999999999999999996  5999999999999999999999999999999999999986


Q ss_pred             cccccCcccccccCcccchhhhcccCChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcc
Q 024896          165 GLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGT  244 (261)
Q Consensus       165 ~~~~~~~~~~kk~~~~kk~~~K~~Rm~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~  244 (261)
                      ..++..+..++    +++.++|++|+|++||+|+||+|||+|+||+||+|+++|+||++||||||++||+||++|||+|+
T Consensus       161 ~~~~~~~~~rk----K~k~e~Kr~R~dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~NkKg~~k~t  236 (254)
T KOG2905|consen  161 RSSSNIAYERK----KAKEEGKRTRRDKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNKKGPYKNT  236 (254)
T ss_pred             cccchhHHHHH----hhhhccccccccHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhccCcccCc
Confidence            43333333332    14789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccchhhhccccCCCC
Q 024896          245 YELKPEYKKSVEDGGA  260 (261)
Q Consensus       245 weLKpEYk~~~~~~~~  260 (261)
                      ||||||||++.+++..
T Consensus       237 yeLKPEYK~~~~ee~~  252 (254)
T KOG2905|consen  237 YELKPEYKKYKEEEKK  252 (254)
T ss_pred             eecCHHHhhhhhhhhc
Confidence            9999999999988653

>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=1e-69  Score=494.52  Aligned_cols=230  Identities=43%  Similarity=0.672  Sum_probs=122.6

Q ss_pred             CCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEEecccCCCCCCCCcceeeccccC
Q 024896           12 KGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKD   91 (261)
Q Consensus        12 ~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~l~~~~~~~~~iPkey~l~~~~~   91 (261)
                      +++||+++|+++|||||||+|||++|.+..+ +++++||+|+|+.++++  ..+++|.|+.....+..||++|+|+|++.
T Consensus         1 ~~~LD~s~a~~~vWLvKVPk~l~e~W~~~~~-~~~~~iG~lri~~~~~~--~~~v~l~L~~~~~~~~~iPkey~L~~~~~   77 (275)
T PF02270_consen    1 DGDLDTSKADRSVWLVKVPKFLSEKWSKAPD-DDEIEIGKLRISKDPNG--KPKVSLTLNDSLANHGNIPKEYDLDMSKD   77 (275)
T ss_dssp             -TBEE-HHHHTEEEEEEEEHHHHHHHTTSBT-T--TEEEEEEEEEE-TT--EEEEEEEE-HHHHT-T-S--EEEEEEE--
T ss_pred             Ccccccccccccccccccccccccccccccc-ccccccccccccccccc--ccccccccccccccccccccccccccccc
Confidence            4799999999999999999999999997654 46789999999987443  33455555544345569999999999999


Q ss_pred             C-ceeeeeeecCC-------------------------------------------cceeEEEEeeeeeEEeeCCCChHH
Q 024896           92 F-VPMSVFSESNQ-------------------------------------------GKVAMEGKVEHKFDMKPHEKNMEE  127 (261)
Q Consensus        92 ~-~~~~VFse~~~-------------------------------------------~~~~l~G~V~~e~~~~P~~~~~~~  127 (261)
                      . +|+|||||.+.                                           ++++|+|+|+|+|+|+|+.  +++
T Consensus        78 ~~~n~~VFse~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~G~I~~~~~~~P~~--~~~  155 (275)
T PF02270_consen   78 NVQNMYVFSESDQPGFKAKNKERAGAPNAGIPASLLREKKKKDRKRKYQPYVKTIPKKTALEGRIVHECDCRPVL--NDE  155 (275)
T ss_dssp             TTEEEEEEEEETT----------------------------------------ETT--EEEEEEEEEEEEE---------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCceEEEEEEEEEEEeEECC--CHH
Confidence            6 69999998753                                           4789999999999999996  579


Q ss_pred             HHHHHHHHhHHhhccccceEEeecCCCcccccCCCcccccccCcc-cccccCcccchhhhcccCChhHHHHHHHHHhhhC
Q 024896          128 YGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSK-DKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQ  206 (261)
Q Consensus       128 Y~~l~~~R~~~a~~pkr~v~~ld~~~~~~~~p~~~~~~~~~~~~~-~~kk~~~~kk~~~K~~Rm~k~eLld~LF~~Fe~~  206 (261)
                      |++++++|+.++++|+|++++|+......+.|++.+.    .+.. +.   .++|++++|++|||+++|+|+||+|||+|
T Consensus       156 Y~~~~~~r~~~a~~~kr~~~~i~~~~~~~~~~~~~~~----~~~~~~~---~~~k~~~~K~~R~~~~eL~d~lF~~Fe~~  228 (275)
T PF02270_consen  156 YRRLKRERIEKANKPKRTVQQIDEDVSQSYKPVSFHS----ANSKFFI---KKKKKQEEKRARMDKNELLDLLFKLFEKH  228 (275)
T ss_dssp             -------------------------------------------------------------THHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHhcCCCCeeEEeccccccCCCCccccc----ccchhcc---cccccccccceeCCHHHHHHHHHHHHHhC
Confidence            9999999999999999999999986555666643322    1111 11   22467899999999999999999999999


Q ss_pred             CCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcccccchhhhc
Q 024896          207 PNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKK  253 (261)
Q Consensus       207 ~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~  253 (261)
                      +||+||+|+++|+||++||||||++||+|||+|||+|+|+||||||+
T Consensus       229 ~ywslK~L~~~t~QP~~yLKeiL~eIa~~~k~g~~~~~w~LKpeyk~  275 (275)
T PF02270_consen  229 QYWSLKDLRQRTQQPEAYLKEILEEIAVLNKRGPHKNMWELKPEYKH  275 (275)
T ss_dssp             S-B-HHHHHHH--S-HHHHHHHHHHH--EE--TT---EE----SS--
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHhccCCcCCcEecchHHcC
Confidence            99999999999999999999999999999999999999999999986

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=1.3e-61  Score=422.17  Aligned_cols=242  Identities=32%  Similarity=0.487  Sum_probs=203.5

Q ss_pred             CCCCCcCCCCCCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEEecccCCCCCCCC
Q 024896            2 EDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRP   81 (261)
Q Consensus         2 ~~~~~~~~~~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~l~~~~~~~~~iP   81 (261)
                      +.|+-||+.-  |||+.+.+.+|||||||.||+++|.+.+ .+.|..+|++|+..+|.     .++|.|.. .++++++|
T Consensus        11 ~e~~~yed~~--dLdl~~~~~kVWLvkvP~FLaekw~sr~-~~~g~~lg~~r~~~d~a-----~isLlL~n-e~~n~~~P   81 (297)
T COG5090          11 EEDDRYEDDA--DLDLNNRHTKVWLVKVPLFLAEKWLSRE-AEIGELLGTKRTSTDPA-----VISLLLSN-EFCNGGFP   81 (297)
T ss_pred             cccccccccc--cccccccCceEEEEeccHHHHHHHhcch-hhhhhhhceeeecCCcc-----eEEEEecc-CCccCCCC
Confidence            4566777755  8999999999999999999999999654 34567799999986643     45555532 36788999


Q ss_pred             cceeeccccCCc-eeeeeeec----CCcceeEEEEeeeeeEEeeCCCChHHHHHHHHHHhHHhhccccceEEeecCCCcc
Q 024896           82 KSYSLNMFKDFV-PMSVFSES----NQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVH  156 (261)
Q Consensus        82 key~l~~~~~~~-~~~VFse~----~~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~~~R~~~a~~pkr~v~~ld~~~~~~  156 (261)
                      ++|+|.+.++.+ +-|||.|+    ..+.|+|+|+|.|||++.|..  |++|+++++.|..++..+++.||+||...|+.
T Consensus        82 ~~ydl~i~~k~v~n~yVfre~et~t~~k~tavvGtV~hEC~V~P~v--Nd~Y~r~~q~r~~~~~~~K~~vq~iD~~~g~~  159 (297)
T COG5090          82 SSYDLKIKPKDVNNYYVFRESETSTHEKNTAVVGTVNHECYVTPEV--NDEYLRYKQDRGFKSDSKKSDVQVIDYLKGGK  159 (297)
T ss_pred             cceeeeeccccccceEEEecccccccccccceeeeeccceeecccc--cHHHHHHHHHhhhhhcCccccceeeecccCce
Confidence            999999999877 57899654    357899999999999999986  68999999999999999999999999988877


Q ss_pred             cccCCCcccccccCcccccccCcccchhhhcccCChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhh
Q 024896          157 MRPMPGMVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYN  236 (261)
Q Consensus       157 ~~p~~~~~~~~~~~~~~~kk~~~~kk~~~K~~Rm~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~ln  236 (261)
                      ..+  +..++.+++..+++...++.+...|+.|||++||+|+||+||++|+||++|+|+++++||++||||||++||+||
T Consensus       160 ~~~--~~~s~Rs~~~~fl~~~r~k~~~~~K~~RlpknEvlD~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~iavLn  237 (297)
T COG5090         160 RGE--KFGSLRSSTLEFLARKRKKMLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLN  237 (297)
T ss_pred             ecc--CccccccchHHHHHhcchhhhcchhhcccchhHHHHHHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHHhhh
Confidence            765  222223334455544444456788999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcccccchhhhcccc
Q 024896          237 KRGTNQGTYELKPEYKKSVE  256 (261)
Q Consensus       237 k~Gp~~~~weLKpEYk~~~~  256 (261)
                      |+|||+++|+|+|||+...+
T Consensus       238 Kkgpya~kY~LrPEYK~~~d  257 (297)
T COG5090         238 KKGPYANKYELRPEYKQTMD  257 (297)
T ss_pred             ccCcccceeecCHHHHhHHH
Confidence            99999999999999998754

>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=95.24  E-value=0.022  Score=52.90  Aligned_cols=57  Identities=26%  Similarity=0.362  Sum_probs=52.7

Q ss_pred             CChhHHHHHHHHHhhhCCCcchHHHHHHcCC--cHHHHHHHHHHhhhhhccCCCCcccc
Q 024896          190 RDRGELEDIMFKLFERQPNWALKQLVQETDQ--PAQFLKEILNELCVYNKRGTNQGTYE  246 (261)
Q Consensus       190 m~k~eLld~LF~~Fe~~~yWslK~L~~~t~Q--Pe~yLKevL~eIa~lnk~Gp~~~~we  246 (261)
                      -...+++..|=.|||+.+-|+-+.|...+..  -...||.+|--+|=+=++||++..|-
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  58899999999999999999999994

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=94.95  E-value=0.049  Score=53.52  Aligned_cols=70  Identities=21%  Similarity=0.445  Sum_probs=60.6

Q ss_pred             hcccCChhHHHHHHHHHhh--hCCCcchHHHHHHc-CCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccc
Q 024896          186 KRTRRDRGELEDIMFKLFE--RQPNWALKQLVQET-DQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSV  255 (261)
Q Consensus       186 K~~Rm~k~eLld~LF~~Fe--~~~yWslK~L~~~t-~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~  255 (261)
                      |..-.-++-|.-.+|.+|.  ...--++.+|.... .|.+.=+++-|++.|.|.|.|...+.|.|||.|+--.
T Consensus       234 ~~t~~~knrL~~~iyRlf~~~~~~ri~~~di~~~Fp~~se~~iRkrLKe~~~~~R~g~~~~~W~lk~~~~lp~  306 (457)
T PF12157_consen  234 KVTNFSKNRLKMIIYRLFNKSQPRRIKVDDIKKHFPDQSESQIRKRLKEFADFQRTGDDSGWWVLKPGFRLPD  306 (457)
T ss_pred             hHHHHHHHHHHHHHHHHHhhccCCccCHHHHHHhCCCCcHHHHHHHHHHHHhccCCCCCCCeEEECCCCCCCC
Confidence            4555778889999999998  44469999999985 7899999999999999999999999999999877443

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

Probab=92.48  E-value=0.13  Score=55.79  Aligned_cols=73  Identities=22%  Similarity=0.391  Sum_probs=65.6

Q ss_pred             hhcccCChhHHHHHHHHHhhhCCC----cchHHHHHHc-CCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccccC
Q 024896          185 VKRTRRDRGELEDIMFKLFERQPN----WALKQLVQET-DQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSVED  257 (261)
Q Consensus       185 ~K~~Rm~k~eLld~LF~~Fe~~~y----WslK~L~~~t-~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~~~  257 (261)
                      .|..-+-+|=|+-.||.+|-+..-    -.|.+|.... .|-++-+|.-|++.|.|.|.|+-.|.|.|||.|+-..++
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            466678889999999999988887    8899998876 889999999999999999999999999999999977655

>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=90.82  E-value=0.35  Score=46.80  Aligned_cols=55  Identities=27%  Similarity=0.387  Sum_probs=48.8

Q ss_pred             HHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcccccchhh
Q 024896          194 ELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEY  251 (261)
Q Consensus       194 eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEY  251 (261)
                      -..|.|--+|.++.+-+-++|...|+-|..=+||||++||+++   |....|+||=.+
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            4568888999999999999999999999999999999999988   567889997543

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

>PF04004 Leo1: Leo1-like protein; InterPro: IPR007149 Members of this family are part of the Paf1/RNA polymerase II complex [, ]

Probab=90.57  E-value=2.9  Score=35.77  Aligned_cols=39  Identities=18%  Similarity=0.354  Sum_probs=28.1

Q ss_pred             eeeeeeecC-CcceeEEEEeeeeeEEeeCCCChHHHHHHH
Q 024896           94 PMSVFSESN-QGKVAMEGKVEHKFDMKPHEKNMEEYGRLC  132 (261)
Q Consensus        94 ~~~VFse~~-~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~  132 (261)
                      ..|+|.... .+-+...|.|.+++.++|...++...+++.
T Consensus        99 ~~~L~~~~~~~~~l~~~~~i~~~l~~rP~s~~s~thr~l~  138 (171)
T PF04004_consen   99 HNYLFVRHGSSGVLQGQGHITKKLTFRPASTDSATHRRLT  138 (171)
T ss_pred             cceEEEEcCCcceEEEEEEecccEEEecCCccCHHHHHHH
Confidence            477887654 356889999999999999764344445444

The Paf1 complex probably functions during the elongation phase of transcription [].

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

Probab=87.89  E-value=0.86  Score=44.86  Aligned_cols=56  Identities=23%  Similarity=0.334  Sum_probs=49.5

Q ss_pred             ChhHHHHHHHHHhhhCCCcchHHHHH-HcCCcHHHHHHHHHHhhhhhccCCCCcccc
Q 024896          191 DRGELEDIMFKLFERQPNWALKQLVQ-ETDQPAQFLKEILNELCVYNKRGTNQGTYE  246 (261)
Q Consensus       191 ~k~eLld~LF~~Fe~~~yWslK~L~~-~t~QPe~yLKevL~eIa~lnk~Gp~~~~we  246 (261)
                      .-+|++-.|=.+|++.+-|+-+.|.. .++==.-+||-+|--||-|-.+||++++|-
T Consensus       229 ~~~e~~~~l~eLF~~RPIWtR~al~~~~~~~~~h~LK~~Lp~~AYyfssGPwr~~wi  285 (484)
T KOG2473|consen  229 SLEEVLRSLRELFEERPIWTRRALLYKELGCTHHKLKRFLPLIAYYFSSGPWRRLWI  285 (484)
T ss_pred             hhHHHHHHHHHHHHhCchhhHHhHhhcccCccHHHHHHHHHHHHHHhccCchhceee
Confidence            44677778888999999999999999 566667899999999999999999999994

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

Probab=87.70  E-value=0.68  Score=47.10  Aligned_cols=70  Identities=27%  Similarity=0.324  Sum_probs=58.3

Q ss_pred             hhcccCChhHHHHHHHHHhhhCCC--cchHHHHHHc-CCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccc
Q 024896          185 VKRTRRDRGELEDIMFKLFERQPN--WALKQLVQET-DQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSV  255 (261)
Q Consensus       185 ~K~~Rm~k~eLld~LF~~Fe~~~y--WslK~L~~~t-~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~  255 (261)
                      .|-+-|-++-|.-++|.+|...+-  -.|.+|.... .|-+.-.++-|+|-+.|.|.||- |.|.|||.=.-..
T Consensus       592 RKvt~~~knRLKm~~fRl~n~~~~g~l~I~ql~khFpdq~egq~Rq~lKEfm~y~kdGp~-g~W~Lk~~e~lld  664 (968)
T COG5179         592 RKVTVFCKNRLKMAAFRLFNSKEGGSLRISQLDKHFPDQSEGQKRQWLKEFMDYVKDGPD-GVWVLKPSEALLD  664 (968)
T ss_pred             hhhHHHHhhhHHHHHHHHhhcCCCCceeeehhhhhCCCcchhHHHHHHHHHHHHhhcCCC-ceEEeccccccCC
Confidence            466778889999999999988775  7788887775 78888888888899999999997 9999999654443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	261
1bby_A	69	Dna-Binding Domain From Human Rap30, Nmr, Minimized		4e-10

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 29/65 (44%), Positives = 42/65 (64%)
Query: 188 TRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYEL 247
            R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ V N +G ++ T+EL
Sbjct: 2   ARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWEL 61
Query: 248 KPEYK 252
           KPEY+
Sbjct: 62  KPEYR 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	261
1bby_A	69	RAP30; average structure transcription regulation,	2e-28
1f3u_A	118	Transcription initiation factor IIF, beta subunit;	4e-24

>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 =  102 bits (256), Expect = 2e-28
 Identities = 30/66 (45%), Positives = 43/66 (65%)

Query: 187 RTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYE 246
           R R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ V N +G ++ T+E
Sbjct: 1   RARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWE 60

Query: 247 LKPEYK 252
           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 = 92.8 bits (230), Expect = 4e-24
 Identities = 25/119 (21%), Positives = 57/119 (47%), Gaps = 12/119 (10%)

Query: 10  NGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM- 68
            G+ +L  AK +  VWL+K P  +++ W   +   +   V K+ ++    +++ + FT+ 
Sbjct: 3   RGELDLTGAKQNTGVWLVKVPKYLSQQWAKASGRGE---VGKLRIAKTQGRTE-VSFTLN 58

Query: 69  ------ETTAVSNDSLNRPKSYSLNMFKDFV-PMSVFSESNQGKVAMEGKVEHKFDMKP 120
                         S++ P+ +   +       ++VF+ES+  K+++EG V  + + +P
Sbjct: 59  EDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRP 117

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	261
1bby_A	69	RAP30; average structure transcription regulation,	100.0
1f3u_A	118	Transcription initiation factor IIF, beta subunit;	99.96

>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=4.9e-38  Score=228.33  Aligned_cols=69  Identities=43%  Similarity=0.746  Sum_probs=67.3

Q ss_pred             cccCChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccc
Q 024896          187 RTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSV  255 (261)
Q Consensus       187 ~~Rm~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~  255 (261)
                      ++|||+++|+|+||+|||+|+||+||+|+++|+||++||||||++||+||++|||+|+|+||||||++.
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            589999999999999999999999999999999999999999999999999999999999999999874

>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=99.96  E-value=3e-30  Score=206.82  Aligned_cols=107  Identities=21%  Similarity=0.399  Sum_probs=88.7

Q ss_pred             CCCCCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEEecccC---------CCCCC
Q 024896            9 GNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVS---------NDSLN   79 (261)
Q Consensus         9 ~~~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~l~~~~---------~~~~~   79 (261)
                      ++|+++||+++++++|||||||+|||++|++..   ++++||+|+|..+++ ..  +++|.|+...         +++.+
T Consensus         2 ~~~~~dld~~~~~~~VWLvKvPk~L~e~W~~~~---~~~~vGkvri~~~~g-~~--~v~l~L~~~~~~~~~~~~~~~~~~   75 (118)
T 1f3u_A            2 ERGELDLTGAKQNTGVWLVKVPKYLSQQWAKAS---GRGEVGKLRIAKTQG-RT--EVSFTLNEDLANIHDIGGKPASVS   75 (118)
T ss_dssp             CTTBEECHHHHTTCEEEEEEEEHHHHHHHTTCC---TTCEEEEEEEEEETT-EE--EEEEEECHHHHTCCCTTCCCSTTC
T ss_pred             CcccccccccCCCceEEEEECCHHHHHHHHhCC---CCCceEEEEEecCCC-ce--eEEEEeChhHhhhccccccccccC
Confidence            578899999999999999999999999998644   236899999997753 33  4444443211         24678


Q ss_pred             CCcceeecccc-CCceeeeeeecCCcceeEEEEeeeeeEEeeC
Q 024896           80 RPKSYSLNMFK-DFVPMSVFSESNQGKVAMEGKVEHKFDMKPH  121 (261)
Q Consensus        80 iPkey~l~~~~-~~~~~~VFse~~~~~~~l~G~V~~e~~~~P~  121 (261)
                      +|++|+|.|++ +.+||+||||+++++++|||+|+|+|+|+|.
T Consensus        76 iPkeY~l~~~~~~~~~~~VFSE~~~~~~a~EG~V~~k~d~rP~  118 (118)
T 1f3u_A           76 APREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA  118 (118)
T ss_dssp             SCCEEEEEEECCTTSEEEEEEEETTCCEEEEEEEEEEEEECCC
T ss_pred             CChhceEEeeccCCceeEEEeccCCCcEEEEEEEEEEEEeecC
Confidence            99999999998 5789999999999999999999999999994

---

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	261
d2bbya_	69	a.4.5.15 (A:) DNA-binding domain from rap30 {Human	3e-32
d1f3ua_	118	b.65.1.1 (A:) TFIIF beta subunit, Rap30 {Human (Ho	2e-31

>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 =  110 bits (278), Expect = 3e-32
 Identities = 30/67 (44%), Positives = 43/67 (64%)

Query: 187 RTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYE 246
           R R D+  + D++F  FE+   + LK LV  T QP  +LKEIL E+ V N +G ++ T+E
Sbjct: 1   RARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWE 60

Query: 247 LKPEYKK 253
           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 =  110 bits (277), Expect = 2e-31
 Identities = 25/120 (20%), Positives = 51/120 (42%), Gaps = 14/120 (11%)

Query: 10  NGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDP--------LQS 61
            G+ +L  AK +  VWL+K P  +++ W   +       V K+ ++           L  
Sbjct: 3   RGELDLTGAKQNTGVWLVKVPKYLSQQWAKAS---GRGEVGKLRIAKTQGRTEVSFTLNE 59

Query: 62  DSMQFTMETTAVSNDSLNRPKSYSLNMFKDFV-PMSVFSESNQGKVAMEGKVEHKFDMKP 120
           D              S++ P+ +   +       ++VF+ES+  K+++EG V  + + +P
Sbjct: 60  DLANIHDIGG--KPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRP 117

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	261
d2bbya_	69	DNA-binding domain from rap30 {Human (Homo sapiens	100.0
d1f3ua_	118	TFIIF beta subunit, Rap30 {Human (Homo sapiens) [T	99.96
d2doaa1	91	RNA polymerase II elongation factor ELL {Human (Ho	91.16
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	81.77

>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=1.1e-38  Score=229.30  Aligned_cols=69  Identities=43%  Similarity=0.746  Sum_probs=67.3

Q ss_pred             cccCChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccc
Q 024896          187 RTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSV  255 (261)
Q Consensus       187 ~~Rm~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~  255 (261)
                      ++|||+++|+|+||+|||+|+|||||+|+++|+||++||||||++||+||++|||+|+|+||||||++.
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            689999999999999999999999999999999999999999999999999999999999999999873

>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=99.96  E-value=7.7e-31  Score=208.35  Aligned_cols=109  Identities=23%  Similarity=0.422  Sum_probs=90.4

Q ss_pred             CCCCCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEEe-------cccCCCCCCCC
Q 024896            9 GNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMET-------TAVSNDSLNRP   81 (261)
Q Consensus         9 ~~~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~l-------~~~~~~~~~iP   81 (261)
                      ++|+.|||+++++++|||||||+|||++|+++.   +.++||+|||..+++ ..+++|.|.-       ....+++.+||
T Consensus         2 ~~~~ldl~~a~~~~~VWLvKvPkyls~~W~k~~---~~~~vGklri~~~~~-k~ev~l~l~~~~~~~~~~~~~~~~~~iP   77 (118)
T d1f3ua_           2 ERGELDLTGAKQNTGVWLVKVPKYLSQQWAKAS---GRGEVGKLRIAKTQG-RTEVSFTLNEDLANIHDIGGKPASVSAP   77 (118)
T ss_dssp             CTTBEECHHHHTTCEEEEEEEEHHHHHHHTTCC---TTCEEEEEEEEEETT-EEEEEEEECHHHHTCCCTTCCCSTTCSC
T ss_pred             CccccccccccCCceEEEEECCHHHHHHHhhCC---CCCcceEEEeccCCC-CcceEEecCchHhhhhccccCCCcCCCC
Confidence            578888889999999999999999999998643   245899999998775 3455665531       11124567899


Q ss_pred             cceeeccccCC-ceeeeeeecCCcceeEEEEeeeeeEEeeC
Q 024896           82 KSYSLNMFKDF-VPMSVFSESNQGKVAMEGKVEHKFDMKPH  121 (261)
Q Consensus        82 key~l~~~~~~-~~~~VFse~~~~~~~l~G~V~~e~~~~P~  121 (261)
                      ++|+|.|++.. +||+||||.+++++++||+|+|+|+|||+
T Consensus        78 key~l~~~~~~~q~~~VFSe~~~~k~~~EG~V~~k~d~RPa  118 (118)
T d1f3ua_          78 REHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA  118 (118)
T ss_dssp             CEEEEEEECCTTSEEEEEEEETTCCEEEEEEEEEEEEECCC
T ss_pred             hhhcEecccccCCceEEEEecCCCcEEEEEEEEEEeecCCC
Confidence            99999999986 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=91.16  E-value=0.027  Score=40.46  Aligned_cols=30  Identities=23%  Similarity=0.341  Sum_probs=24.6

Q ss_pred             HHHHHHHHHhhhhhccCCCCcccccchhhhccc
Q 024896          223 QFLKEILNELCVYNKRGTNQGTYELKPEYKKSV  255 (261)
Q Consensus       223 ~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~  255 (261)
                      .-|.+||++||.++..   .|+|+|||+|-.--
T Consensus        39 ~~l~~iL~~Va~~~~~---~g~Y~LK~~~~~Ev   68 (91)
T d2doaa1          39 DALDGLLQQVANMSAK---DGTCTLQDCMYKDV   68 (91)
T ss_dssp             HHHHHHHHHSSEECSS---SCEEECCSSGGGGC
T ss_pred             HHHHHHHHHHheecCC---CceEeeHHHHHhHc
Confidence            4699999999998743   68999999986543

>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=81.77  E-value=0.97  Score=29.63  Aligned_cols=43  Identities=14%  Similarity=0.084  Sum_probs=37.8

Q ss_pred             hhHHHHHHHHHhhhCCC--cchHHHHHHcCCcHHHHHHHHHHhhh
Q 024896          192 RGELEDIMFKLFERQPN--WALKQLVQETDQPAQFLKEILNELCV  234 (261)
Q Consensus       192 k~eLld~LF~~Fe~~~y--WslK~L~~~t~QPe~yLKevL~eIa~  234 (261)
                      ...|...|-.+|.+..+  |++|+|...++.++.=++++|.-.|.
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            46789999999988755  99999999999999999999987664