Psyllid ID: psy996

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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-
Protein Sequence
MNFIFLFPAPPGISNNKDSSSKKKEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYITV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHccccccHHHHHccccccccHHHHHcccHHHHccccccccHHHHHccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccccccEEEEEEEEccccccccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccEEEEccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHccccccHHHHHHccHHHHcccccccccHHHHcHHHHHHHHHHHHHHHHHHHHccccccccccEEEccccccccEEEEEEEEccccccccEEEEEEEEc
Coil and Loop (DISEMBL)
mnfiflfpappgisnnkdssskKKEAKeekkedkkpsvtqyppqkshnltdSVRLKCREMLQNSiqvgdldmdGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRianlkdpknpmlsrnyiFGAISASKLATMTAEvqtrsadepmttFEMANDEMKTLRNKFIKESIDDAQLATvqgtktdllkcgkckkrnctynqvqtrsadepmttlhhFYITV
Flexible Loop (DISEMBL)
mnfiflfpappgisnnkdssskkkeakeekkedkkpsvtqyppqkshnltdsVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYnefkntdnryknrvrsrianlkdpknpmlsRNYIFGAISASKLATMTAEVqtrsadepmttfEMANDEMKTLRNKFIKESIDdaqlatvqgtktdllkcgkckkrnctynqvqtrsadepmttlhhfyitv
Low Complexity Region (SEG)
MNFIFLFPAPPGIsnnkdssskkkeakeekkedkkPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGlasleelateleeaIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYITV
Disordered region (IsUnstruct)
***IFL*************************************************KCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRY******************LSRNYIFGAISASKL*******************************KFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQT*******TTLHHFYI**
Disordered Region (DISOPRED)
*NFIFL************************************************LKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATM****************EMANDEMKTLRNKFIKESID*A******GTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYITV
Disordered Region (DISEMBL)
MNFIFLFPAPPGIS********************************HNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYITV
Disordered Region (DISPRO)
*NFIF**P**********************************PQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEV******EPMT**E*ANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYITV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNFIFLFPAPPGISNNKDSSSKKKEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYITV
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	221	2.2.26 [Sep-21-2011]
P20232	313	Transcription elongation	yes	N/A	0.728	0.514	0.612	3e-57
Q29RL9	301	Transcription elongation	yes	N/A	0.850	0.624	0.471	1e-44
P23193	301	Transcription elongation	no	N/A	0.733	0.538	0.525	2e-44
Q4KLL0	301	Transcription elongation	no	N/A	0.733	0.538	0.525	2e-44
P10711	301	Transcription elongation	yes	N/A	0.733	0.538	0.525	3e-44
Q2KI09	349	Transcription elongation	no	N/A	0.683	0.432	0.536	6e-43
P23881	347	Transcription elongation	no	N/A	0.742	0.472	0.513	7e-43
O75764	348	Transcription elongation	no	N/A	0.683	0.433	0.536	8e-43
Q15560	299	Transcription elongation	no	N/A	0.873	0.645	0.432	7e-42
Q148K0	300	Transcription elongation	no	N/A	0.814	0.6	0.448	2e-41

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

 Score =  221 bits (564), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 109/178 (61%), Positives = 136/178 (76%), Gaps = 17/178 (9%)

Query: 37  SVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNT 96
           S T +P   S  +TD+VR+KCREML  ++++G++  +G    EE+A ELE+AIY+EF NT
Sbjct: 140 SQTSFP---SGGMTDAVRIKCREMLATALKIGEVP-EGCGEPEEMAAELEDAIYSEFNNT 195

Query: 97  DNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAN 156
           D +YKNR+RSR+ANLKDPKNP L  N++ GA++A +LA MT E             EMA+
Sbjct: 196 DMKYKNRIRSRVANLKDPKNPGLRGNFMCGAVTAKQLAKMTPE-------------EMAS 242

Query: 157 DEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           DEMK LR KF+KE+I+DAQLATVQGTKTDLLKC KCKKRNCTYNQ+QTRSADEPMTT 
Sbjct: 243 DEMKKLREKFVKEAINDAQLATVQGTKTDLLKCAKCKKRNCTYNQLQTRSADEPMTTF 300

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 =  179 bits (455), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 106/225 (47%), Positives = 138/225 (61%), Gaps = 37/225 (16%)

Query: 12  GISNNKDSSSKKK----------EAKEE---------KKED---KKPSVTQYPPQKSHNL 49
           G S +KDS  KKK          EA+EE         +K++   +   V+ +P  ++ + 
Sbjct: 79  GPSTDKDSEEKKKDTAVTSQNSPEAREESSSSGNMSSRKDETNARDTYVSSFP--RAPST 136

Query: 50  TDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIA 109
           +DSVRLKCREML  +++ GD  +   A  EEL +++EEAIY E +NTD +YKNRVRSRI+
Sbjct: 137 SDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRIS 196

Query: 110 NLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKE 169
           NLKD KNP L +N + G I     A MTAE             EMA+DE+K +R    KE
Sbjct: 197 NLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASDELKEMRKNLTKE 243

Query: 170 SIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           +I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT 
Sbjct: 244 AIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTF 288

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|P23193|TCEA1_HUMAN Transcription elongation factor A protein 1 OS=Homo sapiens GN=TCEA1 PE=1 SV=2

 Score =  178 bits (452), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 93/177 (52%), Positives = 119/177 (67%), Gaps = 15/177 (8%)

Query: 38  VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTD 97
           V+ +P  ++ + +DSVRLKCREML  +++ GD  +   A  EEL +++EEAIY E +NTD
Sbjct: 127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTD 184

Query: 98  NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
            +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct: 185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query: 158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT 
Sbjct: 232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTF 288

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

 Score =  178 bits (452), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 93/177 (52%), Positives = 119/177 (67%), Gaps = 15/177 (8%)

Query: 38  VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTD 97
           V+ +P  ++ + +DSVRLKCREML  +++ GD  +   A  EEL +++EEAIY E +NTD
Sbjct: 127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTD 184

Query: 98  NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
            +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct: 185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query: 158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT 
Sbjct: 232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTF 288

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

 Score =  178 bits (451), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 93/177 (52%), Positives = 119/177 (67%), Gaps = 15/177 (8%)

Query: 38  VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTD 97
           V+ +P  ++ + +DSVRLKCREML  +++ GD  +   A  EEL +++EEAIY E +NTD
Sbjct: 127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTD 184

Query: 98  NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
            +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct: 185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query: 158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT 
Sbjct: 232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTF 288

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|Q2KI09|TCEA3_BOVIN Transcription elongation factor A protein 3 OS=Bos taurus GN=TCEA3 PE=2 SV=1

 Score =  174 bits (440), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 88/164 (53%), Positives = 114/164 (69%), Gaps = 13/164 (7%)

Query: 51  DSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIAN 110
           DSVR KC EML  +++  D   D   + +++A+E+E+ IY E K+TD +Y+NRVRSRI+N
Sbjct: 186 DSVRDKCVEMLSAALKADDDYKDYGVNCDKMASEIEDHIYQELKSTDMKYRNRVRSRISN 245

Query: 111 LKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKES 170
           LKDP+NP L RN + GAISA  +A MTAE             EMA+DE++ LRN   +E+
Sbjct: 246 LKDPRNPGLRRNVLSGAISAGLIAKMTAE-------------EMASDELRELRNAMTQEA 292

Query: 171 IDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           I + Q+A   GT TDL +C KCKK+NCTYNQVQTRSADEPMTT 
Sbjct: 293 IREHQMAKTGGTTTDLFQCSKCKKKNCTYNQVQTRSADEPMTTF 336

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

 Score =  173 bits (439), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 92/179 (51%), Positives = 119/179 (66%), Gaps = 15/179 (8%)

Query: 36  PSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKN 95
           P+V    P   +   DSVR KC EML  +++  D   D   + ++LA+E+E+ IY E K+
Sbjct: 171 PAVCLLAP--CYLTGDSVRDKCVEMLSAALKAEDNFKDYGVNCDKLASEIEDHIYQELKS 228

Query: 96  TDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMA 155
           TD +Y+NRVRSRI+NLKDP+NP L RN + GAIS   +A MTAE             EMA
Sbjct: 229 TDMKYRNRVRSRISNLKDPRNPGLRRNVLSGAISPELIAKMTAE-------------EMA 275

Query: 156 NDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           +DE++ LRN   +E+I + Q+A   GT TDLL+C KCKK+NCTYNQVQTRSADEPMTT 
Sbjct: 276 SDELRELRNAMTQEAIREHQMAKTGGTTTDLLRCSKCKKKNCTYNQVQTRSADEPMTTF 334

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|O75764|TCEA3_HUMAN Transcription elongation factor A protein 3 OS=Homo sapiens GN=TCEA3 PE=2 SV=2

 Score =  173 bits (439), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 88/164 (53%), Positives = 114/164 (69%), Gaps = 13/164 (7%)

Query: 51  DSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIAN 110
           DSVR KC EML  +++  D   D   + +++A+E+E+ IY E K+TD +Y+NRVRSRI+N
Sbjct: 185 DSVRDKCVEMLSAALKADDDYKDYGVNCDKMASEIEDHIYQELKSTDMKYRNRVRSRISN 244

Query: 111 LKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKES 170
           LKDP+NP L RN + GAISA  +A MTAE             EMA+DE++ LRN   +E+
Sbjct: 245 LKDPRNPGLRRNVLSGAISAGLIAKMTAE-------------EMASDELRELRNAMTQEA 291

Query: 171 IDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           I + Q+A   GT TDL +C KCKK+NCTYNQVQTRSADEPMTT 
Sbjct: 292 IREHQMAKTGGTTTDLFQCSKCKKKNCTYNQVQTRSADEPMTTF 335

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

 Score =  170 bits (431), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 90/208 (43%), Positives = 124/208 (59%), Gaps = 15/208 (7%)

Query: 7   FPAPPGISNNKDSSSKKKEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQ 66
            P P    +  ++    ++  E  +    P +T +PP       D+VR KCREML  ++Q
Sbjct: 94  MPLPTSSRDASEAPDPSRKRPELPRAPSTPRITTFPPVPV--TCDAVRNKCREMLTAALQ 151

Query: 67  VGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFG 126
                +   A  E L+ ++EE I+ +  NTD +YKNRVRSRI+NLKD KNP L RN + G
Sbjct: 152 TDHDHVAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCG 211

Query: 127 AISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDL 186
           AI+  ++A MT+E             EMA+DE+K +R    KE+I + Q+A   GT+TDL
Sbjct: 212 AITPQQIAVMTSE-------------EMASDELKEIRKAMTKEAIREHQMARTGGTQTDL 258

Query: 187 LKCGKCKKRNCTYNQVQTRSADEPMTTL 214
             CGKC+K+NCTY QVQTRS+DEPMTT 
Sbjct: 259 FTCGKCRKKNCTYTQVQTRSSDEPMTTF 286

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

 Score =  168 bits (426), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 92/205 (44%), Positives = 123/205 (60%), Gaps = 25/205 (12%)

Query: 20  SSKKKEAKEEKKEDKK----------PSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGD 69
           +S  KEA E +   +K          P +T +PP       D+VR KCREML  ++Q   
Sbjct: 98  TSSSKEASEAQDPSRKRPELPRMPSTPRITTFPPVPV--TCDAVRTKCREMLTAALQTDH 155

Query: 70  LDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAIS 129
             +   A  E LA ++EE I+ +  NTD +YKNRVRSR++NLKD KNP L R  + GAI+
Sbjct: 156 DHVAIGADCECLAGQIEECIFRDVGNTDMKYKNRVRSRLSNLKDAKNPGLRRKVLCGAIT 215

Query: 130 ASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKC 189
             ++A MT+E             EMA+DE+K +R    KE+I + Q+A   GT+TDL  C
Sbjct: 216 PQQIAVMTSE-------------EMASDELKEIRKAMTKEAIREHQMARTGGTQTDLFTC 262

Query: 190 GKCKKRNCTYNQVQTRSADEPMTTL 214
           GKC+K+NCTY QVQTRS+DEPMTT 
Sbjct: 263 GKCRKKNCTYTQVQTRSSDEPMTTF 287

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	221
195115581	323	GI17330 [Drosophila mojavensis] gi|19391	0.755	0.517	0.629	2e-59
125987179	313	GA17632 [Drosophila pseudoobscura pseudo	0.764	0.539	0.627	8e-59
289742185	326	transcription elongation factor tFIIS [G	0.760	0.515	0.635	2e-58
195030242	350	GH10818 [Drosophila grimshawi] gi|193903	0.733	0.462	0.636	2e-58
194760841	315	GF15561 [Drosophila ananassae] gi|190616	0.755	0.530	0.623	6e-58
170036777	301	transcription elongation factor S-II [Cu	0.742	0.544	0.636	4e-56
17136888	313	RNA polymerase II elongation factor, iso	0.728	0.514	0.612	1e-55
195475592	313	GE19417 [Drosophila yakuba] gi|194176169	0.701	0.495	0.633	2e-55
91084035	294	PREDICTED: similar to transcription elon	0.823	0.619	0.650	2e-55
195338531	311	GM14545 [Drosophila sechellia] gi|194129	0.719	0.511	0.613	3e-55

>gi|195115581|ref|XP_002002335.1| GI17330 [Drosophila mojavensis] gi|193912910|gb|EDW11777.1| GI17330 [Drosophila mojavensis]

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 117/186 (62%), Positives = 146/186 (78%), Gaps = 19/186 (10%)

Query: 31  KEDKKPSVTQ--YPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEA 88
           +++KKPS  Q  +P   +  +TD+VRLKCREML N++++G++  +G A  EE+A ELE+A
Sbjct: 142 RDEKKPSSAQTSFP---AGGMTDAVRLKCREMLTNALKIGEVP-EGCAEPEEMAAELEDA 197

Query: 89  IYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEP 148
           IY+EFKNTD +YKNR+RSR+ANLKDPKNP L  N++ GA+SA +LA MT E         
Sbjct: 198 IYSEFKNTDMKYKNRIRSRVANLKDPKNPGLRGNFMCGAVSAKQLAKMTPE--------- 248

Query: 149 MTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSAD 208
               EMA+DEMK LR KF+KE+I+DAQLATVQGTKTDLLKCGKCKKRNCTYNQ+QTRSAD
Sbjct: 249 ----EMASDEMKKLREKFVKEAINDAQLATVQGTKTDLLKCGKCKKRNCTYNQLQTRSAD 304

Query: 209 EPMTTL 214
           EPMTT 
Sbjct: 305 EPMTTF 310

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125987179|ref|XP_001357352.1| GA17632 [Drosophila pseudoobscura pseudoobscura] gi|195155927|ref|XP_002018852.1| GL25727 [Drosophila persimilis] gi|54645683|gb|EAL34421.1| GA17632 [Drosophila pseudoobscura pseudoobscura] gi|194115005|gb|EDW37048.1| GL25727 [Drosophila persimilis]

 Score =  232 bits (592), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 118/188 (62%), Positives = 147/188 (78%), Gaps = 19/188 (10%)

Query: 29  EKKEDKKPSVTQ--YPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELE 86
           +K+E+KK S +Q  +P   S  +TD+VRLKCREML  ++++G++  +G A  EE+A ELE
Sbjct: 130 DKREEKKVSSSQTSFP---SGGMTDAVRLKCREMLTTALKMGEVP-EGCAEPEEMAAELE 185

Query: 87  EAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSAD 146
           +AIY+EFKNTD +YKNR+RSR+ANLKDPKNP L  N++ GA+SA +LA MT E       
Sbjct: 186 DAIYSEFKNTDMKYKNRIRSRVANLKDPKNPGLRGNFMCGAVSAKQLAKMTPE------- 238

Query: 147 EPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRS 206
                 EMA+DEMK LR KF+KE+I+DAQLATVQGTKTDLLKCGKCKKRNCTYNQ+QTRS
Sbjct: 239 ------EMASDEMKKLREKFVKEAINDAQLATVQGTKTDLLKCGKCKKRNCTYNQLQTRS 292

Query: 207 ADEPMTTL 214
           ADEPMTT 
Sbjct: 293 ADEPMTTF 300

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289742185|gb|ADD19840.1| transcription elongation factor tFIIS [Glossina morsitans morsitans]

 Score =  231 bits (589), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/184 (63%), Positives = 141/184 (76%), Gaps = 16/184 (8%)

Query: 31  KEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIY 90
           K+D+K   T +P   S  +TD+VRLKCREML N+++ GD+  +G    EE+A ELEEAIY
Sbjct: 146 KDDRKLIQTSFPA--SSGMTDAVRLKCREMLCNALKTGDIP-EGWPEPEEMAIELEEAIY 202

Query: 91  NEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMT 150
            EF+NTD +YKNRVRSR+ANLKDPKNP L  N++ GAI+A +LA MT E           
Sbjct: 203 AEFRNTDMKYKNRVRSRVANLKDPKNPTLRGNFMCGAITAQQLAKMTPE----------- 251

Query: 151 TFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEP 210
             EMA+DEMK LR KF+KE+I+DAQLATVQGTKTDLLKCGKCKKRNCTYNQ+QTRS+DEP
Sbjct: 252 --EMASDEMKKLREKFVKEAINDAQLATVQGTKTDLLKCGKCKKRNCTYNQLQTRSSDEP 309

Query: 211 MTTL 214
           MTT 
Sbjct: 310 MTTF 313

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195030242|ref|XP_001987977.1| GH10818 [Drosophila grimshawi] gi|193903977|gb|EDW02844.1| GH10818 [Drosophila grimshawi]

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 112/176 (63%), Positives = 135/176 (76%), Gaps = 14/176 (7%)

Query: 39  TQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDN 98
           T +P      + D+VRLKCREML  ++++G++  DG A  EE+A ELE+AIY EFKNTD 
Sbjct: 176 TTFPSGGGGGMKDAVRLKCREMLATALKMGEVP-DGCAEPEEMAAELEDAIYMEFKNTDM 234

Query: 99  RYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDE 158
           +YKNR+RSR+ANLKDPKNP L  N++ GA+SA +LA MT E             EMA+DE
Sbjct: 235 KYKNRIRSRVANLKDPKNPGLRGNFMCGAVSAKQLAKMTPE-------------EMASDE 281

Query: 159 MKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           MK LR KF+KE+I+DAQLATVQGTKTDLLKCGKCKKRNCTYNQ+QTRSADEPMTT 
Sbjct: 282 MKKLREKFVKEAINDAQLATVQGTKTDLLKCGKCKKRNCTYNQLQTRSADEPMTTF 337

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194760841|ref|XP_001962641.1| GF15561 [Drosophila ananassae] gi|190616338|gb|EDV31862.1| GF15561 [Drosophila ananassae]

 Score =  229 bits (584), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 116/186 (62%), Positives = 144/186 (77%), Gaps = 19/186 (10%)

Query: 31  KEDKKPSVTQ--YPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEA 88
           +E+K+ S +Q  +P   S  +TD+VRLKCREML  ++++G++  +G A  EE+A ELE+A
Sbjct: 134 REEKRASSSQTSFP---SGGMTDAVRLKCREMLTTALKMGEVP-EGCAEPEEMAAELEDA 189

Query: 89  IYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEP 148
           IY EFKNTD +YKNR+RSR+ANLKDPKNP L  N++ GA+SA +LA MT E         
Sbjct: 190 IYAEFKNTDMKYKNRIRSRVANLKDPKNPGLRGNFMCGAVSAKQLAKMTPE--------- 240

Query: 149 MTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSAD 208
               EMA+DEMK LR KF+KE+I+DAQLATVQGTKTDLLKCGKCKKRNCTYNQ+QTRSAD
Sbjct: 241 ----EMASDEMKKLREKFVKEAINDAQLATVQGTKTDLLKCGKCKKRNCTYNQLQTRSAD 296

Query: 209 EPMTTL 214
           EPMTT 
Sbjct: 297 EPMTTF 302

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170036777|ref|XP_001846238.1| transcription elongation factor S-II [Culex quinquefasciatus] gi|167879681|gb|EDS43064.1| transcription elongation factor S-II [Culex quinquefasciatus]

 Score =  223 bits (568), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 114/179 (63%), Positives = 137/179 (76%), Gaps = 15/179 (8%)

Query: 36  PSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKN 95
           P+ T +PP  S N TD+VRLKCREML ++I+V     +G  + EEL  ELEEAI++EF+N
Sbjct: 125 PTQTSFPP--SSNTTDAVRLKCREMLASAIRVDGEPPEGCQTPEELGDELEEAIFSEFRN 182

Query: 96  TDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMA 155
           TD +YKNRVRSR+ANLKD KNP L  NYI GAI+A +LA MT E             EMA
Sbjct: 183 TDMKYKNRVRSRVANLKDLKNPSLRSNYINGAITAQRLAKMTPE-------------EMA 229

Query: 156 NDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           +DEMK LR++F+KE+I+DAQLAT QGTKTDLLKCGKCKKRNCTYNQ+QTRS+DEPMTT 
Sbjct: 230 SDEMKNLRDRFVKEAINDAQLATNQGTKTDLLKCGKCKKRNCTYNQLQTRSSDEPMTTF 288

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17136888|ref|NP_476967.1| RNA polymerase II elongation factor, isoform A [Drosophila melanogaster] gi|442627872|ref|NP_001260457.1| RNA polymerase II elongation factor, isoform B [Drosophila melanogaster] gi|135660|sp|P20232.1|TFS2_DROME RecName: Full=Transcription elongation factor S-II; AltName: Full=RNA polymerase II elongation factor DMS-II; AltName: Full=TFIIS gi|7921|emb|CAA37710.1| unnamed protein product [Drosophila melanogaster] gi|6713129|gb|AAA92864.2| transcription elongation factor [Drosophila melanogaster] gi|7298202|gb|AAF53436.1| RNA polymerase II elongation factor, isoform A [Drosophila melanogaster] gi|15291997|gb|AAK93267.1| LD34766p [Drosophila melanogaster] gi|220942248|gb|ACL83667.1| TfIIS-PA [synthetic construct] gi|440213800|gb|AGB92992.1| RNA polymerase II elongation factor, isoform B [Drosophila melanogaster]

 Score =  221 bits (564), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 109/178 (61%), Positives = 136/178 (76%), Gaps = 17/178 (9%)

Query: 37  SVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNT 96
           S T +P   S  +TD+VR+KCREML  ++++G++  +G    EE+A ELE+AIY+EF NT
Sbjct: 140 SQTSFP---SGGMTDAVRIKCREMLATALKIGEVP-EGCGEPEEMAAELEDAIYSEFNNT 195

Query: 97  DNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAN 156
           D +YKNR+RSR+ANLKDPKNP L  N++ GA++A +LA MT E             EMA+
Sbjct: 196 DMKYKNRIRSRVANLKDPKNPGLRGNFMCGAVTAKQLAKMTPE-------------EMAS 242

Query: 157 DEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           DEMK LR KF+KE+I+DAQLATVQGTKTDLLKC KCKKRNCTYNQ+QTRSADEPMTT 
Sbjct: 243 DEMKKLREKFVKEAINDAQLATVQGTKTDLLKCAKCKKRNCTYNQLQTRSADEPMTTF 300

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195475592|ref|XP_002090068.1| GE19417 [Drosophila yakuba] gi|194176169|gb|EDW89780.1| GE19417 [Drosophila yakuba]

 Score =  221 bits (563), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 107/169 (63%), Positives = 133/169 (78%), Gaps = 14/169 (8%)

Query: 46  SHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVR 105
           S  +TD+VR+KCREML  ++++G++  +G    EE+A ELE+AIY+EFKNTD +YKNR+R
Sbjct: 146 SGGMTDAVRIKCREMLAAALKIGEVP-EGCGEPEEMAAELEDAIYSEFKNTDMKYKNRIR 204

Query: 106 SRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNK 165
           SR+ANLKDPKNP L  N++ GA++A +LA MT E             EMA+DEMK LR K
Sbjct: 205 SRVANLKDPKNPGLRGNFMCGAVTAKQLAKMTPE-------------EMASDEMKKLREK 251

Query: 166 FIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           F+KE+I+DAQLATVQGTKTDLLKC KCKKRNCTYNQ+QTRSADEPMTT 
Sbjct: 252 FVKEAINDAQLATVQGTKTDLLKCAKCKKRNCTYNQLQTRSADEPMTTF 300

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91084035|ref|XP_966732.1| PREDICTED: similar to transcription elongation factor S-II [Tribolium castaneum] gi|270008004|gb|EFA04452.1| hypothetical protein TcasGA2_TC014756 [Tribolium castaneum]

 Score =  221 bits (562), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 132/203 (65%), Positives = 148/203 (72%), Gaps = 21/203 (10%)

Query: 19  SSSKKKEAKEEK--KEDK-----KPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLD 71
           S+SK K  KEEK  +EDK     K    Q+PP  S N TD+VRLKCREML  +I+    +
Sbjct: 93  STSKPKRDKEEKSSREDKDRDKEKKLPNQFPPS-SSNTTDAVRLKCREMLAAAIRCDTEE 151

Query: 72  MDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISAS 131
            +G AS E+LA ELEEAI+ EFKNTD RYKNRVRSRIANLKD KNP L  N+  GAI AS
Sbjct: 152 FEGCASPEDLAEELEEAIFQEFKNTDMRYKNRVRSRIANLKDVKNPNLRTNFRIGAIPAS 211

Query: 132 KLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGK 191
           +LA MTAE             EMANDE+K LR +F KE+I+DAQLATVQGTKTDLLKCGK
Sbjct: 212 RLAVMTAE-------------EMANDEIKQLRERFTKEAINDAQLATVQGTKTDLLKCGK 258

Query: 192 CKKRNCTYNQVQTRSADEPMTTL 214
           CKKRNCTYNQVQTRSADEPMTT 
Sbjct: 259 CKKRNCTYNQVQTRSADEPMTTF 281

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195338531|ref|XP_002035878.1| GM14545 [Drosophila sechellia] gi|194129758|gb|EDW51801.1| GM14545 [Drosophila sechellia]

 Score =  220 bits (561), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 108/176 (61%), Positives = 135/176 (76%), Gaps = 17/176 (9%)

Query: 39  TQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDN 98
           T +P   S  +TD+VR+KCREML  ++++G++  +G    EE+A ELE+AIY+EF NTD 
Sbjct: 140 TSFP---SGGMTDAVRIKCREMLATALKIGEVP-EGCGEPEEMAAELEDAIYSEFNNTDM 195

Query: 99  RYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDE 158
           +YKNR+RSR+ANLKDPKNP L  N++ GA++A +LA MT E             EMA+DE
Sbjct: 196 KYKNRIRSRVANLKDPKNPGLRGNFMCGAVTAKQLARMTPE-------------EMASDE 242

Query: 159 MKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           MK LR KF+KE+I+DAQLATVQGTKTDLLKC KCKKRNCTYNQ+QTRSADEPMTT 
Sbjct: 243 MKKLREKFVKEAINDAQLATVQGTKTDLLKCAKCKKRNCTYNQLQTRSADEPMTTF 298

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	221
FB|FBgn0010422	313	TfIIS "RNA polymerase II elong	0.696	0.492	0.589	8.8e-47
ZFIN|ZDB-GENE-030131-8049	309	tcea1 "transcription elongatio	0.728	0.521	0.505	2.1e-38
UNIPROTKB|F1NP37	280	TCEA1 "Uncharacterized protein	0.723	0.571	0.494	4.9e-37
ZFIN|ZDB-GENE-040426-1860	409	tcea3 "transcription elongatio	0.678	0.366	0.533	4.9e-37
UNIPROTKB|F1MIT2	280	TCEA1 "Transcription elongatio	0.728	0.575	0.488	3.5e-36
UNIPROTKB|Q29RL9	301	TCEA1 "Transcription elongatio	0.728	0.534	0.488	3.5e-36
UNIPROTKB|E2QVN6	301	TCEA1 "Uncharacterized protein	0.728	0.534	0.488	3.5e-36
UNIPROTKB|P23193	301	TCEA1 "Transcription elongatio	0.728	0.534	0.488	3.5e-36
MGI|MGI:1196624	301	Tcea1 "transcription elongatio	0.728	0.534	0.488	3.5e-36
RGD|1309880	301	Tcea1 "transcription elongatio	0.728	0.534	0.488	3.5e-36

FB|FBgn0010422 TfIIS "RNA polymerase II elongation factor" [Drosophila melanogaster (taxid:7227)]

 Score = 490 (177.5 bits), Expect = 8.8e-47, P = 8.8e-47
 Identities = 99/168 (58%), Positives = 123/168 (73%)

Query:    46 SHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTDNRYKNRVR 105
             S  +TD+VR+KCREML  ++++G++  +G              IY+EF NTD +YKNR+R
Sbjct:   146 SGGMTDAVRIKCREMLATALKIGEVP-EGCGEPEEMAAELEDAIYSEFNNTDMKYKNRIR 204

Query:   106 SRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNK 165
             SR+ANLKDPKNP L  N++ GA++A +LA MT E             EMA+DEMK LR K
Sbjct:   205 SRVANLKDPKNPGLRGNFMCGAVTAKQLAKMTPE-------------EMASDEMKKLREK 251

Query:   166 FIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             F+KE+I+DAQLATVQGTKTDLLKC KCKKRNCTYNQ+QTRSADEPMTT
Sbjct:   252 FVKEAINDAQLATVQGTKTDLLKCAKCKKRNCTYNQLQTRSADEPMTT 299

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

GO:0005634 "nucleus" evidence=ISS;NAS

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA 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

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

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 89/176 (50%), Positives = 112/176 (63%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             +  +P  ++   +DSVR+KCREML N++Q GD  +                I+ EFKNTD
Sbjct:   135 IATFP--RAPGTSDSVRIKCREMLSNALQTGDDYITIGSDCDELGAQIEECIFLEFKNTD 192

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRI+NLKD KNP L RN + G +S  ++A MTAE             EMA+D
Sbjct:   193 MKYKNRVRSRISNLKDAKNPNLRRNVLCGNVSPDRIAKMTAE-------------EMASD 239

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I D Q+AT  GT+TDL  CGKCKK+ CTY QVQTRSADEPMTT
Sbjct:   240 ELKEMRKNLTKEAIRDHQVATSGGTQTDLFTCGKCKKKKCTYTQVQTRSADEPMTT 295

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

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

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 87/176 (49%), Positives = 109/176 (61%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             +  +P  ++ + +DSVR+KCREML  +++ GD D                 I+ E KNTD
Sbjct:   107 IPSFP--RAPSTSDSVRVKCREMLSAALRTGD-DYIAIGADEEELETIHTPIFQELKNTD 163

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRIANLKD KNP L +N + G I   K A MTAE             EMA+D
Sbjct:   164 MKYKNRVRSRIANLKDAKNPNLRKNVLCGNIPPDKFAKMTAE-------------EMASD 210

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct:   211 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 266

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-040426-1860 tcea3 "transcription elongation factor A (SII), 3" [Danio rerio (taxid:7955)]

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 87/163 (53%), Positives = 106/163 (65%)

Query:    51 DSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTDNRYKNRVRSRIAN 110
             DS+R KC EML  +++  D   D               IY E K TD +YKNRVRSRI+N
Sbjct:   246 DSIRDKCIEMLTAALRTDDDYKDYGTNCEAMGAEIEDYIYQETKATDMKYKNRVRSRISN 305

Query:   111 LKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKES 170
             LKDPKNP L +N + GAI  S++A+MTAE             EMA+DE+K LRN   +E+
Sbjct:   306 LKDPKNPNLRKNVLAGAIELSRIASMTAE-------------EMASDELKQLRNVLTQEA 352

Query:   171 IDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             I + Q+A   GT TDLL+CGKCKK+NCTYNQVQTRSADEPMTT
Sbjct:   353 IREHQMAKTGGTTTDLLQCGKCKKKNCTYNQVQTRSADEPMTT 395

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

UNIPROTKB|F1MIT2 TCEA1 "Transcription elongation factor A protein 1" [Bos taurus (taxid:9913)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 86/176 (48%), Positives = 109/176 (61%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             V+ +P  ++ + +DSVRLKCREML  +++ GD  +                IY E +NTD
Sbjct:   106 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTD 163

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct:   164 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 210

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct:   211 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 266

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

GO:0030218 "erythrocyte differentiation" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q29RL9 TCEA1 "Transcription elongation factor A protein 1" [Bos taurus (taxid:9913)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 86/176 (48%), Positives = 109/176 (61%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             V+ +P  ++ + +DSVRLKCREML  +++ GD  +                IY E +NTD
Sbjct:   127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTD 184

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct:   185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct:   232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 287

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

GO:0030218 "erythrocyte differentiation" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2QVN6 TCEA1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 86/176 (48%), Positives = 109/176 (61%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             V+ +P  ++ + +DSVRLKCREML  +++ GD  +                IY E +NTD
Sbjct:   127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTD 184

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct:   185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct:   232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 287

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

GO:0030218 "erythrocyte differentiation" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P23193 TCEA1 "Transcription elongation factor A protein 1" [Homo sapiens (taxid:9606)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 86/176 (48%), Positives = 109/176 (61%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             V+ +P  ++ + +DSVRLKCREML  +++ GD  +                IY E +NTD
Sbjct:   127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTD 184

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct:   185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct:   232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 287

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0030218 "erythrocyte differentiation" evidence=IEA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

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

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

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:1196624 Tcea1 "transcription elongation factor A (SII) 1" [Mus musculus (taxid:10090)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 86/176 (48%), Positives = 109/176 (61%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             V+ +P  ++ + +DSVRLKCREML  +++ GD  +                IY E +NTD
Sbjct:   127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTD 184

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct:   185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct:   232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 287

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IDA

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

GO:0006355 "regulation of 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:0030218 "erythrocyte differentiation" evidence=IMP

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

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

GO:0046872 "metal ion binding" evidence=IEA

RGD|1309880 Tcea1 "transcription elongation factor A (SII) 1" [Rattus norvegicus (taxid:10116)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 86/176 (48%), Positives = 109/176 (61%)

Query:    38 VTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTD 97
             V+ +P  ++ + +DSVRLKCREML  +++ GD  +                IY E +NTD
Sbjct:   127 VSSFP--RAPSTSDSVRLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTD 184

Query:    98 NRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
              +YKNRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+D
Sbjct:   185 MKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASD 231

Query:   158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             E+K +R    KE+I + Q+A   GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct:   232 ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 287

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005730 "nucleolus" evidence=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:0030218 "erythrocyte differentiation" evidence=ISO

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

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

---

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)
P10711	TCEA1_MOUSE	No assigned EC number	0.5254	0.7330	0.5382	yes	N/A
P52652	TFS2_CAEEL	No assigned EC number	0.3963	0.8461	0.6071	yes	N/A
P20232	TFS2_DROME	No assigned EC number	0.6123	0.7285	0.5143	yes	N/A
Q29RL9	TCEA1_BOVIN	No assigned EC number	0.4711	0.8506	0.6245	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	221
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	1e-47
pfam07500	115	pfam07500, TFIIS_M, Transcription factor S-II (TFI	3e-32
smart00510	102	smart00510, TFS2M, Domain in the central regions o	9e-27
pfam01096	39	pfam01096, TFIIS_C, Transcription factor S-II (TFI	9e-12
smart00440	40	smart00440, ZnF_C2C2, C2C2 Zinc finger	1e-09
COG1594	113	COG1594, RPB9, DNA-directed RNA polymerase, subuni	2e-06
pfam01096	39	pfam01096, TFIIS_C, Transcription factor S-II (TFI	3e-04

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

 Score =  158 bits (400), Expect = 1e-47
 Identities = 77/206 (37%), Positives = 105/206 (50%), Gaps = 15/206 (7%)

Query: 8   PAPPGISNNKDSSSKKKEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQV 67
            +   +     S S K E  +      + +   + P    N  D VR KCRE+L +++  
Sbjct: 95  ESVNSVKQEAKSQSDKIEQPKYVSSSPRNAKNDFVPTAVTN--DKVRDKCRELLYDALAK 152

Query: 68  GDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGA 127
                      E  A ++EE  +N    T+  YK R RS  +NL+D  NP L  N + G 
Sbjct: 153 DSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGE 212

Query: 128 ISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLL 187
           I+  KLATMTAE             EMA+ E+K  R +  KE++ +AQ A +Q   TDL 
Sbjct: 213 ITPEKLATMTAE-------------EMASAELKQEREEITKENLFEAQGAKIQKAVTDLF 259

Query: 188 KCGKCKKRNCTYNQVQTRSADEPMTT 213
            CGKCK++ CTY Q+QTRSADEPMTT
Sbjct: 260 TCGKCKQKKCTYYQLQTRSADEPMTT 285

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

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

 Score =  112 bits (283), Expect = 3e-32
 Identities = 50/127 (39%), Positives = 72/127 (56%), Gaps = 13/127 (10%)

Query: 50  TDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIA 109
            D VR KCRE+L +++  G  D      +E LA E+EE ++  + NT  +YKN+ RS + 
Sbjct: 2   NDKVRDKCRELLYDALAKGSEDSMSEEEVERLAAEIEEELFKLYGNTGKKYKNKYRSLMF 61

Query: 110 NLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKE 169
           NLKDPKNP L R  + G IS  +L  M+ E             E+A+DE+K  R +  KE
Sbjct: 62  NLKDPKNPDLRRKVLNGEISPERLVNMSPE-------------ELASDELKKEREEIEKE 108

Query: 170 SIDDAQL 176
           ++ +AQL
Sbjct: 109 ALREAQL 115

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 = 98.5 bits (246), Expect = 9e-27
 Identities = 47/115 (40%), Positives = 63/115 (54%), Gaps = 13/115 (11%)

Query: 51  DSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIAN 110
           D VR KC+EML  ++Q      +      ELA ++E  +++EF  TD +YKN+ RS   N
Sbjct: 1   DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFN 60

Query: 111 LKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNK 165
           LKD KNP L R  + G I+  KLATMTAE             E+A+ E+K  R K
Sbjct: 61  LKDKKNPDLRRKVLNGEITPEKLATMTAE-------------ELASAELKEKREK 102

Length = 102

>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS)

 Score = 57.6 bits (140), Expect = 9e-12
 Identities = 18/32 (56%), Positives = 21/32 (65%), Gaps = 3/32 (9%)

Query: 188 KCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219
           KC KC  R   + Q+QTRSADEPMT    FY+
Sbjct: 2   KCPKCGHREAVFFQLQTRSADEPMTL---FYV 30

Length = 39

>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger

 Score = 51.6 bits (124), Expect = 1e-09
 Identities = 16/29 (55%), Positives = 20/29 (68%)

Query: 187 LKCGKCKKRNCTYNQVQTRSADEPMTTLH 215
            +C KC  R  T+ Q+QTRSADEPMT  +
Sbjct: 1   AECPKCGNREATFYQLQTRSADEPMTVFY 29

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases. Length = 40

>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 21/52 (40%), Positives = 25/52 (48%), Gaps = 5/52 (9%)

Query: 167 IKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFY 218
           +    D+ Q A      T   KC KC  +   Y Q+QTRSADEP T    FY
Sbjct: 55  VLVVEDETQGAKTL--PTAKEKCPKCGNKEAYYWQLQTRSADEPETR---FY 101

Length = 113

>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS)

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 11/14 (78%), Positives = 13/14 (92%)

Query: 139 EVQTRSADEPMTTF 152
           ++QTRSADEPMT F
Sbjct: 15  QLQTRSADEPMTLF 28

Length = 39

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	221
TIGR01385	299	TFSII transcription elongation factor S-II. This m	100.0
KOG1105|consensus	296		100.0
smart00510	102	TFS2M Domain in the central regions of transcripti	99.92
PF07500	115	TFIIS_M: Transcription factor S-II (TFIIS), centra	99.91
KOG2906|consensus	105		99.56
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	99.53
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	99.48
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	99.28
PHA02998	195	RNA polymerase subunit; Provisional	99.24
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	99.24
KOG1634|consensus	778		99.1
KOG2907|consensus	116		98.59
KOG2691|consensus	113		98.59
KOG2906|consensus	105		97.26
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	96.09
PHA02998	195	RNA polymerase subunit; Provisional	96.01
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	95.31
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	95.02
KOG2907|consensus	116		94.36
KOG1105|consensus	296		93.4
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	92.88
TIGR01385	299	TFSII transcription elongation factor S-II. This m	91.1

>TIGR01385 TFSII transcription elongation factor S-II

Probab=100.00  E-value=1.1e-44  Score=326.21  Aligned_cols=166  Identities=43%  Similarity=0.618  Sum_probs=155.8

Q ss_pred             ccCCCCCCCCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChh
Q psy996           39 TQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPM  118 (221)
Q Consensus        39 ~~~pp~~~~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~  118 (221)
                      +.+.|  .+.++|++|++|+++|++||..+.++.+...++..+|.+||.++|+.++.++..|+.++|+|+|||||++||+
T Consensus       126 ~~~~~--~~~t~d~~Rdk~r~~L~~aL~~~~~~~~~~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~  203 (299)
T TIGR01385       126 NDFVP--TAVTNDKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPD  203 (299)
T ss_pred             CCCCC--CccCCcHHHHHHHHHHHHHHhhcCCCCccccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHH
Confidence            34444  4579999999999999999998777666666788999999999999999888899999999999999999999


Q ss_pred             hhhccccCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHhhhhcCcccccccccccCCCcee
Q psy996          119 LSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCT  198 (221)
Q Consensus       119 L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~~~~~~~~T~~~~C~kC~~~~~~  198 (221)
                      ||.+|++|+|+|++|+.|+++             ||||+|++++++++.+++|+++|++..+++.|++|+|++||+++|+
T Consensus       204 Lr~~vl~G~i~p~~lv~Ms~e-------------Emas~e~k~~~e~~~ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~  270 (299)
T TIGR01385       204 LRHNVLTGEITPEKLATMTAE-------------EMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCT  270 (299)
T ss_pred             HHHHHHcCCCCHHHHhcCCHH-------------HcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccCCCCCCccce
Confidence            999999999999999999999             9999999999999999999999999999999999999999999999


Q ss_pred             EEEEeccCCCCCceEEEEeec
Q psy996          199 YNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       199 y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      |+|+|||+||||||+||+|++
T Consensus       271 ~~q~QtrsaDEpmT~f~~C~~  291 (299)
T TIGR01385       271 YYQLQTRSADEPMTTFVTCEE  291 (299)
T ss_pred             EEEecccCCCCCCeEEEEcCC
Confidence            999999999999999999985

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

Probab=100.00  E-value=3.8e-42  Score=307.58  Aligned_cols=193  Identities=49%  Similarity=0.721  Sum_probs=167.9

Q ss_pred             CCCCCCCCCCCchh---hhccccccCCCCCCCccCCCCCCCCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHH
Q psy996           10 PPGISNNKDSSSKK---KEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELE   86 (221)
Q Consensus        10 ~~~~~~~~~~s~~~---~~~~~~~~~~~~~~~~~~pp~~~~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE   86 (221)
                      .||+-..+..|.-+   +..-+.++++.+++  . +|  .+..+|.+|++|+++|+.||...++....+.++..+|.+||
T Consensus        94 ~p~~~~~~~~s~~~~~~ks~~~~~~~~~~~~--~-~~--~~~~~d~~r~k~~e~l~~al~~~~~~~~~~~~~~~~a~~iE  168 (296)
T KOG1105|consen   94 DPGEASSKSPSGAKQPEKSRGDSKRDKHSGS--K-DP--VPITNDPVRDKCRELLYAALTTEDDSRVTGADPLELAVQIE  168 (296)
T ss_pred             CCCcCCcCCccCCCCccccccccccccccCc--C-CC--CCCCCchHHHHHHHHHHHHhcccccccccCCCHHHHHHHHH
Confidence            34555555544433   22334444433342  2 33  55679999999999999999977766666788999999999


Q ss_pred             HHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhccccCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHH
Q psy996           87 EAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKF  166 (221)
Q Consensus        87 ~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~  166 (221)
                      ++||..++.++.+|+.++|++++||+|++||+||++||+|+|+|++|+.|+++             ||+|++++++++++
T Consensus       169 ~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~e-------------EMaS~~lk~~~~k~  235 (296)
T KOG1105|consen  169 EAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSE-------------EMASEELKEERQKL  235 (296)
T ss_pred             HHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChh-------------hhccHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999             99999999999999


Q ss_pred             HHHhHHHHHhhhhcCcccccccccccCCCceeEEEEeccCCCCCceEEEEeecc
Q psy996          167 IKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYIT  220 (221)
Q Consensus       167 ~~e~l~~~q~~~~~~~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~~  220 (221)
                      .+++|++||++..++++|+.|.|++|++++|+|+|+||||+||||||||+|...
T Consensus       236 ~keal~~~q~~~~~gt~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ec  289 (296)
T KOG1105|consen  236 TKEALREHQMAKIQGTQTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNEC  289 (296)
T ss_pred             HHHHHHHHhhcccccccccceeeccccccceeEEeeccCCCCCCcceeeeeccc
Confidence            999999999999999999999999999999999999999999999999999753

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

Probab=99.92  E-value=1e-24  Score=168.93  Aligned_cols=101  Identities=46%  Similarity=0.603  Sum_probs=94.4

Q ss_pred             cHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhccccCcCCh
Q psy996           51 DSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISA  130 (221)
Q Consensus        51 d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp  130 (221)
                      |++|++|+++|+++|..+.+..+...++..+|.+||.++|+.++..+..|++++|+|+|||||++||+|+.+|++|+|+|
T Consensus         1 d~~R~~~~~~L~~al~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~vl~G~i~p   80 (102)
T smart00510        1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP   80 (102)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCcccccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCH
Confidence            57999999999999998876655555788999999999999998878899999999999999999999999999999999


Q ss_pred             hhhhcCChhhhhccCCCCchhHhhccHHHHHHHH
Q psy996          131 SKLATMTAEVQTRSADEPMTTFEMANDEMKTLRN  164 (221)
Q Consensus       131 ~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~  164 (221)
                      ++|+.|+++             ||||+|+|++++
T Consensus        81 ~~lv~Ms~~-------------ElAs~elk~~~e  101 (102)
T smart00510       81 EKLATMTAE-------------ELASAELKEKRE  101 (102)
T ss_pred             HHHhcCCHH-------------HcCCHHHHHHHh
Confidence            999999999             999999999986

>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=99.91  E-value=3.9e-25  Score=173.47  Aligned_cols=115  Identities=42%  Similarity=0.635  Sum_probs=106.2

Q ss_pred             CCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhccccCcC
Q psy996           49 LTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAI  128 (221)
Q Consensus        49 ~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~i  128 (221)
                      +++++|++++++|+++|....+..+....+..+|.+||.+||..++.++..|++++|+|+|||||++|+.|+.+|++|.|
T Consensus         1 ~~~~~R~k~~~~L~~~l~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~~il~g~i   80 (115)
T PF07500_consen    1 TNDKVRDKARKLLYKALQKRSDEQDDPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRRRILSGEI   80 (115)
T ss_dssp             -TCHHHHHHHHHHHHHHHHCCCCCCCTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHHHHHHSSS
T ss_pred             CCcHHHHHHHHHHHHHHHhcCccccchhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHHHHHcCCC
Confidence            57899999999999999998665334568899999999999999988889999999999999999999999999999999


Q ss_pred             ChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHh
Q psy996          129 SASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQL  176 (221)
Q Consensus       129 sp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~  176 (221)
                      +|.+||.|+++             ||+|+++|++++++.+++++++|+
T Consensus        81 ~p~~lv~ms~~-------------Elas~e~k~~~e~~~~~~l~~~~~  115 (115)
T PF07500_consen   81 SPEELVTMSPE-------------ELASEELKEEREKIRKESLKQSQM  115 (115)
T ss_dssp             TTCHHHHCTTT-------------TTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred             CHHHHhcCCHH-------------HhCCHHHHHHHHHHHHHHHHHhhC
Confidence            99999999999             999999999999999999988764

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.

>KOG2906|consensus

Probab=99.56  E-value=4e-16  Score=119.21  Aligned_cols=73  Identities=29%  Similarity=0.394  Sum_probs=60.2

Q ss_pred             ChhhhhHHHHHHHhcCCCCChhhhhccccCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHh
Q psy996           97 DNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQL  176 (221)
Q Consensus        97 ~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~  176 (221)
                      .++|...|...|.+.+.++-+++ ++|+.|.-++++.                                           
T Consensus        26 tCpY~~~I~~ei~~r~~~~~Kev-d~vlgg~~a~~nv-------------------------------------------   61 (105)
T KOG2906|consen   26 TCPYVFPISREISSRKYPKLKEV-DDVLGGDEAWENV-------------------------------------------   61 (105)
T ss_pred             CCCceeeEeeeeeccccCchhhh-hhhcCCcccccch-------------------------------------------
Confidence            47888888877777777776776 4888887766554                                           


Q ss_pred             hhhcCcccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          177 ATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       177 ~~~~~~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                           ++|+. +|++||+.+++|.|+||||||||||+||.|.+
T Consensus        62 -----~~t~~-~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~   98 (105)
T KOG2906|consen   62 -----DQTEA-TCPTCGHERAYFMQLQTRSADEPMTTFYKCCK   98 (105)
T ss_pred             -----hhccC-cCCCCCCCceEEEEeeeccCCCcHhHhhhhhc
Confidence                 45555 99999999999999999999999999999975

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=99.53  E-value=6.9e-15  Score=95.93  Aligned_cols=33  Identities=48%  Similarity=0.685  Sum_probs=31.5

Q ss_pred             ccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          187 LKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       187 ~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      +.|++||+++++|+|+|+||||||||+||.|++
T Consensus         1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~   33 (40)
T smart00440        1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTK   33 (40)
T ss_pred             CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCC
Confidence            579999999999999999999999999999975

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.48  E-value=2.7e-14  Score=92.61  Aligned_cols=33  Identities=45%  Similarity=0.699  Sum_probs=28.7

Q ss_pred             ccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          187 LKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       187 ~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      ++|++||++++.|+|+|+||||||||+||.|.+
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~   33 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCN   33 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESS
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCC
Confidence            589999999999999999999999999999974

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. 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. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=99.28  E-value=2.4e-12  Score=101.52  Aligned_cols=37  Identities=43%  Similarity=0.551  Sum_probs=33.5

Q ss_pred             ccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          183 KTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       183 ~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      .+..+.||+||+++++|+|+||||||||||+||+|..
T Consensus        69 ~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~  105 (113)
T COG1594          69 PTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTR  105 (113)
T ss_pred             ccccccCCCCCCceeEEEeeehhccCCCceEEEEecc
Confidence            3346899999999999999999999999999999963

>PHA02998 RNA polymerase subunit; Provisional

Probab=99.24  E-value=5.4e-12  Score=106.04  Aligned_cols=35  Identities=37%  Similarity=0.432  Sum_probs=32.9

Q ss_pred             ccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          185 DLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       185 ~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      ...+|++||+++++|+|+||||||||||+||.|..
T Consensus       142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~  176 (195)
T PHA02998        142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRD  176 (195)
T ss_pred             cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCC
Confidence            45799999999999999999999999999999975

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=99.24  E-value=6.7e-12  Score=96.60  Aligned_cols=36  Identities=36%  Similarity=0.537  Sum_probs=33.2

Q ss_pred             cccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       184 T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      +....|++||+++++|+|+|+||||||||+||+|++
T Consensus        60 ~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~   95 (104)
T TIGR01384        60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTK   95 (104)
T ss_pred             cccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCC
Confidence            345799999999999999999999999999999974

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>KOG1634|consensus

Probab=99.10  E-value=8.4e-11  Score=116.63  Aligned_cols=84  Identities=32%  Similarity=0.497  Sum_probs=77.4

Q ss_pred             hcHHHHHHHHHHHHHHHhc-CCChhhhhHHHHHHHhcCCCCChhhhhccccCcCChhhhhcCChhhhhccCCCCchhHhh
Q psy996           76 ASLEELATELEEAIYNEFK-NTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEM  154 (221)
Q Consensus        76 ~~~~~lA~~IE~~i~~~~~-~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fEl  154 (221)
                      .+...++..||.++|..|+ ..+..|+.++|+|+|||||.+|+.|+.+|..|+|++++|+.|+.+             ||
T Consensus       267 ~d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msae-------------el  333 (778)
T KOG1634|consen  267 QDPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAE-------------EL  333 (778)
T ss_pred             cchhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCch-------------hh
Confidence            3556777899999999999 788999999999999999999999999999999999999999999             99


Q ss_pred             ccHHHHHHHHHHHHHhHH
Q psy996          155 ANDEMKTLRNKFIKESID  172 (221)
Q Consensus       155 as~e~k~~r~k~~~e~l~  172 (221)
                      |+.++.+||++..++...
T Consensus       334 As~eL~~~rEek~ee~~~  351 (778)
T KOG1634|consen  334 ASPELAEWREEKAEEMNE  351 (778)
T ss_pred             cCchHHHHHHHHHHHHHh
Confidence            999999999988777653

>KOG2907|consensus

Probab=98.59  E-value=1.3e-08  Score=79.86  Aligned_cols=36  Identities=33%  Similarity=0.414  Sum_probs=33.0

Q ss_pred             cccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       184 T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      +-...||+||+.+..|..+|+|||||.-|+||+|.+
T Consensus        72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~k  107 (116)
T KOG2907|consen   72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPK  107 (116)
T ss_pred             chhccCcccCCchhhhhhhhcccccCCceEEEEcCc
Confidence            335699999999999999999999999999999964

>KOG2691|consensus

Probab=98.59  E-value=3.4e-08  Score=77.02  Aligned_cols=38  Identities=34%  Similarity=0.470  Sum_probs=35.0

Q ss_pred             cccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          182 TKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       182 ~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      ..|....||+||++++.|+|.|+|.+|+.|+.||.|++
T Consensus        69 Prts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~  106 (113)
T KOG2691|consen   69 PRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCS  106 (113)
T ss_pred             CccccccCCccCCcceEEEecccccccceEEEEEEecc
Confidence            35577899999999999999999999999999999985

>KOG2906|consensus

Probab=97.26  E-value=6e-05  Score=58.15  Aligned_cols=21  Identities=57%  Similarity=0.662  Sum_probs=17.8

Q ss_pred             CChhhhhccCCCCchhHhhcc
Q psy996          136 MTAEVQTRSADEPMTTFEMAN  156 (221)
Q Consensus       136 m~~q~Q~rsadep~t~fElas  156 (221)
                      ++.|||+||||||||+|+-+-
T Consensus        77 yF~qlQtRSADEPmT~FYkC~   97 (105)
T KOG2906|consen   77 YFMQLQTRSADEPMTTFYKCC   97 (105)
T ss_pred             EEEEeeeccCCCcHhHhhhhh
Confidence            667899999999999987543

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=96.09  E-value=0.0011  Score=43.11  Aligned_cols=17  Identities=65%  Similarity=0.868  Sum_probs=14.2

Q ss_pred             hhhhhccCCCCchhHhh
Q psy996          138 AEVQTRSADEPMTTFEM  154 (221)
Q Consensus       138 ~q~Q~rsadep~t~fEl  154 (221)
                      .++|+||||||||.|..
T Consensus        14 ~q~Q~RsaDE~mT~fy~   30 (40)
T smart00440       14 FQLQTRSADEPMTVFYV   30 (40)
T ss_pred             EEEcccCCCCCCeEEEE
Confidence            46899999999999643

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PHA02998 RNA polymerase subunit; Provisional

Probab=96.01  E-value=0.0021  Score=54.61  Aligned_cols=17  Identities=41%  Similarity=0.438  Sum_probs=14.4

Q ss_pred             CChhhhhccCCCCchhH
Q psy996          136 MTAEVQTRSADEPMTTF  152 (221)
Q Consensus       136 m~~q~Q~rsadep~t~f  152 (221)
                      ...++|+||||||||+|
T Consensus       155 ~f~qlQTRSADEPmT~F  171 (195)
T PHA02998        155 TPMMIQTRAADEPPLVR  171 (195)
T ss_pred             EEEEEeeccCCCCceEE
Confidence            44569999999999995

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=95.31  E-value=0.0054  Score=48.46  Aligned_cols=17  Identities=59%  Similarity=0.696  Sum_probs=15.0

Q ss_pred             CChhhhhccCCCCchhH
Q psy996          136 MTAEVQTRSADEPMTTF  152 (221)
Q Consensus       136 m~~q~Q~rsadep~t~f  152 (221)
                      +..++|+||||||||+|
T Consensus        84 ~y~~~QtRsaDEp~T~F  100 (113)
T COG1594          84 YYWQLQTRSADEPETRF  100 (113)
T ss_pred             EEEeeehhccCCCceEE
Confidence            56679999999999995

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=95.02  E-value=0.0047  Score=39.84  Aligned_cols=17  Identities=65%  Similarity=0.868  Sum_probs=14.2

Q ss_pred             hhhhhccCCCCchhHhh
Q psy996          138 AEVQTRSADEPMTTFEM  154 (221)
Q Consensus       138 ~q~Q~rsadep~t~fEl  154 (221)
                      .++|+||||||||.|..
T Consensus        14 ~~~Q~rsaDE~~T~fy~   30 (39)
T PF01096_consen   14 FQIQTRSADEPMTLFYV   30 (39)
T ss_dssp             EEESSSSSSSSSEEEEE
T ss_pred             EEeeccCCCCCCeEEEE
Confidence            36899999999999643

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. 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. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>KOG2907|consensus

Probab=94.36  E-value=0.015  Score=46.00  Aligned_cols=16  Identities=50%  Similarity=0.520  Sum_probs=13.2

Q ss_pred             ChhhhhccCCCCchhH
Q psy996          137 TAEVQTRSADEPMTTF  152 (221)
Q Consensus       137 ~~q~Q~rsadep~t~f  152 (221)
                      ..-+|+|||||.+|.|
T Consensus        87 Y~T~QlRSADEGQTVF  102 (116)
T KOG2907|consen   87 YHTLQLRSADEGQTVF  102 (116)
T ss_pred             hhhhhcccccCCceEE
Confidence            3449999999999984

>KOG1105|consensus

Probab=93.40  E-value=0.018  Score=52.52  Aligned_cols=34  Identities=41%  Similarity=0.522  Sum_probs=27.4

Q ss_pred             hccccCcCChhhhhcCChhhhhccCCCCchhHhhcc
Q psy996          121 RNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAN  156 (221)
Q Consensus       121 ~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas  156 (221)
                      ..+.+|.+.-.++  -..|+|+||+|||||+|..|.
T Consensus       254 d~fkcgkckk~~c--ty~q~Qtrs~DePmtTfv~C~  287 (296)
T KOG1105|consen  254 DLFKCGKCKKKNC--TYTQLQTRSADEPMTTFVTCN  287 (296)
T ss_pred             cceeeccccccce--eEEeeccCCCCCCcceeeeec
Confidence            3678888888777  447899999999999986554

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=92.88  E-value=0.025  Score=43.27  Aligned_cols=16  Identities=56%  Similarity=0.601  Sum_probs=13.7

Q ss_pred             ChhhhhccCCCCchhH
Q psy996          137 TAEVQTRSADEPMTTF  152 (221)
Q Consensus       137 ~~q~Q~rsadep~t~f  152 (221)
                      +.++|+||||||||.|
T Consensus        75 f~~~Q~RsadE~~T~f   90 (104)
T TIGR01384        75 YWLLQTRRADEPETRF   90 (104)
T ss_pred             EEEeccCCCCCCcEEE
Confidence            4458999999999995

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>TIGR01385 TFSII transcription elongation factor S-II

Probab=91.10  E-value=0.048  Score=49.87  Aligned_cols=29  Identities=48%  Similarity=0.610  Sum_probs=21.4

Q ss_pred             ccccCcCChhhhhcCChhhhhccCCCCchhH
Q psy996          122 NYIFGAISASKLATMTAEVQTRSADEPMTTF  152 (221)
Q Consensus       122 ~Il~G~isp~~l~~m~~q~Q~rsadep~t~f  152 (221)
                      .+.|+.+.-.++  .+.|+|+||||||||+|
T Consensus       258 ~~~C~~C~~~~~--~~~q~QtrsaDEpmT~f  286 (299)
T TIGR01385       258 LFTCGKCKQKKC--TYYQLQTRSADEPMTTF  286 (299)
T ss_pred             cccCCCCCCccc--eEEEecccCCCCCCeEE
Confidence            455666655454  44679999999999995

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	221
3ndq_A	108	Structure Of Human Tfiis Domain Ii Length = 108		9e-17
2lw4_A	113	Solution Nmr Structure Of Human Transcription Elong		2e-16
1tfi_A	50	A Novel Zn Finger Motif In The Basal Transcriptiona		6e-11
1y1v_S	179	Refined Rna Polymerase Ii-tfiis Complex Length = 17		2e-10
1pqv_S	309	Rna Polymerase Ii-Tfiis Complex Length = 309		2e-10
3gtm_S	173	Co-Complex Of Backtracked Rna Polymerase Ii With Tf		7e-10
3po3_S	178	Arrested Rna Polymerase Ii Reactivation Intermediat		8e-09
2dme_A	120	Solution Structure Of The Tfiis Domain Ii Of Human		6e-05

>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii Length = 108

Iteration: 1
 Score = 83.6 bits (205), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 49/114 (42%), Positives = 63/114 (55%), Gaps = 13/114 (11%)
Query: 45  KSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTDNRYKNRV 104
           ++ + +DSVRLKCREML  +++ GD  +                IY E +NTD +YKNRV
Sbjct: 8   RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRV 67
Query: 105 RSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDE 158
           RSRI+NLKD KNP L +N + G I     A MTAE             EMA+DE
Sbjct: 68  RSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASDE 108

>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 = 82.4 bits (202), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 47/113 (41%), Positives = 63/113 (55%), Gaps = 13/113 (11%)
Query: 51  DSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTDNRYKNRVRSRIAN 110
           D+VR KCREML  ++Q     +                I+ +  NTD +YKNRVRSRI+N
Sbjct: 10  DAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISN 69
Query: 111 LKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLR 163
           LKD KNP L RN + GAI+  ++A MT+E             EMA+DE+K +R
Sbjct: 70  LKDAKNPDLRRNVLCGAITPQQIAVMTSE-------------EMASDELKEIR 109

>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional Machinery: Three-Dimensional Nmr Studies Of The Nucleic- Acid Binding Domain Of Transcriptional Elongation Factor Tfiis Length = 50

Iteration: 1
 Score = 63.9 bits (154), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 28/34 (82%), Positives = 30/34 (88%)
Query: 181 GTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT 
Sbjct: 4   GTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTF 37

>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex Length = 179

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 60/115 (52%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
           YK R R   +N+    NP L      G I+   LAT  A+             ++A   +
Sbjct: 65  YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 111
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           K    +  K+++ +AQ AT++ + TD   CGKCK++  +Y Q+QTRSADEP+TT 
Sbjct: 112 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTF 166

>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex Length = 309

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 60/115 (52%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
           YK R R   +N+    NP L      G I+   LAT  A+             ++A   +
Sbjct: 195 YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 241
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           K    +  K+++ +AQ AT++ + TD   CGKCK++  +Y Q+QTRSADEP+TT 
Sbjct: 242 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTF 296

>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis Length = 173

Iteration: 1
 Score = 60.5 bits (145), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 59/115 (51%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
           YK R R   +N+    NP L      G I+   LAT  A+             ++A   +
Sbjct: 59  YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 105
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           K    +  K+++ +AQ AT++ + TD   CGKCK++  +Y Q+QTRSAD P+TT 
Sbjct: 106 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADHPLTTF 160

>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate Length = 178

Iteration: 1
 Score = 57.0 bits (136), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 38/115 (33%), Positives = 58/115 (50%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
           YK R R   +N+    NP L      G I+   LAT  A+             ++A   +
Sbjct: 64  YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 110
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
           K    +  K+++ +AQ AT++ + TD   CGKCK++  +Y Q+QTRSA  P+TT 
Sbjct: 111 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTF 165

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 13/77 (16%)
Query: 89  IYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEP 148
           +++ F++TD +YKN+ RS + NLKDPKN +L +  + G ++   L  M+ E         
Sbjct: 51  LFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPE--------- 101
Query: 149 MTTFEMANDEMKTLRNK 165
               E+A+ E+   R +
Sbjct: 102 ----ELASKELAAWRRR 114

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	221
3po3_S	178	Transcription elongation factor S-II; RNA polymera	3e-35
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	5e-29
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	1e-26
3ndq_A	108	Transcription elongation factor A protein 1; helix	2e-25
1tfi_A	50	Transcriptional elongation factor SII; transcripti	6e-16
1tfi_A	50	Transcriptional elongation factor SII; transcripti	3e-04
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	7e-11
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	4e-09
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	1e-07
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	7e-05

>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 =  122 bits (306), Expect = 3e-35
 Identities = 44/164 (26%), Positives = 69/164 (42%), Gaps = 13/164 (7%)

Query: 50  TDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIA 109
              +R +  + L + +                A E E    N     +  YK R R   +
Sbjct: 14  HHKLRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYS 73

Query: 110 NLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKE 169
           N+    NP L      G I+   LAT  A              ++A   +K    +  K+
Sbjct: 74  NVISKNNPDLKHKIANGDITPEFLATCDA-------------KDLAPAPLKQKIEEIAKQ 120

Query: 170 SIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
           ++ +AQ AT++ + TD   CGKCK++  +Y Q+QTRSA  P+TT
Sbjct: 121 NLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTT 164

>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 =  109 bits (272), Expect = 5e-29
 Identities = 52/206 (25%), Positives = 85/206 (41%), Gaps = 13/206 (6%)

Query: 8   PAPPGISNNKDSSSKKKEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQV 67
                    + +SS+    K++K    KP  ++     +      +R +  + L + +  
Sbjct: 103 VGESVNGVQQPASSQSDAMKQDKYVSTKPRNSKNDGVDTAIYHHKLRDQVLKALYDVLAK 162

Query: 68  GDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGA 127
                         A E E    N     +  YK R R   +N+    NP L      G 
Sbjct: 163 ESEHPPQSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGD 222

Query: 128 ISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLL 187
           I+   LAT  A              ++A   +K    +  K+++ +AQ AT++ + TD  
Sbjct: 223 ITPEFLATCDA-------------KDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRF 269

Query: 188 KCGKCKKRNCTYNQVQTRSADEPMTT 213
            CGKCK++  +Y Q+QTRSADEP+TT
Sbjct: 270 TCGKCKEKKVSYYQLQTRSADEPLTT 295

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

 Score = 98.1 bits (244), Expect = 1e-26
 Identities = 34/129 (26%), Positives = 62/129 (48%), Gaps = 16/129 (12%)

Query: 45  KSHNLTDSVRLKCREMLQNSIQVGDLDMDGL---ASLEELATELEEAIYNEFKNTDNRYK 101
            S    D +R   R  L++ +     D +         ++AT++E+ +++ F++TD +YK
Sbjct: 4   GSSGSADQIRQSVRHSLKDILMKRLTDSNLKVPEEKAAKVATKIEKELFSFFRDTDAKYK 63

Query: 102 NRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKT 161
           N+ RS + NLKDPKN +L +  + G ++   L  M+ E             E+A+ E+  
Sbjct: 64  NKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPE-------------ELASKELAA 110

Query: 162 LRNKFIKES 170
            R +    S
Sbjct: 111 WRRRSGPSS 119

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

 Score = 94.7 bits (235), Expect = 2e-25
 Identities = 56/117 (47%), Positives = 73/117 (62%), Gaps = 13/117 (11%)

Query: 42  PPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYK 101
              ++ + +DSVRLKCREML  +++ GD  +   A  EEL +++EEAIY E +NTD +YK
Sbjct: 5   FTPRAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYK 64

Query: 102 NRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDE 158
           NRVRSRI+NLKD KNP L +N + G I     A MTAE             EMA+DE
Sbjct: 65  NRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASDE 108

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 50

 Score = 68.2 bits (167), Expect = 6e-16
 Identities = 28/35 (80%), Positives = 30/35 (85%)

Query: 179 VQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTT 213
             GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT
Sbjct: 2   TGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT 36

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 50

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 13/14 (92%), Positives = 14/14 (100%)

Query: 139 EVQTRSADEPMTTF 152
           +VQTRSADEPMTTF
Sbjct: 24  QVQTRSADEPMTTF 37

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Length = 57

 Score = 55.2 bits (133), Expect = 7e-11
 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 3/35 (8%)

Query: 184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFY 218
           T  + C KC      + ++QTR+ DEP T    FY
Sbjct: 13  TTKITCPKCGNDTAYWWEMQTRAGDEPSTI---FY 44

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 113

 Score = 52.1 bits (124), Expect = 4e-09
 Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 7/72 (9%)

Query: 152 FEMANDEMKTLRNKFIKESIDDAQL----ATVQGTKTDLLKCGKCKKRNCTYNQVQTRSA 207
           +       K  R++    ++++  +    +T         +C +C +    + Q  +R  
Sbjct: 34  YSEIAATSKVYRHELQSSNVENTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRG 93

Query: 208 DEPMTTLHHFYI 219
           D  MT     Y+
Sbjct: 94  DTMMTL---IYV 102

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae} Length = 133

 Score = 48.3 bits (114), Expect = 1e-07
 Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 3/62 (4%)

Query: 158 EMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHF 217
               L     + +     + +         +C KC  R   + Q+Q RSADEPMTT   F
Sbjct: 64  YRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTT---F 120

Query: 218 YI 219
           Y 
Sbjct: 121 YK 122

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ... Length = 122

 Score = 40.2 bits (93), Expect = 7e-05
 Identities = 11/67 (16%), Positives = 19/67 (28%), Gaps = 3/67 (4%)

Query: 153 EMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMT 212
                    L     + +     + +         +C KC  R   + Q Q R  D  M 
Sbjct: 39  GSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMV 98

Query: 213 TLHHFYI 219
               F++
Sbjct: 99  L---FFV 102

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	221
3po3_S	178	Transcription elongation factor S-II; RNA polymera	100.0
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	100.0
2lw4_A	113	Transcription elongation factor A protein 2; struc	99.95
3ndq_A	108	Transcription elongation factor A protein 1; helix	99.95
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	99.89
1tfi_A	50	Transcriptional elongation factor SII; transcripti	99.6
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	99.37
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	99.24
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	99.23
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	99.12
1tfi_A	50	Transcriptional elongation factor SII; transcripti	96.0
3po3_S	178	Transcription elongation factor S-II; RNA polymera	94.45
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	94.4
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	94.18
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	93.49
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	93.35
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	92.34

>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=100.00  E-value=4.3e-44  Score=300.32  Aligned_cols=158  Identities=28%  Similarity=0.362  Sum_probs=145.3

Q ss_pred             CCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcC-CCh-hhhhHHHHHHHhcCCCCChhhhhccc
Q psy996           47 HNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKN-TDN-RYKNRVRSRIANLKDPKNPMLSRNYI  124 (221)
Q Consensus        47 ~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~-~~~-~Yk~k~Rsl~~nLk~~kN~~L~~~Il  124 (221)
                      +.++|++|++|+++|++||..++++.+  .++..+|.+||++||+.++. ++. .|++++|+|++||||++||.|+.+|+
T Consensus        11 ~~~~d~vRdk~~~lL~~aL~~~~~~~~--~~~~~~A~~IE~~if~~~~~~~~~k~Yk~k~Rsl~~NLKd~~N~~Lr~~vl   88 (178)
T 3po3_S           11 AIYHHKLRDQVLKALYDVLAKESEHPP--QSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIA   88 (178)
T ss_dssp             ----CHHHHHHHHHHHHHTTSSSSCST--THHHHHHHHHHHHHHHHTSCSSSSTHHHHHHHHHHHHHHSSSCSHHHHHHH
T ss_pred             CcCCChHHHHHHHHHHHHHhcCCCCch--hhHHHHHHHHHHHHHHHhcCCCchhhhhhhhhHHHHHcCCCCCHHHHHHHh
Confidence            348999999999999999999776544  36789999999999999986 455 89999999999999999999999999


Q ss_pred             cCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHhhhhcCcccccccccccCCCceeEEEEec
Q psy996          125 FGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQT  204 (221)
Q Consensus       125 ~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~~~~~~~~T~~~~C~kC~~~~~~y~q~Qt  204 (221)
                      +|+|+|+.|+.|+++             ||||+|++++++++.+++|.+++.+..++++|+.+.||+||+++++|+|+|+
T Consensus        89 ~g~isp~~lv~Ms~e-------------Elas~elk~~~e~~~~e~l~~~~~~~~~~~~t~~~~Cp~C~~~~a~~~q~Q~  155 (178)
T 3po3_S           89 NGDITPEFLATCDAK-------------DLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQT  155 (178)
T ss_dssp             HCCCTTHHHHCCTTT-------------TSSCSHHHHHHHHHHHHHHHHTBCCCCCCCCBSSSCCSSSCCSCEECCCCCC
T ss_pred             cCCCCHHHHHhcCch-------------hhCCHHHHHHHHHHHHHHHHHhhhccccCCCcCCcCCCCCCCCceEEEEeec
Confidence            999999999999999             9999999999999999999999999888888999999999999999999999


Q ss_pred             cCCCCCceEEEEeec
Q psy996          205 RSADEPMTTLHHFYI  219 (221)
Q Consensus       205 RsaDEpmT~f~~C~~  219 (221)
                      ||||||||+||+|++
T Consensus       156 rsaDE~mt~f~~C~~  170 (178)
T 3po3_S          156 RSAAAPLTTFCTCEA  170 (178)
T ss_dssp             SCTTSCCCCCEEETT
T ss_pred             ccCCCCCcEEEEcCC
Confidence            999999999999975

>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=100.00  E-value=5.8e-41  Score=302.07  Aligned_cols=158  Identities=29%  Similarity=0.377  Sum_probs=148.1

Q ss_pred             CCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChh--hhhHHHHHHHhcCCCCChhhhhccc
Q psy996           47 HNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNR--YKNRVRSRIANLKDPKNPMLSRNYI  124 (221)
Q Consensus        47 ~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~--Yk~k~Rsl~~nLk~~kN~~L~~~Il  124 (221)
                      +.++|.+|++|+++|+++|..+.++.+.  ++..+|.+||.+||+.++.++..  |++++|+|+|||||++||.|+.+|+
T Consensus       142 ~~~~d~~R~k~r~~L~~aL~~~~~~~~~--~~~~~A~~IE~al~~~~~~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr~~vl  219 (309)
T 1pqv_S          142 AIYHHKLRDQVLKALYDVLAKESEHPPQ--SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIA  219 (309)
T ss_pred             CcCChHHHHHHHHHHHHHHhcCCCccch--hHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHcCcCCChHHHHHHH
Confidence            4578999999999999999987665443  67899999999999999877767  9999999999999999999999999


Q ss_pred             cCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHhhhhcCcccccccccccCCCceeEEEEec
Q psy996          125 FGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQT  204 (221)
Q Consensus       125 ~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~~~~~~~~T~~~~C~kC~~~~~~y~q~Qt  204 (221)
                      .|+|+|++|+.|+++             |||++|++++++++.+++|++++++...++.|+.+.|++||+++|+|+|+|+
T Consensus       220 ~g~i~p~~lv~Ms~e-------------Elasde~k~~~~~~~~e~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~q~Q~  286 (309)
T 1pqv_S          220 NGDITPEFLATCDAK-------------DLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQT  286 (309)
T ss_pred             cCCCCHHHHhcCCHH-------------HhCCHHHHHHHHHHHHHHHHHhhhccccccCcccccCCCCCCCeeEEEEeec
Confidence            999999999999999             9999999999999999999999998877788899999999999999999999


Q ss_pred             cCCCCCceEEEEeec
Q psy996          205 RSADEPMTTLHHFYI  219 (221)
Q Consensus       205 RsaDEpmT~f~~C~~  219 (221)
                      ||||||||+||+|++
T Consensus       287 rsaDe~~t~f~~C~~  301 (309)
T 1pqv_S          287 RSADEPLTTFCTCEA  301 (309)
T ss_pred             ccCCCCCcEEEEeCC
Confidence            999999999999975

>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=1.1e-29  Score=198.86  Aligned_cols=111  Identities=48%  Similarity=0.688  Sum_probs=102.2

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhh
Q psy996           41 YPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLS  120 (221)
Q Consensus        41 ~pp~~~~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~  120 (221)
                      +||  .|.++|++|++|+++|++||..+.+..+...++..+|.+||.++|..|+.++..|+.++|+|+|||||++||+|+
T Consensus         2 ~~p--~p~t~D~vRdk~~e~L~~aL~~~~~~~~~~~~~~~~A~~IE~~~f~~~~~~~~~Yk~k~Rsl~~NLkd~~Np~Lr   79 (113)
T 2lw4_A            2 HMP--VPVTCDAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLR   79 (113)
T ss_dssp             CCC--SCCCCSTTHHHHHHHHHHHHHSSTHHHHHTCCHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHCSSSSHHH
T ss_pred             CCC--CCCCCcHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHH
Confidence            456  788999999999999999999876554445678899999999999999998899999999999999999999999


Q ss_pred             hccccCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHH
Q psy996          121 RNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKF  166 (221)
Q Consensus       121 ~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~  166 (221)
                      .+|++|.|+|.+||.|+++             ||||+|+|++|+++
T Consensus        80 ~~vl~G~i~p~~l~~Ms~e-------------EmAs~elk~~r~~~  112 (113)
T 2lw4_A           80 RNVLCGAITPQQIAVMTSE-------------EMASDELKEIRKAM  112 (113)
T ss_dssp             HHHHTTSSCHHHHHHSCHH-------------HHHCTTTTTCSSSC
T ss_pred             HHHHcCCCCHHHHhcCCHH-------------HcCCHHHHHHHHHc
Confidence            9999999999999999999             99999999988754

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

Probab=99.95  E-value=2e-28  Score=190.35  Aligned_cols=107  Identities=53%  Similarity=0.734  Sum_probs=91.2

Q ss_pred             CCccCCCCCCCCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCC
Q psy996           37 SVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKN  116 (221)
Q Consensus        37 ~~~~~pp~~~~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN  116 (221)
                      .-|.|||  .|.++|++|++|+++|++||..++++.+.+.++..+|.+||++||+.|+.++..|++++|+|+|||||++|
T Consensus         2 ~~~~~~~--~~~t~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~if~~~~~~~~~Yk~k~Rsl~fNLKd~kN   79 (108)
T 3ndq_A            2 IDPFTPR--APSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKN   79 (108)
T ss_dssp             ------C--CCCCCCHHHHHHHHHHHHHTTGGGHHHHHTCCHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHTCTTC
T ss_pred             CCCCCCC--CCCCCChHHHHHHHHHHHHHHcCCCCCcccccHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC
Confidence            4578999  89999999999999999999987655444567899999999999999998889999999999999999999


Q ss_pred             hhhhhccccCcCChhhhhcCChhhhhccCCCCchhHhhccHH
Q psy996          117 PMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDE  158 (221)
Q Consensus       117 ~~L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e  158 (221)
                      |+|+++|++|.|+|++||.|+++             ||||+|
T Consensus        80 p~Lr~~vl~G~isp~~lv~Ms~e-------------EmAS~E  108 (108)
T 3ndq_A           80 PNLRKNVLCGNIPPDLFARMTAE-------------EMASDE  108 (108)
T ss_dssp             HHHHHHHHHTSSCHHHHHHCCTT-------------TC----
T ss_pred             HHHHHHHHcCCcCHHHHhCCCHH-------------HccCCC
Confidence            99999999999999999999999             999986

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

Probab=99.89  E-value=2.2e-24  Score=170.37  Aligned_cols=105  Identities=30%  Similarity=0.489  Sum_probs=93.4

Q ss_pred             CCcHHHHHHHHHHHHHhhcCCCC---CCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhcccc
Q psy996           49 LTDSVRLKCREMLQNSIQVGDLD---MDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIF  125 (221)
Q Consensus        49 ~~d~vR~k~~~lL~~aL~~~~d~---~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~  125 (221)
                      ++|.+|++|+++|+++|......   .....++..+|.+||.+||+.|+.++..|+.++|+|+|||||++||.|+.+|++
T Consensus         8 ~~d~~Rd~~r~~L~eaL~~~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~Lr~~vl~   87 (120)
T 2dme_A            8 SADQIRQSVRHSLKDILMKRLTDSNLKVPEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLK   87 (120)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHHHHHHHHHCSCSHHHHHHHHHHTHHHHSSSCCSHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHHHHHHc
Confidence            56899999999999999754221   112346789999999999999998888999999999999999999999999999


Q ss_pred             CcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHH
Q psy996          126 GAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKF  166 (221)
Q Consensus       126 G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~  166 (221)
                      |.|+|++||.|+++             ||||+|+|+||++.
T Consensus        88 G~i~p~~lv~Ms~e-------------EmAS~elk~~r~~~  115 (120)
T 2dme_A           88 GEVTPDHLIRMSPE-------------ELASKELAAWRRRS  115 (120)
T ss_dssp             TSSCTTHHHHSCTT-------------TTTTCCSTTTCTTC
T ss_pred             CCCCHHHHhcCCHH-------------HcCCHHHHHHHHHH
Confidence            99999999999999             99999999998764

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=99.60  E-value=5.1e-16  Score=104.93  Aligned_cols=40  Identities=70%  Similarity=1.080  Sum_probs=37.4

Q ss_pred             cCcccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          180 QGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       180 ~~~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      +++.|+.+.|++||+++++|+|+|+||||||||+||.|.+
T Consensus         3 ~~~~t~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~   42 (50)
T 1tfi_A            3 GGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE   42 (50)
T ss_dssp             SCEECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESS
T ss_pred             CCceeCccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCC
Confidence            4678888999999999999999999999999999999974

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=99.37  E-value=3.1e-13  Score=93.03  Aligned_cols=37  Identities=30%  Similarity=0.479  Sum_probs=33.7

Q ss_pred             ccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          183 KTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       183 ~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      ++..+.||+||+.+++|+|+|+||||||||+||.|..
T Consensus        12 ~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~   48 (57)
T 1qyp_A           12 PTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK   48 (57)
T ss_dssp             CEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESS
T ss_pred             CceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCC
Confidence            3346899999999999999999999999999999974

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.24  E-value=3.2e-12  Score=99.44  Aligned_cols=36  Identities=19%  Similarity=0.371  Sum_probs=33.1

Q ss_pred             cccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       184 T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      +..+.|++||+++++|+|+|+||||||||+||.|.+
T Consensus        70 ~~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~  105 (113)
T 3h0g_I           70 RSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVH  105 (113)
T ss_dssp             BCCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESS
T ss_pred             CcccCCCCCCCceEEEEEEecccCCCCCeeEEEcCC
Confidence            334899999999999999999999999999999964

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=99.23  E-value=4.6e-12  Score=99.77  Aligned_cols=35  Identities=26%  Similarity=0.386  Sum_probs=32.8

Q ss_pred             ccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          185 DLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       185 ~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      ..+.|++||+++++|+|+|+||||||||+||+|.+
T Consensus        71 t~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~  105 (122)
T 1twf_I           71 SDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS  105 (122)
T ss_dssp             CCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETT
T ss_pred             cCCCCCCCCCCEEEEEEecCccCCCCceEEEEeCC
Confidence            35799999999999999999999999999999974

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=99.12  E-value=5.4e-12  Score=101.02  Aligned_cols=35  Identities=43%  Similarity=0.604  Sum_probs=0.0

Q ss_pred             ccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          185 DLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       185 ~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      ..+.|++||+++++|+|+|+||||||||+||.|..
T Consensus        91 t~~~CpkCg~~~a~f~q~Q~RsaDE~mT~fy~C~~  125 (133)
T 3qt1_I           91 SDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVN  125 (133)
T ss_dssp             -----------------------------------
T ss_pred             ccCCCCCCCCceEEEEEEeeecCCCCCcEEEEcCC
Confidence            35799999999999999999999999999999964

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=96.00  E-value=0.00071  Score=45.11  Aligned_cols=18  Identities=72%  Similarity=0.888  Sum_probs=14.8

Q ss_pred             CChhhhhccCCCCchhHh
Q psy996          136 MTAEVQTRSADEPMTTFE  153 (221)
Q Consensus       136 m~~q~Q~rsadep~t~fE  153 (221)
                      ...++|+||||||||+|.
T Consensus        21 ~f~q~Q~RsaDE~mT~Fy   38 (50)
T 1tfi_A           21 TYTQVQTRSADEPMTTFV   38 (50)
T ss_dssp             EEEEECSSSSSSCCEEEE
T ss_pred             EEEEecCcCCCCCceEEE
Confidence            345689999999999964

>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=94.45  E-value=0.01  Score=49.06  Aligned_cols=30  Identities=37%  Similarity=0.511  Sum_probs=21.9

Q ss_pred             ccccCcCChhhhhcCChhhhhccCCCCchhHh
Q psy996          122 NYIFGAISASKLATMTAEVQTRSADEPMTTFE  153 (221)
Q Consensus       122 ~Il~G~isp~~l~~m~~q~Q~rsadep~t~fE  153 (221)
                      .+.++++.-.++  .+.|+|+||||||||+|.
T Consensus       137 ~~~Cp~C~~~~a--~~~q~Q~rsaDE~mt~f~  166 (178)
T 3po3_S          137 RFTCGKCKEKKV--SYYQLQTRSAAAPLTTFC  166 (178)
T ss_dssp             SSCCSSSCCSCE--ECCCCCCSCTTSCCCCCE
T ss_pred             CcCCCCCCCCce--EEEEeecccCCCCCcEEE
Confidence            445666655555  456889999999999953

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=94.40  E-value=0.01  Score=45.55  Aligned_cols=16  Identities=25%  Similarity=0.287  Sum_probs=13.7

Q ss_pred             ChhhhhccCCCCchhH
Q psy996          137 TAEVQTRSADEPMTTF  152 (221)
Q Consensus       137 ~~q~Q~rsadep~t~f  152 (221)
                      +.++|+||||||||+|
T Consensus        85 ~~q~q~rsade~mt~f  100 (113)
T 3h0g_I           85 FYQTHSRRGDTMMTLI  100 (113)
T ss_dssp             EECCCCSSCCCCCCCE
T ss_pred             EEEEecccCCCCCeeE
Confidence            3458999999999995

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=94.18  E-value=0.0064  Score=40.98  Aligned_cols=28  Identities=32%  Similarity=0.324  Sum_probs=18.7

Q ss_pred             cccCcCChhhhhcCChhhhhccCCCCchhH
Q psy996          123 YIFGAISASKLATMTAEVQTRSADEPMTTF  152 (221)
Q Consensus       123 Il~G~isp~~l~~m~~q~Q~rsadep~t~f  152 (221)
                      +.+.+..-.++  ...++|+||||||||.|
T Consensus        16 ~~Cp~Cg~~~~--~~~q~Q~rsadep~T~f   43 (57)
T 1qyp_A           16 ITCPKCGNDTA--YWWEMQTRAGDEPSTIF   43 (57)
T ss_dssp             CCCTTTCCSEE--EEEEECCSSSSCSSEEE
T ss_pred             eECCCCCCCEE--EEEEeecccCCCCCcEE
Confidence            34444443333  44578999999999984

>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=93.49  E-value=0.014  Score=52.03  Aligned_cols=28  Identities=46%  Similarity=0.681  Sum_probs=19.6

Q ss_pred             cccCcCChhhhhcCChhhhhccCCCCchhH
Q psy996          123 YIFGAISASKLATMTAEVQTRSADEPMTTF  152 (221)
Q Consensus       123 Il~G~isp~~l~~m~~q~Q~rsadep~t~f  152 (221)
                      +.|+.+.-.++  .+.++|+||||||||+|
T Consensus       269 ~~C~~C~~~~~--~~~q~Q~rsaDe~~t~f  296 (309)
T 1pqv_S          269 FTCGKCKEKKV--SYYQLQTRSADEPLTTF  296 (309)
T ss_pred             ccCCCCCCCee--EEEEeecccCCCCCcEE
Confidence            34444444444  45679999999999995

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=93.35  E-value=0.015  Score=46.12  Aligned_cols=21  Identities=52%  Similarity=0.610  Sum_probs=0.0

Q ss_pred             CChhhhhccCCCCchhHhhcc
Q psy996          136 MTAEVQTRSADEPMTTFEMAN  156 (221)
Q Consensus       136 m~~q~Q~rsadep~t~fElas  156 (221)
                      .+.|+|+||||||||+|..+.
T Consensus       104 ~f~q~Q~RsaDE~mT~fy~C~  124 (133)
T 3qt1_I          104 VFFQLQIRSADEPMTTFYKCV  124 (133)
T ss_dssp             ---------------------
T ss_pred             EEEEEeeecCCCCCcEEEEcC
Confidence            556799999999999987764

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=92.34  E-value=0.019  Score=44.49  Aligned_cols=17  Identities=29%  Similarity=0.386  Sum_probs=14.1

Q ss_pred             CChhhhhccCCCCchhH
Q psy996          136 MTAEVQTRSADEPMTTF  152 (221)
Q Consensus       136 m~~q~Q~rsadep~t~f  152 (221)
                      .+.++|+||||||||+|
T Consensus        84 ~~~q~q~rsade~~t~f  100 (122)
T 1twf_I           84 VFFQSQQRRKDTSMVLF  100 (122)
T ss_dssp             EEEECSSCCTTCCCCEE
T ss_pred             EEEEecCccCCCCceEE
Confidence            34458999999999995

---

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	221
d1enwa_	114	a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak	9e-20
d1tfia_	50	g.41.3.1 (A:) Transcriptional factor SII, C-termin	1e-16
d1tfia_	50	g.41.3.1 (A:) Transcriptional factor SII, C-termin	4e-04
d1qypa_	57	g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A	4e-10
d1qypa_	57	g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A	0.003
d1twfi2	72	g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase	7e-07

>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 = 79.1 bits (195), Expect = 9e-20
 Identities = 19/92 (20%), Positives = 32/92 (34%), Gaps = 4/92 (4%)

Query: 50  TDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEF--KNTDNRYKNRVRSR 107
              +R +  + L + +           S+   A  +E  +         +  YK R R  
Sbjct: 19  HHKLRDQVLKALYDVLAKE--SEHPPQSILHTAKAIESEMNKVNNCDTNEAAYKARYRII 76

Query: 108 IANLKDPKNPMLSRNYIFGAISASKLATMTAE 139
            +N+    NP L      G I+   LAT  A+
Sbjct: 77  YSNVISKNNPDLKHKIANGDITPEFLATCDAK 108

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 50

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.6 bits (168), Expect = 1e-16
 Identities = 29/41 (70%), Positives = 32/41 (78%), Gaps = 3/41 (7%)

Query: 179 VQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219
             GT+TDL  CGKCKK+NCTY QVQTRSADEPMTT   F +
Sbjct: 2   TGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTT---FVV 39

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 50

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (81), Expect = 4e-04
 Identities = 13/14 (92%), Positives = 14/14 (100%)

Query: 139 EVQTRSADEPMTTF 152
           +VQTRSADEPMTTF
Sbjct: 24  QVQTRSADEPMTTF 37

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Length = 57

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

 Score = 51.7 bits (124), Expect = 4e-10
 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 3/35 (8%)

Query: 184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFY 218
           T  + C KC      + ++QTR+ DEP T    FY
Sbjct: 13  TTKITCPKCGNDTAYWWEMQTRAGDEPSTI---FY 44

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Length = 57

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

 Score = 32.4 bits (74), Expect = 0.003
 Identities = 9/14 (64%), Positives = 11/14 (78%)

Query: 139 EVQTRSADEPMTTF 152
           E+QTR+ DEP T F
Sbjct: 30  EMQTRAGDEPSTIF 43

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 72

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.3 bits (102), Expect = 7e-07
 Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 3/32 (9%)

Query: 188 KCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219
           +C KC  R   + Q Q R  D  M     F++
Sbjct: 25  ECPKCHSRENVFFQSQQRRKDTSMVL---FFV 53

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	221
d1enwa_	114	Elongation factor TFIIS domain 2 {Baker's yeast (S	99.77
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	99.69
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	99.52
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	99.41
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	96.85
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	96.44
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	93.58

>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=99.77  E-value=7.2e-20  Score=141.43  Aligned_cols=92  Identities=21%  Similarity=0.207  Sum_probs=81.7

Q ss_pred             CCCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcC--CChhhhhHHHHHHHhcCCCCChhhhhcc
Q psy996           46 SHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKN--TDNRYKNRVRSRIANLKDPKNPMLSRNY  123 (221)
Q Consensus        46 ~~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~--~~~~Yk~k~Rsl~~nLk~~kN~~L~~~I  123 (221)
                      ...++|++|++|+++|+++|..+.++..  ..+.++|.+||.+||..+++  ++..|++++|+|++|||+++|+.|+.+|
T Consensus        15 ~~~~~d~~R~~~~~~L~~aL~~~~~~~~--~~~~~la~~IE~~lf~~~~~~~~~~~Y~~k~rsi~~NLkd~~N~~L~~~v   92 (114)
T d1enwa_          15 TAIYHHKLRDQVLKALYDVLAKESEHPP--QSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKI   92 (114)
T ss_dssp             CCSSTTTTHHHHHHHHHHHHHHHCSSSC--SCHHHHHHHHTTTTTSSCTTTTTHHHHHHHHHHHHHHHTTSCCCCTTTHH
T ss_pred             CccCCcHHHHHHHHHHHHHHhCcCccch--hHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHcCccchHHHHHHH
Confidence            3458899999999999999997654433  35789999999999999864  3467999999999999999999999999


Q ss_pred             ccCcCChhhhhcCChh
Q psy996          124 IFGAISASKLATMTAE  139 (221)
Q Consensus       124 l~G~isp~~l~~m~~q  139 (221)
                      +.|+|+|.+|+.|+++
T Consensus        93 ~~g~i~p~~l~~M~~~  108 (114)
T d1enwa_          93 ANGDITPEFLATCDAK  108 (114)
T ss_dssp             HHCSSCCSSHHHHTTT
T ss_pred             HcCCCCHHHHhCCCHH
Confidence            9999999999999999

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.5e-18  Score=112.53  Aligned_cols=40  Identities=70%  Similarity=1.080  Sum_probs=38.0

Q ss_pred             cCcccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          180 QGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       180 ~~~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      +++.|++|+|++||++++.|+|+||||||||||+||+|++
T Consensus         3 ~g~~T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~   42 (50)
T d1tfia_           3 GGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE   42 (50)
T ss_dssp             SCEECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESS
T ss_pred             CCcccCCEECCCCCCCccEEEEEEccCCCCCceEEEEccc
Confidence            4688999999999999999999999999999999999975

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=99.52  E-value=3.4e-15  Score=101.80  Aligned_cols=38  Identities=29%  Similarity=0.455  Sum_probs=35.0

Q ss_pred             cccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          182 TKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       182 ~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      .++..+.|++||+++++|+|+||||||||||+||+|.+
T Consensus        11 ~pt~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~   48 (57)
T d1qypa_          11 LPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK   48 (57)
T ss_dssp             SCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESS
T ss_pred             CCcccCCCCCCCCCceEEEEeecccccCCCeEEEEeCC
Confidence            45567899999999999999999999999999999975

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.41  E-value=5.3e-14  Score=99.98  Aligned_cols=35  Identities=26%  Similarity=0.386  Sum_probs=32.9

Q ss_pred             ccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996          185 DLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI  219 (221)
Q Consensus       185 ~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~  219 (221)
                      ....|++||+++++|+|+|+||||||||+||+|.+
T Consensus        22 t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~   56 (72)
T d1twfi2          22 SDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS   56 (72)
T ss_dssp             CCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETT
T ss_pred             cCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCC
Confidence            35799999999999999999999999999999975

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.85  E-value=5.1e-05  Score=49.29  Aligned_cols=20  Identities=65%  Similarity=0.835  Sum_probs=16.0

Q ss_pred             CChhhhhccCCCCchhHhhc
Q psy996          136 MTAEVQTRSADEPMTTFEMA  155 (221)
Q Consensus       136 m~~q~Q~rsadep~t~fEla  155 (221)
                      ...++|+||||||||+|..+
T Consensus        21 ~~~~~QtRSADEp~T~F~~C   40 (50)
T d1tfia_          21 TYTQVQTRSADEPMTTFVVC   40 (50)
T ss_dssp             EEEEECSSSSSSCCEEEEEE
T ss_pred             EEEEEEccCCCCCceEEEEc
Confidence            45679999999999996443

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=96.44  E-value=0.00027  Score=46.91  Aligned_cols=17  Identities=53%  Similarity=0.644  Sum_probs=14.4

Q ss_pred             CChhhhhccCCCCchhH
Q psy996          136 MTAEVQTRSADEPMTTF  152 (221)
Q Consensus       136 m~~q~Q~rsadep~t~f  152 (221)
                      .+.++|+||||||||.|
T Consensus        27 ~~~~~QtRsaDE~~T~f   43 (57)
T d1qypa_          27 YWWEMQTRAGDEPSTIF   43 (57)
T ss_dssp             EEEEECCSSSSCSSEEE
T ss_pred             EEEEeecccccCCCeEE
Confidence            44579999999999994

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.58  E-value=0.0049  Score=42.39  Aligned_cols=28  Identities=18%  Similarity=0.122  Sum_probs=19.4

Q ss_pred             cccCcCChhhhhcCChhhhhccCCCCchhH
Q psy996          123 YIFGAISASKLATMTAEVQTRSADEPMTTF  152 (221)
Q Consensus       123 Il~G~isp~~l~~m~~q~Q~rsadep~t~f  152 (221)
                      +.+.+..-.+.  .+.++|+||||||||.|
T Consensus        24 ~~CpkCg~~~a--~~~q~QtRsaDE~mT~F   51 (72)
T d1twfi2          24 RECPKCHSREN--VFFQSQQRRKDTSMVLF   51 (72)
T ss_dssp             CCCTTTCCCCE--EEEECSSCCTTCCCCEE
T ss_pred             CCCCCCCCCeE--EEEEeecCccCCCceEE
Confidence            34444444444  45579999999999995