Citrus Sinensis ID: 037910

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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-----
Protein Sequence
ILRKEDCGEYNVHGFSIRLRKIKNKNQESEHHPSLLIEFIIMGLSTNQMKNRVSVESKKFKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQSQPPKQEQDRKTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEKELECDAQ
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcccccHHHHcHHHHHHHHHHHHHcccccccHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHcccccccHHHHHHHHHHHccccccccccHHHHHHccEcEEHHHHHcccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccHccccccHHHHHHHHHHHHHHHHHcHHHcccccccccHHHHHEcccccHHHHHHccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
ilrkedcgeynvhgFSIRLRKIknknqesehhpSLLIEFIIMGLSTNQMKNRVSVeskkfkapssrtnkkrkfegedqaafpfmkkplgqsqppkqeqdrKTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKeqvracdpvgVAVSVESVLFknmcpflfnvkdpknpdfWRKVLlgevkpetlvtalpeemasdeRQSRNKQIREDALAKIrdhsvvgekelecdaq
Flexible Loop (DISEMBL)
ilrkedcgeynvhgfsirlrkiknknqesehhPSLLIEFIIMGLSTNQMKNRVsveskkfkapssrtnkkrkfegedQAAFpfmkkplgqsqppkqeqdrktASAVEIKCSDATRTLIRERLAEAFSKvageveemekkeqvracdpVGVAVSVESVLFKNMCPFlfnvkdpknpDFWRKVLLGEVKPEtlvtalpeemasderqsrnKQIREDALAkirdhsvvgekelecdaq
Low Complexity Region (SEG)
ILRKEDCGEYNVHGFSIRLRKIKNKNQESEHHPSLLIEFIIMGLSTNQMKNRVSVESKKFKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQSQPPKQEQDRKTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEKELECDAQ
Disordered region (IsUnstruct)
********EYNVHGFSIRLRK************SLLIEFIIMGLS*******************************************************************ATRTLIRERLAEAFS**************VRACDPVGVAVSVESVLFKNMCPFLFNVKDPKNPDFWRKVLLGEVKPETLVT******************************************
Disordered Region (DISOPRED)
*******GEYNVHG****************************************************************************************************RTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPFLFNVKDPKNPDFWRKVLLGEVKPETLVT******************************************
Disordered Region (DISEMBL)
ILRKEDCGEYNVHGFSIRLRKIKNKNQESEHHPSLLIEFIIMGLSTNQMKNRV*******************FEGEDQAAFPFMKKP*****************AVEIKCSDATRTLIRERLAEAFSKVA**************CDPVGVAVSVESVLFKNMCPFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEE************IREDALAKIRDHSVVGEKELECDAQ
Disordered Region (DISPRO)
ILRKEDCGEYNVHGFSIRLRKIKNKNQESEHHPSLLIEFIIMGLSTNQMKNRVSVESKKFKAPSSRTNKKRKFE**********************************KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVV**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
ILRKEDCGEYNVHGFSIRLRKIKNKNQESEHHPSLLIEFIIMGLSTNQMKNRVSVESKKFKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQSQPPKQEQDRKTASAVEIKCSDATRTLIxxxxxxxxxxxxxxxxxxxxxEQVRACDPVGVAVSVESVLFKNMCPFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEKELECDAQ
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	235	2.2.26 [Sep-21-2011]
Q148K0	300	Transcription elongation	yes	no	0.446	0.35	0.313	5e-05
Q92576	2039	PHD finger protein 3 OS=H	yes	no	0.297	0.034	0.402	5e-05
P23881	347	Transcription elongation	no	no	0.238	0.161	0.426	8e-05
Q63799	299	Transcription elongation	no	no	0.480	0.377	0.330	0.0001
Q9QVN7	299	Transcription elongation	no	no	0.480	0.377	0.330	0.0001
Q15560	299	Transcription elongation	no	no	0.242	0.190	0.4	0.0002
P10711	301	Transcription elongation	no	no	0.468	0.365	0.308	0.0005
Q4KLL0	301	Transcription elongation	no	no	0.468	0.365	0.308	0.0006
P20232	313	Transcription elongation	no	no	0.502	0.376	0.307	0.0006
Q29RL9	301	Transcription elongation	no	no	0.468	0.365	0.3	0.0007

>sp|Q148K0|TCEA2_BOVIN Transcription elongation factor A protein 2 OS=Bos taurus GN=TCEA2 PE=2 SV=1

 Score = 48.1 bits (113), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 60/134 (44%), Gaps = 29/134 (21%)

Query: 106 VEIKCSDATRTLIRERLAEAFSK-------------VAGEVEEMEKKEQVRACDPVGVAV 152
           V + C DA RT  RE L  A                +AG++EE   ++           V
Sbjct: 132 VPVTC-DAVRTKCREMLTAALQTDHDHVAIGADCECLAGQIEECIFRD-----------V 179

Query: 153 SVESVLFKNMC-PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQI 211
               + +KN     L N+KD KNP   RKVL G + P+ +     EEMASDE +   K +
Sbjct: 180 GNTDMKYKNRVRSRLSNLKDAKNPGLRRKVLCGAITPQQIAVMTSEEMASDELKEIRKAM 239

Query: 212 REDALAKIRDHSVV 225
            ++A   IR+H + 
Sbjct: 240 TKEA---IREHQMA 250

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.
Bos taurus (taxid: 9913)

>sp|Q92576|PHF3_HUMAN PHD finger protein 3 OS=Homo sapiens GN=PHF3 PE=1 SV=3

 Score = 48.1 bits (113), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 12/82 (14%)

Query: 165  FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE------RQSRN------KQIR 212
             +FN+KDPKN   ++KVL GEV P+ L+   PEE+AS E      R++R+      K+ R
Sbjct: 984  LMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRRENRHTIEMIEKEQR 1043

Query: 213  EDALAKIRDHSVVGEKELECDA 234
            E     I   +  GE E+E DA
Sbjct: 1044 EVERRPITKITHKGEIEIESDA 1065

Homo sapiens (taxid: 9606)

>sp|P23881|TCEA3_MOUSE Transcription elongation factor A protein 3 OS=Mus musculus GN=Tcea3 PE=1 SV=3

 Score = 47.4 bits (111), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 5/61 (8%)

Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE-RQSRNKQIREDALAKIRDHSV 224
           + N+KDP+NP   R VL G + PE +     EEMASDE R+ RN   +E     IR+H +
Sbjct: 241 ISNLKDPRNPGLRRNVLSGAISPELIAKMTAEEMASDELRELRNAMTQE----AIREHQM 296

Query: 225 V 225
            
Sbjct: 297 A 297

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Mus musculus (taxid: 10090)

>sp|Q63799|TCEA2_RAT Transcription elongation factor A protein 2 OS=Rattus norvegicus GN=Tcea2 PE=2 SV=1

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/124 (33%), Positives = 57/124 (45%), Gaps = 11/124 (8%)

Query: 106 VEIKCSDATRTLIRERLAEAF----SKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKN 161
           V I C DA R   RE L  A       VA  V       Q+  C  + + V    + +KN
Sbjct: 131 VPITC-DAVRNKCREMLTLALQTDHDHVAVGVSCEHLSSQIEEC--IFLDVGNTDMKYKN 187

Query: 162 MC-PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIR 220
                + N+KD KNP   R VL G + P+ +     EEMASDE +   K + ++A   IR
Sbjct: 188 RVRSRISNLKDAKNPGLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAMTKEA---IR 244

Query: 221 DHSV 224
           +H +
Sbjct: 245 EHQM 248

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Rattus norvegicus (taxid: 10116)

>sp|Q9QVN7|TCEA2_MOUSE Transcription elongation factor A protein 2 OS=Mus musculus GN=Tcea2 PE=2 SV=2

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/124 (33%), Positives = 57/124 (45%), Gaps = 11/124 (8%)

Query: 106 VEIKCSDATRTLIRERLAEAF----SKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKN 161
           V I C DA R   RE L  A       VA  V       Q+  C  + + V    + +KN
Sbjct: 131 VPITC-DAVRNKCREMLTLALQTDHDHVAVGVNCEHLSSQIEEC--IFLDVGNTDMKYKN 187

Query: 162 MC-PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIR 220
                + N+KD KNP   R VL G + P+ +     EEMASDE +   K + ++A   IR
Sbjct: 188 RVRSRISNLKDAKNPGLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAMTKEA---IR 244

Query: 221 DHSV 224
           +H +
Sbjct: 245 EHQM 248

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Mus musculus (taxid: 10090)

>sp|Q15560|TCEA2_HUMAN Transcription elongation factor A protein 2 OS=Homo sapiens GN=TCEA2 PE=1 SV=1

 Score = 46.6 bits (109), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVV 225
           + N+KD KNPD  R VL G + P+ +     EEMASDE +   K + ++A   IR+H + 
Sbjct: 193 ISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAMTKEA---IREHQMA 249

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Homo sapiens (taxid: 9606)

>sp|P10711|TCEA1_MOUSE Transcription elongation factor A protein 1 OS=Mus musculus GN=Tcea1 PE=1 SV=2

 Score = 44.7 bits (104), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 57/120 (47%), Gaps = 10/120 (8%)

Query: 111 SDATRTLIRERLAEAF----SKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC-PF 165
           SD+ R   RE LA A       VA   +E E   Q+   + +   +    + +KN     
Sbjct: 137 SDSVRLKCREMLAAALRTGDDYVAIGADEEELGSQIE--EAIYQEIRNTDMKYKNRVRSR 194

Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVV 225
           + N+KD KNP+  + VL G + P+       EEMASDE +   K + ++A   IR+H + 
Sbjct: 195 ISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKEA---IREHQMA 251

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Mus musculus (taxid: 10090)

>sp|Q4KLL0|TCEA1_RAT Transcription elongation factor A protein 1 OS=Rattus norvegicus GN=Tcea1 PE=2 SV=1

 Score = 44.7 bits (104), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 57/120 (47%), Gaps = 10/120 (8%)

Query: 111 SDATRTLIRERLAEAF----SKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC-PF 165
           SD+ R   RE LA A       VA   +E E   Q+   + +   +    + +KN     
Sbjct: 137 SDSVRLKCREMLAAALRTGDDYVAIGADEEELGSQIE--EAIYQEIRNTDMKYKNRVRSR 194

Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVV 225
           + N+KD KNP+  + VL G + P+       EEMASDE +   K + ++A   IR+H + 
Sbjct: 195 ISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKEA---IREHQMA 251

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Rattus norvegicus (taxid: 10116)

>sp|P20232|TFS2_DROME Transcription elongation factor S-II OS=Drosophila melanogaster GN=TfIIS PE=2 SV=1

 Score = 44.3 bits (103), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/130 (30%), Positives = 62/130 (47%), Gaps = 12/130 (9%)

Query: 111 SDATRTLIRERLAEAFS-----KVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKN-MCP 164
           +DA R   RE LA A       +  GE EEM  + +    D +    +   + +KN +  
Sbjct: 150 TDAVRIKCREMLATALKIGEVPEGCGEPEEMAAELE----DAIYSEFNNTDMKYKNRIRS 205

Query: 165 FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSV 224
            + N+KDPKNP      + G V  + L    PEEMASDE +   ++  ++A+   +  +V
Sbjct: 206 RVANLKDPKNPGLRGNFMCGAVTAKQLAKMTPEEMASDEMKKLREKFVKEAINDAQLATV 265

Query: 225 VGEKE--LEC 232
            G K   L+C
Sbjct: 266 QGTKTDLLKC 275

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Drosophila melanogaster (taxid: 7227)

>sp|Q29RL9|TCEA1_BOVIN Transcription elongation factor A protein 1 OS=Bos taurus GN=TCEA1 PE=2 SV=1

 Score = 44.3 bits (103), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 57/120 (47%), Gaps = 10/120 (8%)

Query: 111 SDATRTLIRERLAEAF----SKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC-PF 165
           SD+ R   RE LA A       +A   +E E   Q+   + +   +    + +KN     
Sbjct: 137 SDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIE--EAIYQEIRNTDMKYKNRVRSR 194

Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVV 225
           + N+KD KNP+  + VL G + P+       EEMASDE +   K + ++A   IR+H + 
Sbjct: 195 ISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKEA---IREHQMA 251

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Bos taurus (taxid: 9913)

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	235
297735532	322	unnamed protein product [Vitis vinifera]	0.642	0.468	0.465	4e-26
225439709	367	PREDICTED: transcription elongation fact	0.523	0.335	0.496	7e-26
224087871	352	predicted protein [Populus trichocarpa]	0.459	0.306	0.533	1e-24
255575598	342	transcription elongation factor s-II, pu	0.604	0.415	0.456	5e-24
224139382	334	predicted protein [Populus trichocarpa]	0.459	0.323	0.516	1e-23
255559741	330	transcription elongation factor s-II, pu	0.455	0.324	0.521	3e-23
224286619	328	unknown [Picea sitchensis]	0.459	0.329	0.491	6e-22
116789178	331	unknown [Picea sitchensis]	0.646	0.459	0.422	1e-21
224137638	333	predicted protein [Populus trichocarpa]	0.587	0.414	0.435	2e-21
449499153	290	PREDICTED: transcription elongation fact	0.523	0.424	0.472	3e-21

>gi|297735532|emb|CBI18026.3| unnamed protein product [Vitis vinifera]

 Score =  124 bits (310), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 80/172 (46%), Positives = 102/172 (59%), Gaps = 21/172 (12%)

Query: 57  SKKFKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQSQ-PPKQEQDRKTASAVEIKCSDATR 115
           +K  KA    T +KR    +++  F  +KKP   S  PPK            IKC+DA R
Sbjct: 104 AKAEKASKVETVEKRVENVDERKQFSSVKKPPQASNGPPKL--------TAMIKCNDALR 155

Query: 116 TLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC-----------P 164
             +RE LAEA  KVA E +E + K++V ACDP+ VAVSVESV+F+ M             
Sbjct: 156 DKVRELLAEALFKVASEADE-DIKDEVNACDPIRVAVSVESVMFEKMGRSNGTQKFKYRS 214

Query: 165 FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
            +FN+KDP NPD  RKVLLGEVKP+ L+   PEEMAS++RQ  N QI+E AL
Sbjct: 215 IMFNIKDPNNPDLRRKVLLGEVKPDRLINMSPEEMASNQRQRENSQIKEKAL 266

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225439709|ref|XP_002272768.1| PREDICTED: transcription elongation factor A protein 3 [Vitis vinifera]

 Score =  123 bits (308), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 71/143 (49%), Positives = 88/143 (61%), Gaps = 20/143 (13%)

Query: 85  KKPLGQSQPPKQEQDRKTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRA 144
           K P   + PPK            IKC+DA R  +RE LAEA  KVA E +E + K++V A
Sbjct: 178 KPPQASNGPPKL--------TAMIKCNDALRDKVRELLAEALFKVASEADE-DIKDEVNA 228

Query: 145 CDPVGVAVSVESVLFKNMC-----------PFLFNVKDPKNPDFWRKVLLGEVKPETLVT 193
           CDP+ VAVSVESV+F+ M              +FN+KDP NPD  RKVLLGEVKP+ L+ 
Sbjct: 229 CDPIRVAVSVESVMFEKMGRSNGTQKFKYRSIMFNIKDPNNPDLRRKVLLGEVKPDRLIN 288

Query: 194 ALPEEMASDERQSRNKQIREDAL 216
             PEEMAS++RQ  N QI+E AL
Sbjct: 289 MSPEEMASNQRQRENSQIKEKAL 311

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224087871|ref|XP_002308256.1| predicted protein [Populus trichocarpa] gi|222854232|gb|EEE91779.1| predicted protein [Populus trichocarpa]

 Score =  119 bits (298), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 64/120 (53%), Positives = 83/120 (69%), Gaps = 12/120 (10%)

Query: 108 IKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC---- 163
           +KC+DA R  IRE LAEA SKVA E +E + +++V ACDP+ VAVSVES++F+ +     
Sbjct: 178 VKCNDALRDKIRELLAEALSKVASEADE-DIRDEVEACDPIRVAVSVESMMFEKLGRSNG 236

Query: 164 -------PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
                    +FN+KD  NPDF RKVLLGEV+PE LVT  PEEMAS++R+  N QI+E  L
Sbjct: 237 AQKLKYRSIMFNIKDQNNPDFRRKVLLGEVQPERLVTMGPEEMASEQRKRENNQIKEKVL 296

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255575598|ref|XP_002528699.1| transcription elongation factor s-II, putative [Ricinus communis] gi|223531871|gb|EEF33688.1| transcription elongation factor s-II, putative [Ricinus communis]

 Score =  117 bits (292), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 74/162 (45%), Positives = 91/162 (56%), Gaps = 20/162 (12%)

Query: 66  RTNKKRKFEGEDQAAFPFMKKPLGQSQPPKQEQDRKTASAVEIKCSDATRTLIRERLAEA 125
           RT K  K   E Q A    K       PPK        +A+ +KC+DA R  IRE L EA
Sbjct: 134 RTVKVEKKSEEKQQAIDVKKPSQASVTPPK-------LTAI-VKCNDALRDKIRELLVEA 185

Query: 126 FSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC-----------PFLFNVKDPKN 174
            SKV  E  E + ++++  CDP+ VAVSVES +F+ M              +FN+KDP N
Sbjct: 186 LSKVVSEANE-DGRDEISKCDPIRVAVSVESAMFEKMGRSNGAQKFKYRSIMFNLKDPNN 244

Query: 175 PDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
           PD  RKVLLGEVKPE L++  PEEMAS ERQ    QI+E AL
Sbjct: 245 PDLRRKVLLGEVKPERLISMTPEEMASKERQEEINQIKEKAL 286

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224139382|ref|XP_002323085.1| predicted protein [Populus trichocarpa] gi|222867715|gb|EEF04846.1| predicted protein [Populus trichocarpa]

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 62/120 (51%), Positives = 82/120 (68%), Gaps = 12/120 (10%)

Query: 108 IKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC---- 163
           +KC+DA R  IRE LAEA SKVA E +E + +++V ACDP+ VAVSVES +F+ +     
Sbjct: 160 VKCNDALRDKIRELLAEALSKVASEADE-DIRDEVEACDPIRVAVSVESAMFEKLGRSNG 218

Query: 164 -------PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
                    +FN+KD  NPD  RKVLLG+V+P+ LVT  PEEMAS++R+  N QI+E AL
Sbjct: 219 AQKMKYRSIMFNIKDQNNPDLRRKVLLGQVQPQRLVTMPPEEMASEQRKRENNQIKEKAL 278

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559741|ref|XP_002520890.1| transcription elongation factor s-II, putative [Ricinus communis] gi|223540021|gb|EEF41599.1| transcription elongation factor s-II, putative [Ricinus communis]

 Score =  114 bits (285), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 62/119 (52%), Positives = 79/119 (66%), Gaps = 12/119 (10%)

Query: 109 KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCP---- 164
           KC+D +R  IRE+L EA  KV+ E  E E +++V ACD +GVAV+VES LF N  P    
Sbjct: 157 KCNDPSRDNIREQLYEALCKVSSEANE-EIQKEVNACDAIGVAVAVESALFSNWGPSNGS 215

Query: 165 -------FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
                   +FN +D KNPDF RKVLLG+VKPE +     EEMASDER+ +NK+I+E AL
Sbjct: 216 DRIKYRSLIFNTRDAKNPDFRRKVLLGQVKPERIAELSSEEMASDERRKKNKEIKEKAL 274

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224286619|gb|ACN41014.1| unknown [Picea sitchensis]

 Score =  110 bits (274), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 59/120 (49%), Positives = 78/120 (65%), Gaps = 12/120 (10%)

Query: 108 IKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC---- 163
           IKC+DA R  IRE + EAFSKV  E E  E   ++ ACDPV VAV+VE+++F+ +     
Sbjct: 154 IKCNDAVRDKIREIIYEAFSKVVNEAEG-ENMVRINACDPVRVAVTVETLMFEKLGRSNG 212

Query: 164 -------PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
                    +FN+KD  NPD  R+VLLGE+KPE L+    EEMASD+R+  NKQI++ AL
Sbjct: 213 AQKLKYRSIIFNLKDANNPDLRRRVLLGEIKPEKLIVMTAEEMASDQRKLENKQIKDKAL 272

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116789178|gb|ABK25146.1| unknown [Picea sitchensis]

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 74/175 (42%), Positives = 93/175 (53%), Gaps = 23/175 (13%)

Query: 53  VSVESKKFKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQSQPPKQEQDRKTASAVEIKCSD 112
           V VE    K  S +  KK K E E   +    K     + PPK            IKC+D
Sbjct: 113 VKVEVNASKGESVKVEKKPKVETESIGS---KKASSSSNGPPKLTS--------MIKCND 161

Query: 113 ATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC--------- 163
           A R   RE L EAFSKV  E E  E   +V ACDPV +AVSVE+V+F+ +          
Sbjct: 162 ALRDKFREILYEAFSKVVNEAEG-EDLARVNACDPVRIAVSVETVMFEKLGRSNGAQKFK 220

Query: 164 --PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
               +FN+KD  NPD  R+VLLG++KPE L+    EEMASD R+  NKQI++ AL
Sbjct: 221 YRSIMFNLKDGNNPDLRRRVLLGQIKPEKLIVMTAEEMASDNRKLENKQIKDKAL 275

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137638|ref|XP_002322607.1| predicted protein [Populus trichocarpa] gi|222867237|gb|EEF04368.1| predicted protein [Populus trichocarpa]

 Score =  108 bits (270), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 74/170 (43%), Positives = 96/170 (56%), Gaps = 32/170 (18%)

Query: 60  FKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQSQPPKQEQDRKTASAVEIKCSDATRTLIR 119
           FK PS+    KR  + E+   F   KKP   S+ P             +KCSD  R+ +R
Sbjct: 169 FKKPST----KRITQQENVKDFCSFKKP---SEEP-------------VKCSDGLRSKVR 208

Query: 120 ERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFN 168
             L E+  +VA EV+E +  E VR  DP+ VA  VES++F+ M  F           LFN
Sbjct: 209 HILVESLCRVAKEVKE-DLMEAVRLRDPIIVAADVESLMFERMGLFNGTKQLKYRSILFN 267

Query: 169 VKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAK 218
           +KDPKNPD  RKVLLG++KPE LVT   EEMAS++RQ  N QIR+ +L K
Sbjct: 268 MKDPKNPDLRRKVLLGQIKPEKLVTMTAEEMASNQRQFENDQIRKKSLWK 317

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449499153|ref|XP_004160740.1| PREDICTED: transcription elongation factor A protein 2-like [Cucumis sativus]

 Score =  107 bits (268), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 68/144 (47%), Positives = 86/144 (59%), Gaps = 21/144 (14%)

Query: 85  KKPL-GQSQPPKQEQDRKTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVR 143
           KKP  G + PPK            IK  DA R  IRE L EAFSKV GE +E E  ++V 
Sbjct: 100 KKPSSGAAAPPKLTS--------MIKSKDAARDKIRELLFEAFSKVPGEADE-EFMDEVN 150

Query: 144 ACDPVGVAVSVESVLFKNMC-----------PFLFNVKDPKNPDFWRKVLLGEVKPETLV 192
           A DP+ VAVSVESV+F+N               +FN+KDPKNPDF RKVLLG +KPE ++
Sbjct: 151 ASDPIRVAVSVESVMFENWGGSTGAQKAKYRSIMFNLKDPKNPDFRRKVLLGLIKPERMI 210

Query: 193 TALPEEMASDERQSRNKQIREDAL 216
                +MASD+R+  N++I + AL
Sbjct: 211 NMSTADMASDQRKRENEEIAQKAL 234

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	235
TAIR|locus:2064195	378	TFIIS "transcript elongation f	0.706	0.439	0.360	1.2e-21
TAIR|locus:2052351	737	AT2G42730 [Arabidopsis thalian	0.468	0.149	0.429	1.9e-15
TAIR|locus:2124097	266	AT4G18720 [Arabidopsis thalian	0.446	0.394	0.444	4.2e-15
TAIR|locus:504954948	233	AT5G42325 [Arabidopsis thalian	0.446	0.450	0.423	3.8e-14
FB|FBgn0030663	162	CG8117 [Drosophila melanogaste	0.510	0.740	0.303	7.4e-09
UNIPROTKB|F1NP36	309	TCEA1 "Uncharacterized protein	0.851	0.647	0.246	7.3e-08
UNIPROTKB|F1NP37	280	TCEA1 "Uncharacterized protein	0.838	0.703	0.243	7.3e-07
ZFIN|ZDB-GENE-030131-8049	309	tcea1 "transcription elongatio	0.485	0.368	0.290	9.4e-07
RGD|61825	299	Tcea2 "transcription elongatio	0.553	0.434	0.319	4.6e-06
UNIPROTKB|Q63799	299	Tcea2 "Transcription elongatio	0.553	0.434	0.319	4.6e-06

TAIR|locus:2064195 TFIIS "transcript elongation factor IIS" [Arabidopsis thaliana (taxid:3702)]

 Score = 253 (94.1 bits), Expect = 1.2e-21, P = 1.2e-21
 Identities = 66/183 (36%), Positives = 95/183 (51%)

Query:    47 NQMKNRVSVESKKFKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQS--QPPKQEQDRKTAS 104
             N++   V +E K    P  +     K +   QA          QS  + P +  +     
Sbjct:   144 NKVVTGVKIERK---VPDIKVTNGTKIDYRGQAVKDEKVSKDNQSSMKAPAKAANAPPKL 200

Query:   105 AVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC- 163
                +KC+D  R  IRE L EA  +VAGE ++ E+ E V A DP+ VAVSVES++F+ +  
Sbjct:   201 TAMLKCNDPVRDKIRELLVEALCRVAGEADDYER-ESVNASDPLRVAVSVESLMFEKLGR 259

Query:   164 ----------PFLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIRE 213
                         +FN++D  NPD  R+VL GE+ PE L+T   E+MASD+R+  N QI+E
Sbjct:   260 STGAQKLKYRSIMFNLRDSNNPDLRRRVLTGEISPEKLITLSAEDMASDKRKQENNQIKE 319

Query:   214 DAL 216
              AL
Sbjct:   320 KAL 322

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003746 "translation elongation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA;ISS;IDA

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

GO:0006354 "DNA-dependent transcription, elongation" evidence=IEA;ISS

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

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0009910 "negative regulation of flower development" evidence=IMP

GO:0010162 "seed dormancy process" evidence=RCA;IMP

GO:0034243 "regulation of transcription elongation from RNA polymerase II promoter" evidence=IMP

GO:0005829 "cytosol" evidence=RCA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009845 "seed germination" evidence=IMP;RCA

GO:0009880 "embryonic pattern specification" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=RCA

GO:0010072 "primary shoot apical meristem specification" evidence=RCA

GO:0010182 "sugar mediated signaling pathway" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0010431 "seed maturation" evidence=RCA

GO:0010564 "regulation of cell cycle process" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

GO:0045595 "regulation of cell differentiation" evidence=RCA

GO:0048366 "leaf development" evidence=RCA

GO:0048825 "cotyledon development" evidence=RCA

GO:0050826 "response to freezing" evidence=RCA

GO:0051301 "cell division" evidence=RCA

GO:0009739 "response to gibberellin stimulus" evidence=IMP

TAIR|locus:2052351 AT2G42730 [Arabidopsis thaliana (taxid:3702)]

 Score = 205 (77.2 bits), Expect = 1.9e-15, P = 1.9e-15
 Identities = 52/121 (42%), Positives = 71/121 (58%)

Query:   109 KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNM-C---P 164
             K  D+ R  +RE L  +  KVA E+ + E K +V ACDP  VAVSVES +F+ + C   P
Sbjct:   601 KTGDSKRDKVREILQTSLVKVASEIVDTEMKTRVTACDPSVVAVSVESAMFEKLGCFMGP 660

Query:   165 -------FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALA 217
                     LFN+ D  NPD  RKVL+GE+  E LVT   +EM S++ Q   ++I+E+A  
Sbjct:   661 HKAKYRSILFNMGDSNNPDLRRKVLIGEINGERLVTMERQEMGSEKIQKEVQRIKENARF 720

Query:   218 K 218
             K
Sbjct:   721 K 721

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2124097 AT4G18720 [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 4.2e-15, P = 4.2e-15
 Identities = 52/117 (44%), Positives = 65/117 (55%)

Query:   109 KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNM-C---P 164
             K  D+ R  +RE L  + +KVA EV + E K +V ACDP  VAVSVE+ +F+N+ C   P
Sbjct:   112 KTGDSKRDKVREILQTSLAKVASEVVDTEMKTRVTACDPWVVAVSVETAMFENLGCFMGP 171

Query:   165 -------FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASD-ERQSRNKQIRE 213
                     LFN+ D  NPD  RKVLLGE+  E LV    EEM S     SR   + E
Sbjct:   172 QKAKYRSILFNMGDSNNPDLRRKVLLGEISGERLVKMEKEEMGSSWYTNSRRNPLYE 228

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:504954948 AT5G42325 [Arabidopsis thaliana (taxid:3702)]

 Score = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 47/111 (42%), Positives = 63/111 (56%)

Query:   109 KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRA-CDPVGVAVSVESVLFKNMCPFLF 167
             K  D+ R  + E L  + +KVA EV + E K +V   CDP  VAVSVES +       LF
Sbjct:   111 KTGDSKRDKVHEILQSSLAKVATEVVDTEMKRRVMTVCDPWVVAVSVESAM-----SILF 165

Query:   168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAK 218
             N+ D  NPD  RKVL+GE+  E LV    +EM S++ Q   ++I+E A  K
Sbjct:   166 NMGDSNNPDLRRKVLIGEISGERLVKMEKDEMGSEKIQKEVQRIKERARFK 216

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

FB|FBgn0030663 CG8117 [Drosophila melanogaster (taxid:7227)]

 Score = 134 (52.2 bits), Expect = 7.4e-09, P = 7.4e-09
 Identities = 40/132 (30%), Positives = 69/132 (52%)

Query:   106 VEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF 165
             + IKC +   T ++   +       G+ ++M  K +    D +   ++   V +KN    
Sbjct:     5 IRIKCREMLATALK---SGNMPPGCGDPDDMAAKLE----DAIYGDLNGCKVKYKNRIRS 57

Query:   166 -LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE-RQSRNKQIREDALAKIRDHS 223
              L N++DPKNP+  +K LLG++ PE L    PEEMASD+ +Q R K + +D++   +   
Sbjct:    58 RLANLRDPKNPELRQKFLLGQITPEELSKMTPEEMASDDMKQMRQKYV-QDSINAAQMAK 116

Query:   224 VVGEK--ELECD 233
             V G K  + +C+
Sbjct:   117 VQGTKTDQFKCE 128

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

GO:0005634 "nucleus" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|F1NP36 TCEA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 143 (55.4 bits), Expect = 7.3e-08, P = 7.3e-08
 Identities = 54/219 (24%), Positives = 100/219 (45%)

Query:    14 GFSIR-LRKIKNKNQESEHHPSLLIEF--IIMGLSTNQMKNRVSVESKKFKAPSSRTNKK 70
             G S+  +RK     + +    SL+  +  ++ G ST+    + S E KK  A SS+ + +
Sbjct:    51 GMSVNAIRKQSTDEEVTSLAKSLIKSWKKLLDGPSTD----KDSEEKKKEPASSSQNSPE 106

Query:    71 RKFEGEDQAAFPFMKKP---LGQSQPPKQEQDRKTASAVEIKCSDATRTLIRERLAEAFS 127
              + E    +     K+       S  P   +   T+ +V +KC +     +R    + + 
Sbjct:   107 AREESSSSSNSSSRKEEGSAPSNSFIPSFPRAPSTSDSVRVKCREMLSAALRT--GDDYI 164

Query:   128 KVAGEVEEMEKK-EQVRACDPVGVAVSVESVLFKNMCPF-LFNVKDPKNPDFWRKVLLGE 185
              +  + EE+  + E+ +A  P+   +    + +KN     + N+KD KNP+  + VL G 
Sbjct:   165 AIGADEEELGSQIEEAKA--PIFQELKNTDMKYKNRVRSRIANLKDAKNPNLRKNVLCGN 222

Query:   186 VKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSV 224
             + P+       EEMASDE +   K + ++A   IR+H +
Sbjct:   223 IPPDKFAKMTAEEMASDELKEMRKNLTKEA---IREHQM 258

GO:0003677 "DNA binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0030218 "erythrocyte differentiation" evidence=IEA

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

UNIPROTKB|F1NP37 TCEA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 134 (52.2 bits), Expect = 7.3e-07, P = 7.3e-07
 Identities = 53/218 (24%), Positives = 96/218 (44%)

Query:    14 GFSIR-LRKIKNKNQESEHHPSLLIEF--IIMGLSTNQMKNRVSVESKKFKAPSSRTNKK 70
             G S+  +RK     + +    SL+  +  ++ G ST+    + S E KK  A SS+ + +
Sbjct:    26 GMSVNAIRKQSTDEEVTSLAKSLIKSWKKLLDGPSTD----KDSEEKKKEPASSSQNSPE 81

Query:    71 RKFEGEDQAAFPFMKKP---LGQSQPPKQEQDRKTASAVEIKCSDATRTLIRERLAEAFS 127
              + E    +     K+       S  P   +   T+ +V +KC +     +R    + + 
Sbjct:    82 AREESSSSSNSSSRKEEGSAPSNSFIPSFPRAPSTSDSVRVKCREMLSAALRT--GDDYI 139

Query:   128 KVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-LFNVKDPKNPDFWRKVLLGEV 186
              +  + EE+E         P+   +    + +KN     + N+KD KNP+  + VL G +
Sbjct:   140 AIGADEEELETIHT-----PIFQELKNTDMKYKNRVRSRIANLKDAKNPNLRKNVLCGNI 194

Query:   187 KPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSV 224
              P+       EEMASDE +   K + ++A   IR+H +
Sbjct:   195 PPDKFAKMTAEEMASDELKEMRKNLTKEA---IREHQM 229

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

ZFIN|ZDB-GENE-030131-8049 tcea1 "transcription elongation factor A (SII), 1" [Danio rerio (taxid:7955)]

 Score = 134 (52.2 bits), Expect = 9.4e-07, P = 9.4e-07
 Identities = 36/124 (29%), Positives = 61/124 (49%)

Query:   102 TASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKN 161
             T+ +V IKC +     ++    + +  +  + +E+    Q+  C  + +      + +KN
Sbjct:   144 TSDSVRIKCREMLSNALQT--GDDYITIGSDCDELGA--QIEEC--IFLEFKNTDMKYKN 197

Query:   162 MCPF-LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIR 220
                  + N+KD KNP+  R VL G V P+ +     EEMASDE +   K + ++A   IR
Sbjct:   198 RVRSRISNLKDAKNPNLRRNVLCGNVSPDRIAKMTAEEMASDELKEMRKNLTKEA---IR 254

Query:   221 DHSV 224
             DH V
Sbjct:   255 DHQV 258

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006414 "translational elongation" evidence=IEA

GO:0003746 "translation elongation factor activity" evidence=IEA

RGD|61825 Tcea2 "transcription elongation factor A (SII), 2" [Rattus norvegicus (taxid:10116)]

 Score = 128 (50.1 bits), Expect = 4.6e-06, P = 4.6e-06
 Identities = 47/147 (31%), Positives = 65/147 (44%)

Query:    85 KKPLGQSQPPKQEQDRK--TASAVEIKCSDATRTLIRERLAEAFSK----VAGEVEEMEK 138
             KKP     PP+     +  T   V I C DA R   RE L  A       VA  V     
Sbjct:   112 KKP----DPPRTSSTPRITTFPQVPITC-DAVRNKCREMLTLALQTDHDHVAVGVSCEHL 166

Query:   139 KEQVRACDPVGVAVSVESVLFKNMCPF-LFNVKDPKNPDFWRKVLLGEVKPETLVTALPE 197
               Q+  C  + + V    + +KN     + N+KD KNP   R VL G + P+ +     E
Sbjct:   167 SSQIEEC--IFLDVGNTDMKYKNRVRSRISNLKDAKNPGLRRNVLCGAITPQQIAVMTSE 224

Query:   198 EMASDERQSRNKQIREDALAKIRDHSV 224
             EMASDE +   K + ++A   IR+H +
Sbjct:   225 EMASDELKEIRKAMTKEA---IREHQM 248

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO;TAS

GO:0005813 "centrosome" evidence=IEA;ISO

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

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

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

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q63799 Tcea2 "Transcription elongation factor A protein 2" [Rattus norvegicus (taxid:10116)]

 Score = 128 (50.1 bits), Expect = 4.6e-06, P = 4.6e-06
 Identities = 47/147 (31%), Positives = 65/147 (44%)

Query:    85 KKPLGQSQPPKQEQDRK--TASAVEIKCSDATRTLIRERLAEAFSK----VAGEVEEMEK 138
             KKP     PP+     +  T   V I C DA R   RE L  A       VA  V     
Sbjct:   112 KKP----DPPRTSSTPRITTFPQVPITC-DAVRNKCREMLTLALQTDHDHVAVGVSCEHL 166

Query:   139 KEQVRACDPVGVAVSVESVLFKNMCPF-LFNVKDPKNPDFWRKVLLGEVKPETLVTALPE 197
               Q+  C  + + V    + +KN     + N+KD KNP   R VL G + P+ +     E
Sbjct:   167 SSQIEEC--IFLDVGNTDMKYKNRVRSRISNLKDAKNPGLRRNVLCGAITPQQIAVMTSE 224

Query:   198 EMASDERQSRNKQIREDALAKIRDHSV 224
             EMASDE +   K + ++A   IR+H +
Sbjct:   225 EMASDELKEIRKAMTKEA---IREHQM 248

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" 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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00037504001 SubName- Full=Chromosome chr8 scaffold_88, whole genome shotgun sequence; (367 aa) (Vitis vinifera)

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	235
pfam07500	115	pfam07500, TFIIS_M, Transcription factor S-II (TFI	2e-18
smart00510	102	smart00510, TFS2M, Domain in the central regions o	2e-15
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	2e-14

>gnl|CDD|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central domain

 Score = 77.3 bits (191), Expect = 2e-18
 Identities = 41/118 (34%), Positives = 58/118 (49%), Gaps = 19/118 (16%)

Query: 110 CSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCP----- 164
            +D  R   RE L +A +K + +             +   +A  +E  LFK         
Sbjct: 1   TNDKVRDKCRELLYDALAKGSEDSMSE--------EEVERLAAEIEEELFKLYGNTGKKY 52

Query: 165 ------FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDAL 216
                  +FN+KDPKNPD  RKVL GE+ PE LV   PEE+ASDE +   ++I ++AL
Sbjct: 53  KNKYRSLMFNLKDPKNPDLRRKVLNGEISPERLVNMSPEELASDELKKEREEIEKEAL 110

Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity. Length = 115

>gnl|CDD|128786 smart00510, TFS2M, Domain in the central regions of transcription elongation factor S-II (and elsewhere)

 Score = 69.3 bits (170), Expect = 2e-15
 Identities = 33/99 (33%), Positives = 47/99 (47%), Gaps = 15/99 (15%)

Query: 118 IRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------L 166
           +R++  E   K     +  + +E     DP  +AV +E+ +F                  
Sbjct: 3   VRDKCQEMLYKAL--QKISDPEEI--ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLY 58

Query: 167 FNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQ 205
           FN+KD KNPD  RKVL GE+ PE L T   EE+AS E +
Sbjct: 59  FNLKDKKNPDLRRKVLNGEITPEKLATMTAEELASAELK 97

Length = 102

>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II

 Score = 70.3 bits (172), Expect = 2e-14
 Identities = 41/152 (26%), Positives = 62/152 (40%), Gaps = 28/152 (18%)

Query: 85  KKPLGQSQPPKQEQDRKTASAVEIK---------CSDATRTLIRERLAEAFSKVAGEVEE 135
            K   +SQ  K EQ +  +S+              +D  R   RE L +A +K +     
Sbjct: 100 VKQEAKSQSDKIEQPKYVSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHP-- 157

Query: 136 MEKKEQVRACDPVGVAVSVESVLFKN-----------MCPFLFNVKDPKNPDFWRKVLLG 184
                  ++ DP   A+ +E + F N                 N++D  NPD    VL G
Sbjct: 158 ------PQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTG 211

Query: 185 EVKPETLVTALPEEMASDERQSRNKQIREDAL 216
           E+ PE L T   EEMAS E +   ++I ++ L
Sbjct: 212 EITPEKLATMTAEEMASAELKQEREEITKENL 243

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. Length = 299

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	235
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.96
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	99.94
smart00510	102	TFS2M Domain in the central regions of transcripti	99.93
PF07500	115	TFIIS_M: Transcription factor S-II (TFIIS), centra	99.92
KOG1634	778	consensus Predicted transcription factor DATF1, co	99.11

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.96  E-value=9.1e-29  Score=226.47  Aligned_cols=117  Identities=29%  Similarity=0.419  Sum_probs=105.6

Q ss_pred             cccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCC
Q 037910          105 AVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPK  173 (235)
Q Consensus       105 ~~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~K  173 (235)
                      ++...++|++|++|+++||+||..+..+.+.        .+++..+|.+||.+||..|+.+           +|||||++
T Consensus       129 ~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~~--------~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~k  200 (299)
T TIGR01385       129 VPTAVTNDKVRDKCRELLYDALAKDSDHPPQ--------SIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKN  200 (299)
T ss_pred             CCCccCCcHHHHHHHHHHHHHHhhcCCCCcc--------ccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCC
Confidence            3567899999999999999999986543332        3577889999999999999865           99999999


Q ss_pred             ChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccceE
Q 037910          174 NPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEKE  229 (235)
Q Consensus       174 Np~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~~  229 (235)
                      ||+||++|++|+|+|++||.||++||||+|+|++|+++.+++|++||+++..|..+
T Consensus       201 Np~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~~~~~~~~~~~t  256 (299)
T TIGR01385       201 NPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVT  256 (299)
T ss_pred             CHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCc
Confidence            99999999999999999999999999999999999999999999999999887654

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]

Probab=99.94  E-value=1.9e-26  Score=210.86  Aligned_cols=115  Identities=32%  Similarity=0.495  Sum_probs=104.8

Q ss_pred             cccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCCh
Q 037910          107 EIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNP  175 (235)
Q Consensus       107 ~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp  175 (235)
                      .+.++|++|++|+++||+||....        ...+.++++..+|.+||.+||..++++           +|||+|++||
T Consensus       128 ~~~~~d~~r~k~~e~l~~al~~~~--------~~~~~~~~~~~~a~~iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np  199 (296)
T KOG1105|consen  128 VPITNDPVRDKCRELLYAALTTED--------DSRVTGADPLELAVQIEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNP  199 (296)
T ss_pred             CCCCCchHHHHHHHHHHHHhcccc--------cccccCCCHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCH
Confidence            455789999999999999999432        123446788999999999999998876           9999999999


Q ss_pred             hhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccceE
Q 037910          176 DFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEKE  229 (235)
Q Consensus       176 ~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~~  229 (235)
                      +||++||+|+|+|++|+.||++||||++||++|+++.++||++||++.++|+.|
T Consensus       200 ~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~k~~keal~~~q~~~~~gt~t  253 (296)
T KOG1105|consen  200 DLRRNVLTGEISPERLATMTSEEMASEELKEERQKLTKEALREHQMAKIQGTQT  253 (296)
T ss_pred             HHHHHHhcCCCCHHHhccCChhhhccHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence            999999999999999999999999999999999999999999999999999876

>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere)

Probab=99.93  E-value=1.3e-26  Score=182.73  Aligned_cols=91  Identities=40%  Similarity=0.584  Sum_probs=82.0

Q ss_pred             chHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCChhhhhh
Q 037910          112 DATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNPDFWRK  180 (235)
Q Consensus       112 D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp~Lr~~  180 (235)
                      |++|++|+++||+||.......+.        .+++..+|.+||.+||..|+.+           +|||||++||+||++
T Consensus         1 d~~R~~~~~~L~~al~~~~~~~~~--------~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~   72 (102)
T smart00510        1 DKVRDKCQEMLYKALQKISDPEEI--------ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRK   72 (102)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCcc--------cccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            689999999999999997654432        3467889999999999998854           999999999999999


Q ss_pred             hhcCCCCccccccCCcccCCcHHHHHHHHH
Q 037910          181 VLLGEVKPETLVTALPEEMASDERQSRNKQ  210 (235)
Q Consensus       181 VL~GeIsP~~Lv~MSseEMASdELK~erek  210 (235)
                      ||+|+|+|++||.||++||||+|||++|++
T Consensus        73 vl~G~i~p~~lv~Ms~~ElAs~elk~~~e~  102 (102)
T smart00510       73 VLNGEITPEKLATMTAEELASAELKEKREK  102 (102)
T ss_pred             HHcCCCCHHHHhcCCHHHcCCHHHHHHHhC
Confidence            999999999999999999999999999873

>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites

Probab=99.92  E-value=1.2e-26  Score=183.99  Aligned_cols=104  Identities=38%  Similarity=0.598  Sum_probs=93.5

Q ss_pred             CCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCChhhh
Q 037910          110 CSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNPDFW  178 (235)
Q Consensus       110 t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp~Lr  178 (235)
                      |++++|++|+++|+++|...... .+.       ..++..+|.+||.+||..|+..           +|||||++||+||
T Consensus         1 ~~~~~R~k~~~~L~~~l~~~~~~-~~~-------~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~   72 (115)
T PF07500_consen    1 TNDKVRDKARKLLYKALQKRSDE-QDD-------PEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLR   72 (115)
T ss_dssp             -TCHHHHHHHHHHHHHHHHCCCC-CCC-------TCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHH
T ss_pred             CCcHHHHHHHHHHHHHHHhcCcc-ccc-------hhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHH
Confidence            67999999999999999998654 221       3567899999999999999644           9999999999999


Q ss_pred             hhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhc
Q 037910          179 RKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRD  221 (235)
Q Consensus       179 ~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~  221 (235)
                      .+|++|+|+|.+||.||++||||+++|++++++.+++++++|+
T Consensus        73 ~~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~~~l~~~~~  115 (115)
T PF07500_consen   73 RRILSGEISPEELVTMSPEELASEELKEEREKIRKESLKQSQM  115 (115)
T ss_dssp             HHHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred             HHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999999999999999999999999985

TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.

>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]

Probab=99.11  E-value=4.2e-11  Score=121.20  Aligned_cols=71  Identities=35%  Similarity=0.450  Sum_probs=65.3

Q ss_pred             ChHHHHHHHHHHHHHhhCCc------------ccCCCCCCChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHH
Q 037910          146 DPVGVAVSVESVLFKNMCPF------------LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIRE  213 (235)
Q Consensus       146 d~~~lA~eIE~aLF~~~~~s------------~fNLKD~KNp~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~e  213 (235)
                      ++.-++..||..||..||..            +|||||+|||.||.+|+.|+|+|++||.|+++||||.||++||++..+
T Consensus       268 d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rEek~e  347 (778)
T KOG1634|consen  268 DPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWREEKAE  347 (778)
T ss_pred             chhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHHHHHH
Confidence            45567779999999999933            999999999999999999999999999999999999999999999988


Q ss_pred             HHH
Q 037910          214 DAL  216 (235)
Q Consensus       214 eAL  216 (235)
                      +.+
T Consensus       348 e~~  350 (778)
T KOG1634|consen  348 EMN  350 (778)
T ss_pred             HHH
Confidence            765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	235
2dme_A	120	Solution Structure Of The Tfiis Domain Ii Of Human		1e-05
2lw4_A	113	Solution Nmr Structure Of Human Transcription Elong		3e-05

>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd Finger Protein 3 Length = 120

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 28/39 (71%)
Query: 165 FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE 203
            +FN+KDPKN   ++KVL GEV P+ L+   PEE+AS E
Sbjct: 69  LMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKE 107

>pdb|2LW4|A Chain A, Solution Nmr Structure Of Human Transcription Elongation Factor A Protein 2, Central Domain, Northeast Structural Genomics Consortium (Nesg) Target Hr8682b Length = 113

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 24/38 (63%)
Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE 203
           + N+KD KNPD  R VL G + P+ +     EEMASDE
Sbjct: 67  ISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDE 104

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	235
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	2e-15
3ndq_A	108	Transcription elongation factor A protein 1; helix	1e-13
3po3_S	178	Transcription elongation factor S-II; RNA polymera	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	8e-04

>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 120

 Score = 68.8 bits (168), Expect = 2e-15
 Identities = 32/116 (27%), Positives = 49/116 (42%), Gaps = 16/116 (13%)

Query: 111 SDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCP------ 164
           +D  R  +R  L +   K   +      +E         VA  +E  LF           
Sbjct: 9   ADQIRQSVRHSLKDILMKRLTDSNLKVPEE-----KAAKVATKIEKELFSFFRDTDAKYK 63

Query: 165 -----FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDA 215
                 +FN+KDPKN   ++KVL GEV P+ L+   PEE+AS E  +  ++    +
Sbjct: 64  NKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRRSGPSS 119

>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens} Length = 108

 Score = 63.9 bits (155), Expect = 1e-13
 Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 19/106 (17%)

Query: 109 KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCP---- 164
             SD+ R   RE LA A                    D   +   +E  +++ +      
Sbjct: 11  STSDSVRLKCREMLAAAL--------RTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMK 62

Query: 165 -------FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE 203
                   + N+KD KNP+  + VL G + P+       EEMASDE
Sbjct: 63  YKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 108

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Length = 178

 Score = 51.0 bits (121), Expect = 3e-08
 Identities = 18/125 (14%), Positives = 41/125 (32%), Gaps = 3/125 (2%)

Query: 101 KTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFK 160
           K             R  + + L +  +K +    +            +    + ++    
Sbjct: 4   KNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAA 63

Query: 161 NMCPF---LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALA 217
               +     NV    NPD   K+  G++ PE L T   +++A    + + ++I +  L 
Sbjct: 64  YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLY 123

Query: 218 KIRDH 222
             +  
Sbjct: 124 NAQGA 128

>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 = 40.2 bits (93), Expect = 4e-04
 Identities = 22/161 (13%), Positives = 47/161 (29%), Gaps = 48/161 (29%)

Query: 98  QDRKTASAVEIKCSDATRTLIRERLAEAFSKVAGEV-------------EEMEKKEQVRA 144
           Q+ K  +A  + C    + L+  R  +    ++                   E K  +  
Sbjct: 254 QNAKAWNAFNLSC----KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309

Query: 145 CDPVGVAVSVESVLFKNMC---PFLFNV-----KDPKN-PDFWRKVLLGEVKP--ETLVT 193
                +    +  L + +    P   ++     +D     D W+ V   ++    E+ + 
Sbjct: 310 Y----LDCRPQD-LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364

Query: 194 AL-PEEMASDERQSRNKQIRE--DALAKIRDHSVVGEKELE 231
            L P E             R+  D L+     + +    L 
Sbjct: 365 VLEPAEY------------RKMFDRLSVFPPSAHIPTILLS 393

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Length = 309

 Score = 39.0 bits (89), Expect = 8e-04
 Identities = 21/171 (12%), Positives = 50/171 (29%), Gaps = 3/171 (1%)

Query: 46  TNQMKNRVSVESKKFKAPSSRTNKKRKFEGEDQAAFPFMKKPLGQSQPPKQEQDRKTASA 105
               + +   +         +T       G  Q A               + ++ K    
Sbjct: 80  KRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAMKQDKYVSTKPRNSKNDGV 139

Query: 106 VEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF 165
                    R  + + L +  +K +    +            +    + ++        +
Sbjct: 140 DTAIYHHKLRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAAYKARY 199

Query: 166 L---FNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIRE 213
                NV    NPD   K+  G++ PE L T   +++A    + + ++I +
Sbjct: 200 RIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAK 250

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	235
3po3_S	178	Transcription elongation factor S-II; RNA polymera	99.95
2lw4_A	113	Transcription elongation factor A protein 2; struc	99.95
3ndq_A	108	Transcription elongation factor A protein 1; helix	99.93
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	99.93
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.93

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A

Probab=99.95  E-value=2.9e-29  Score=213.39  Aligned_cols=121  Identities=18%  Similarity=0.224  Sum_probs=100.7

Q ss_pred             ccccccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-------------ccC
Q 037910          102 TASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-------------LFN  168 (235)
Q Consensus       102 l~~~~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-------------~fN  168 (235)
                      .+..+.+.++|++|++|+++||+||.....+.+.          ++..+|.+||.+||..|++.             +||
T Consensus         5 ~d~v~~~~~~d~vRdk~~~lL~~aL~~~~~~~~~----------~~~~~A~~IE~~if~~~~~~~~~k~Yk~k~Rsl~~N   74 (178)
T 3po3_S            5 NDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ----------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSN   74 (178)
T ss_dssp             ----------CHHHHHHHHHHHHHTTSSSSCSTT----------HHHHHHHHHHHHHHHHTSCSSSSTHHHHHHHHHHHH
T ss_pred             CCCcCcCcCCChHHHHHHHHHHHHHhcCCCCchh----------hHHHHHHHHHHHHHHHhcCCCchhhhhhhhhHHHHH
Confidence            3444678899999999999999999997655543          34789999999999999861             999


Q ss_pred             CCCCCChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccce--EEee
Q 037910          169 VKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEK--ELEC  232 (235)
Q Consensus       169 LKD~KNp~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~--~~~~  232 (235)
                      |||++||+||++|++|+|+|.+||.||++||||+|+|++++++++++|+++|.++..|..  .+.|
T Consensus        75 LKd~~N~~Lr~~vl~g~isp~~lv~Ms~eElas~elk~~~e~~~~e~l~~~~~~~~~~~~t~~~~C  140 (178)
T 3po3_S           75 VISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTC  140 (178)
T ss_dssp             HHSSSCSHHHHHHHHCCCTTHHHHCCTTTTSSCSHHHHHHHHHHHHHHHHTBCCCCCCCCBSSSCC
T ss_pred             cCCCCCHHHHHHHhcCCCCHHHHHhcCchhhCCHHHHHHHHHHHHHHHHHhhhccccCCCcCCcCC
Confidence            999999999999999999999999999999999999999999999999999999988843  4555

>2lw4_A Transcription elongation factor A protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.95  E-value=1.2e-30  Score=208.02  Aligned_cols=98  Identities=32%  Similarity=0.437  Sum_probs=87.0

Q ss_pred             ccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCC
Q 037910          106 VEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKN  174 (235)
Q Consensus       106 ~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KN  174 (235)
                      +.+.|+|++|++|+++||+||.......        ....++..+|.+||.++|..|+++           +|||||++|
T Consensus         4 p~p~t~D~vRdk~~e~L~~aL~~~~~~~--------~~~~~~~~~A~~IE~~~f~~~~~~~~~Yk~k~Rsl~~NLkd~~N   75 (113)
T 2lw4_A            4 PVPVTCDAVRNKCREMLTAALQTDHDHV--------AIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKN   75 (113)
T ss_dssp             CSCCCCSTTHHHHHHHHHHHHHSSTHHH--------HHTCCHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHCSSS
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCCcc--------cccchHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCC
Confidence            4688999999999999999998642111        124577899999999999999875           999999999


Q ss_pred             hhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHH
Q 037910          175 PDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQI  211 (235)
Q Consensus       175 p~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki  211 (235)
                      |+||++||+|+|+|++||.||++||||+|||+||+++
T Consensus        76 p~Lr~~vl~G~i~p~~l~~Ms~eEmAs~elk~~r~~~  112 (113)
T 2lw4_A           76 PDLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAM  112 (113)
T ss_dssp             SHHHHHHHTTSSCHHHHHHSCHHHHHCTTTTTCSSSC
T ss_pred             HHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHc
Confidence            9999999999999999999999999999999999865

>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens}

Probab=99.93  E-value=4.1e-27  Score=186.21  Aligned_cols=90  Identities=30%  Similarity=0.436  Sum_probs=75.9

Q ss_pred             ccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCC
Q 037910          106 VEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKN  174 (235)
Q Consensus       106 ~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KN  174 (235)
                      +.+.|+|++|++|+++||+||.......+        ...++..+|.+||.+||..|+++           +|||||++|
T Consensus         8 ~~~~t~d~vR~k~~~lL~~aL~~~~d~~~--------~~~~~~~lA~~IE~~if~~~~~~~~~Yk~k~Rsl~fNLKd~kN   79 (108)
T 3ndq_A            8 RAPSTSDSVRLKCREMLAAALRTGDDYIA--------IGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKN   79 (108)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHTTGGGHHHH--------HTCCHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHTCTTC
T ss_pred             CCCCCCChHHHHHHHHHHHHHHcCCCCCc--------ccccHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC
Confidence            35779999999999999999998541111        13577899999999999999865           999999999


Q ss_pred             hhhhhhhhcCCCCccccccCCcccCCcHH
Q 037910          175 PDFWRKVLLGEVKPETLVTALPEEMASDE  203 (235)
Q Consensus       175 p~Lr~~VL~GeIsP~~Lv~MSseEMASdE  203 (235)
                      |+||++|++|+|+|++||+||++||||+|
T Consensus        80 p~Lr~~vl~G~isp~~lv~Ms~eEmAS~E  108 (108)
T 3ndq_A           80 PNLRKNVLCGNIPPDLFARMTAEEMASDE  108 (108)
T ss_dssp             HHHHHHHHHTSSCHHHHHHCCTTTC----
T ss_pred             HHHHHHHHcCCcCHHHHhCCCHHHccCCC
Confidence            99999999999999999999999999997

>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.93  E-value=6.7e-28  Score=193.85  Aligned_cols=99  Identities=31%  Similarity=0.439  Sum_probs=85.8

Q ss_pred             cCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCChhh
Q 037910          109 KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNPDF  177 (235)
Q Consensus       109 ~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp~L  177 (235)
                      .++|++|++|+++|+++|.....+.+...     ..+++..+|.+||.+||..|+.+           +|||||++||+|
T Consensus         7 ~~~d~~Rd~~r~~L~eaL~~~~~~~~~~~-----~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~L   81 (120)
T 2dme_A            7 GSADQIRQSVRHSLKDILMKRLTDSNLKV-----PEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNIL   81 (120)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHTTTTCCC-----CHHHHHHHHHHHHHHHHHHHCSCSHHHHHHHHHHTHHHHSSSCCSH
T ss_pred             CCCchHHHHHHHHHHHHHHHhcccccccc-----chhHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHH
Confidence            35689999999999999998876543211     01345789999999999999875           999999999999


Q ss_pred             hhhhhcCCCCccccccCCcccCCcHHHHHHHHHHH
Q 037910          178 WRKVLLGEVKPETLVTALPEEMASDERQSRNKQIR  212 (235)
Q Consensus       178 r~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~  212 (235)
                      |++||+|+|+|++||.||++||||+|||+||+++.
T Consensus        82 r~~vl~G~i~p~~lv~Ms~eEmAS~elk~~r~~~~  116 (120)
T 2dme_A           82 FKKVLKGEVTPDHLIRMSPEELASKELAAWRRRSG  116 (120)
T ss_dssp             HHHHHHTSSCTTHHHHSCTTTTTTCCSTTTCTTCC
T ss_pred             HHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHh
Confidence            99999999999999999999999999999998764

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A

Probab=99.93  E-value=8.9e-26  Score=205.30  Aligned_cols=122  Identities=19%  Similarity=0.231  Sum_probs=105.7

Q ss_pred             hccccccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-------------cc
Q 037910          101 KTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-------------LF  167 (235)
Q Consensus       101 kl~~~~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-------------~f  167 (235)
                      +.+.+....++|++|++|+++|++||.....+.+.          ++..+|.+||.+||..|+++             +|
T Consensus       135 ~~~~~~~~~~~d~~R~k~r~~L~~aL~~~~~~~~~----------~~~~~A~~IE~al~~~~~~~~~~~~Yk~k~Rsl~~  204 (309)
T 1pqv_S          135 KNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ----------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYS  204 (309)
T ss_pred             CCCCCCcCcCChHHHHHHHHHHHHHHhcCCCccch----------hHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHH
Confidence            45555566889999999999999999875433322          45789999999999988643             99


Q ss_pred             CCCCCCChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccce--EEee
Q 037910          168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEK--ELEC  232 (235)
Q Consensus       168 NLKD~KNp~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~--~~~~  232 (235)
                      ||||++||+||++||.|+|+|++||.||++||||+|+|++|+++++++|++||+++..+..  .+.|
T Consensus       205 NLKd~~N~~Lr~~vl~g~i~p~~lv~Ms~eElasde~k~~~~~~~~e~l~~~~~~~~~~~~~~~~~C  271 (309)
T 1pqv_S          205 NVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTC  271 (309)
T ss_pred             HcCcCCChHHHHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhhccccccCcccccC
Confidence            9999999999999999999999999999999999999999999999999999999877643  4555

---

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	235
d1enwa_	114	a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak	6e-12

>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 114

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: Elongation factor TFIIS domain 2
family: Elongation factor TFIIS domain 2
domain: Elongation factor TFIIS domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.3 bits (141), Expect = 6e-12
 Identities = 19/103 (18%), Positives = 35/103 (33%), Gaps = 23/103 (22%)

Query: 111 SDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCP------ 164
               R  + + L +  +K +    +            +  A ++ES + K          
Sbjct: 19  HHKLRDQVLKALYDVLAKESEHPPQ----------SILHTAKAIESEMNKVNNCDTNEAA 68

Query: 165 -------FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMA 200
                     NV    NPD   K+  G++ PE L T   +++A
Sbjct: 69  YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	235
d1enwa_	114	Elongation factor TFIIS domain 2 {Baker's yeast (S	99.84

>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: Elongation factor TFIIS domain 2
family: Elongation factor TFIIS domain 2
domain: Elongation factor TFIIS domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=2.5e-22  Score=158.26  Aligned_cols=91  Identities=22%  Similarity=0.224  Sum_probs=79.2

Q ss_pred             hccccccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-------------cc
Q 037910          101 KTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-------------LF  167 (235)
Q Consensus       101 kl~~~~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-------------~f  167 (235)
                      |....+...++|++|++|+++||++|.....+.++          .+..+|.+||.+||..|++.             +|
T Consensus         9 k~d~v~~~~~~d~~R~~~~~~L~~aL~~~~~~~~~----------~~~~la~~IE~~lf~~~~~~~~~~~Y~~k~rsi~~   78 (114)
T d1enwa_           9 KNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ----------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYS   78 (114)
T ss_dssp             TTTCCCCCSSTTTTHHHHHHHHHHHHHHHCSSSCS----------CHHHHHHHHTTTTTSSCTTTTTHHHHHHHHHHHHH
T ss_pred             cCCCCCCccCCcHHHHHHHHHHHHHHhCcCccchh----------HHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHH
Confidence            44444567899999999999999999986654443          34789999999999998743             99


Q ss_pred             CCCCCCChhhhhhhhcCCCCccccccCCcccCCc
Q 037910          168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMAS  201 (235)
Q Consensus       168 NLKD~KNp~Lr~~VL~GeIsP~~Lv~MSseEMAS  201 (235)
                      ||||++||+||++|++|+|+|.+||.|+++|||.
T Consensus        79 NLkd~~N~~L~~~v~~g~i~p~~l~~M~~~ElaP  112 (114)
T d1enwa_          79 NVISKNNPDLKHKIANGDITPEFLATCDAKDLAP  112 (114)
T ss_dssp             HHTTSCCCCTTTHHHHCSSCCSSHHHHTTTTTCS
T ss_pred             HcCccchHHHHHHHHcCCCCHHHHhCCCHHHcCC
Confidence            9999999999999999999999999999999996