Citrus Sinensis ID: 038232

---

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-------
Protein Sequence
CKASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccHHHHHcHHccccccHHHccccHHHcccHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHccHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
CKASSRKKIQDFASDLIVSWRNMSLEqmrderkgsytipgdiepakiekvdkrtSEECQEISGVGIVKVQkvdqnatslssnvvrpesvvtektnssdnlsrsmIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEkwdrydgpykiKYKAVLgnlkdpknpdfrrnvhlgqvkpetiVGMTAKEMAGDkmlscyqr
Flexible Loop (DISEMBL)
ckassrkkiqdfasdlIVSWRNMSLeqmrderkgsytipgdiepakiekvdkrTSEECQEisgvgivkvqkvdqnatslssnvvrpesvvtektnssdnlsrsmiRCNDCFREVVREKVCDALSkvsgeadeeirdevnacdsVRVAIALESAmfekwdrydgPYKIKYKAVLgnlkdpknpdfrrnvhlgqvkpetivgmtakemagdkmlscyqr
Low Complexity Region (SEG)
CKASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR
Disordered region (IsUnstruct)
*************SDLIVSWR***************************************ISGVGIVKV**********************************MIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKD*******RNVHLGQV***TIV******************
Disordered Region (DISOPRED)
****SRK***DFASDLIVSWR******************************************************************************************REVVREKVCDALSKVSGE******DEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEM******S****
Disordered Region (DISEMBL)
*********QDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEK*********QEISGVGIVKVQKVDQNATSLSSNVVRP*************LSRSMIRCNDCFREVVREKVCDALS*********IRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR
Disordered Region (DISPRO)
*KASSRKKIQDFASDLIVSWRNMSLE*******************************************************************************RCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDK*******
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
CKASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR
Positional Conservation
no confident homologs detected

---

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	217	2.2.26 [Sep-21-2011]
P23881	347	Transcription elongation	yes	no	0.433	0.270	0.360	5e-10
O75764	348	Transcription elongation	yes	no	0.594	0.370	0.305	5e-09
Q2KI09	349	Transcription elongation	yes	no	0.433	0.269	0.350	1e-08
Q15560	299	Transcription elongation	no	no	0.322	0.234	0.4	2e-08
P23193	301	Transcription elongation	no	no	0.774	0.558	0.280	9e-08
Q92576	2039	PHD finger protein 3 OS=H	no	no	0.479	0.051	0.321	1e-07
Q4KLL0	301	Transcription elongation	no	no	0.502	0.362	0.314	2e-07
P10711	301	Transcription elongation	no	no	0.502	0.362	0.314	2e-07
P20232	313	Transcription elongation	no	no	0.304	0.210	0.393	3e-07
Q29RL9	301	Transcription elongation	no	no	0.331	0.239	0.347	3e-07

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

 Score = 64.3 bits (155), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 59/97 (60%), Gaps = 3/97 (3%)

Query: 115 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLG 174
           VR+K  + LS  + +A++  +D    CD  ++A  +E  ++++    D  Y+ + ++ + 
Sbjct: 186 VRDKCVEMLS-AALKAEDNFKDYGVNCD--KLASEIEDHIYQELKSTDMKYRNRVRSRIS 242

Query: 175 NLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
           NLKDP+NP  RRNV  G + PE I  MTA+EMA D++
Sbjct: 243 NLKDPRNPGLRRNVLSGAISPELIAKMTAEEMASDEL 279

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 = 61.2 bits (147), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 41/134 (30%), Positives = 73/134 (54%), Gaps = 5/134 (3%)

Query: 80  SSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFR--EVVREKVCDALSKVSGEADEEIRDE 137
           +S+  + ES  T  +  +   + SM     C+   + VR+K  + LS  + +AD++ +D 
Sbjct: 150 NSSKSKAESPKTPSSPLTPTFASSMCLLAPCYLTGDSVRDKCVEMLS-AALKADDDYKDY 208

Query: 138 VNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPET 197
              CD  ++A  +E  ++++    D  Y+ + ++ + NLKDP+NP  RRNV  G +    
Sbjct: 209 GVNCD--KMASEIEDHIYQELKSTDMKYRNRVRSRISNLKDPRNPGLRRNVLSGAISAGL 266

Query: 198 IVGMTAKEMAGDKM 211
           I  MTA+EMA D++
Sbjct: 267 IAKMTAEEMASDEL 280

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

 Score = 59.7 bits (143), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 58/97 (59%), Gaps = 3/97 (3%)

Query: 115 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLG 174
           VR+K  + LS  + +AD++ +D    CD  ++A  +E  ++++    D  Y+ + ++ + 
Sbjct: 188 VRDKCVEMLS-AALKADDDYKDYGVNCD--KMASEIEDHIYQELKSTDMKYRNRVRSRIS 244

Query: 175 NLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
           NLKDP+NP  RRNV  G +    I  MTA+EMA D++
Sbjct: 245 NLKDPRNPGLRRNVLSGAISAGLIAKMTAEEMASDEL 281

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

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 42/70 (60%)

Query: 142 DSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGM 201
           D  R++  +E  +F      D  YK + ++ + NLKD KNPD RRNV  G + P+ I  M
Sbjct: 162 DCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVM 221

Query: 202 TAKEMAGDKM 211
           T++EMA D++
Sbjct: 222 TSEEMASDEL 231

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

 Score = 57.0 bits (136), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 62/221 (28%), Positives = 98/221 (44%), Gaps = 53/221 (23%)

Query: 2   KASSRKKIQDFASDLIVSWRNM----SLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEE 57
           K S+ +++   A  LI SW+ +    S E+  DE+K         EPA    +  + S E
Sbjct: 55  KQSTDEEVTSLAKSLIKSWKKLLDGPSTEKDLDEKKK--------EPA----ITSQNSPE 102

Query: 58  CQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRC---NDCFREV 114
            +E S               + S NV    S   ++TN+ D    S  R    +D  R  
Sbjct: 103 AREES---------------TSSGNV----SNRKDETNARDTYVSSFPRAPSTSDSVRLK 143

Query: 115 VREKVCDALSK----VSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYK 170
            RE +  AL      ++  ADEE            +   +E A++++    D  YK + +
Sbjct: 144 CREMLAAALRTGDDYIAIGADEE-----------ELGSQIEEAIYQEIRNTDMKYKNRVR 192

Query: 171 AVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
           + + NLKD KNP+ R+NV  G + P+    MTA+EMA D++
Sbjct: 193 SRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDEL 233

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

 Score = 56.2 bits (134), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 62/109 (56%), Gaps = 5/109 (4%)

Query: 109  DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIK 168
            D  R+ VR  + D L K   +++ ++ +E  A    +VA  +E  +F  +   D  YK K
Sbjct: 925  DQIRQSVRHSLKDILMKRLTDSNLKVPEEKAA----KVATKIEKELFSFFRDTDAKYKNK 980

Query: 169  YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR 217
            Y++++ NLKDPKN    + V  G+V P+ ++ M+ +E+A  K L+ ++R
Sbjct: 981  YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELAS-KELAAWRR 1028

Homo sapiens (taxid: 9606)

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

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 40/127 (31%), Positives = 63/127 (49%), Gaps = 18/127 (14%)

Query: 92  EKTNSSDNLSRSMIRC---NDCFREVVREKVCDALSK----VSGEADEEIRDEVNACDSV 144
           ++TN+ D    S  R    +D  R   RE +  AL      V+  ADEE           
Sbjct: 118 DETNARDTYVSSFPRAPSTSDSVRLKCREMLAAALRTGDDYVAIGADEE----------- 166

Query: 145 RVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAK 204
            +   +E A++++    D  YK + ++ + NLKD KNP+ R+NV  G + P+    MTA+
Sbjct: 167 ELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE 226

Query: 205 EMAGDKM 211
           EMA D++
Sbjct: 227 EMASDEL 233

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 = 55.5 bits (132), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 40/127 (31%), Positives = 63/127 (49%), Gaps = 18/127 (14%)

Query: 92  EKTNSSDNLSRSMIRC---NDCFREVVREKVCDALSK----VSGEADEEIRDEVNACDSV 144
           ++TN+ D    S  R    +D  R   RE +  AL      V+  ADEE           
Sbjct: 118 DETNARDTYVSSFPRAPSTSDSVRLKCREMLAAALRTGDDYVAIGADEE----------- 166

Query: 145 RVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAK 204
            +   +E A++++    D  YK + ++ + NLKD KNP+ R+NV  G + P+    MTA+
Sbjct: 167 ELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE 226

Query: 205 EMAGDKM 211
           EMA D++
Sbjct: 227 EMASDEL 233

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

 Score = 55.5 bits (132), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 40/66 (60%)

Query: 146 VAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKE 205
           +A  LE A++ +++  D  YK + ++ + NLKDPKNP  R N   G V  + +  MT +E
Sbjct: 180 MAAELEDAIYSEFNNTDMKYKNRIRSRVANLKDPKNPGLRGNFMCGAVTAKQLAKMTPEE 239

Query: 206 MAGDKM 211
           MA D+M
Sbjct: 240 MASDEM 245

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 = 55.5 bits (132), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 140 ACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIV 199
             D   +   +E A++++    D  YK + ++ + NLKD KNP+ R+NV  G + P+   
Sbjct: 162 GADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFA 221

Query: 200 GMTAKEMAGDKM 211
            MTA+EMA D++
Sbjct: 222 RMTAEEMASDEL 233

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	217
225439709	367	PREDICTED: transcription elongation fact	0.930	0.550	0.373	2e-36
224087871	352	predicted protein [Populus trichocarpa]	0.926	0.571	0.390	4e-34
449441244	369	PREDICTED: transcription elongation fact	0.921	0.542	0.380	7e-34
297735532	322	unnamed protein product [Vitis vinifera]	0.834	0.562	0.398	3e-33
224139382	334	predicted protein [Populus trichocarpa]	0.880	0.571	0.389	1e-32
255575598	342	transcription elongation factor s-II, pu	0.907	0.576	0.380	3e-32
255559741	330	transcription elongation factor s-II, pu	0.870	0.572	0.402	1e-30
388514187	369	unknown [Medicago truncatula]	0.930	0.547	0.371	6e-30
449499153	290	PREDICTED: transcription elongation fact	0.751	0.562	0.407	2e-29
356509090	368	PREDICTED: putative transcription elonga	0.963	0.567	0.351	6e-29

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

 Score =  158 bits (399), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 136/230 (59%), Gaps = 28/230 (12%)

Query: 8   KIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGD-------IEPAKIEKVDKRTSEECQE 60
           KIQ  ASDL+  W+ + +++ R+++ G     G         E  K+E   K    + ++
Sbjct: 70  KIQSLASDLLEMWKKVVIDETRNKKNGGLDNNGSAKAEVSKTETVKVEMAHKAGGVKVEK 129

Query: 61  ISGVGIVKVQKVDQNATSLSSNVVRPESVVTEK--------------------TNSSDNL 100
            S V  VK++K D+ +++   +V R E++  EK                    +N    L
Sbjct: 130 ASKVETVKIEKFDRGSSTKPGSVSRSETIKVEKRVENVDERKQFSSVKKPPQASNGPPKL 189

Query: 101 SRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDR 160
           + +MI+CND  R+ VRE + +AL KV+ EADE+I+DEVNACD +RVA+++ES MFEK  R
Sbjct: 190 T-AMIKCNDALRDKVRELLAEALFKVASEADEDIKDEVNACDPIRVAVSVESVMFEKMGR 248

Query: 161 YDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDK 210
            +G  K KY++++ N+KDP NPD RR V LG+VKP+ ++ M+ +EMA ++
Sbjct: 249 SNGTQKFKYRSIMFNIKDPNNPDLRRKVLLGEVKPDRLINMSPEEMASNQ 298

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 86/220 (39%), Positives = 140/220 (63%), Gaps = 19/220 (8%)

Query: 6   RKKIQDFASDLIVSWRNMSLEQMRDERKGSY----TIPGDI---EPAKIEKVDKRTSEEC 58
           ++KI+  ASDL+  W+ M +++ R ++ GS     ++  ++   E  K+EK+ K +  + 
Sbjct: 68  KEKIRAVASDLLEMWKKMVIDETR-KKNGSIDSKSSVKAEVSKSETVKVEKLRKTSVVKV 126

Query: 59  QEISGVGIVKVQKVDQNAT----SLSSNVVRPESVVTEKTNSSDNLS----RSMIRCNDC 110
           +  S    VKV+K+DQ+ T     +S   ++  SV   K  S   +     +++++CND 
Sbjct: 127 ERASTSETVKVEKMDQDKTVKVEKMSKQEIQTSSV---KQPSQSPIGPPKLKTLVKCNDA 183

Query: 111 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYK 170
            R+ +RE + +ALSKV+ EADE+IRDEV ACD +RVA+++ES MFEK  R +G  K+KY+
Sbjct: 184 LRDKIRELLAEALSKVASEADEDIRDEVEACDPIRVAVSVESMMFEKLGRSNGAQKLKYR 243

Query: 171 AVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDK 210
           +++ N+KD  NPDFRR V LG+V+PE +V M  +EMA ++
Sbjct: 244 SIMFNIKDQNNPDFRRKVLLGEVQPERLVTMGPEEMASEQ 283

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441244|ref|XP_004138392.1| PREDICTED: transcription elongation factor A protein 3-like [Cucumis sativus]

 Score =  149 bits (376), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 91/239 (38%), Positives = 131/239 (54%), Gaps = 39/239 (16%)

Query: 6   RKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGD--------IEPAKIEKVDKRTSEE 57
           +KKIQ+ ASDLI  W+ + +++    +K       D         E  K+EK  K +S +
Sbjct: 67  KKKIQEHASDLIEMWKEIVIKETNKNKKNGNASSKDSPKIGSPSAESVKVEKFQKSSSMK 126

Query: 58  CQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTE-------KTNSSDNLSR-------- 102
            + +S     KV++ D+N  + S    + ESVV+E       KT+S   + R        
Sbjct: 127 VERVS-----KVEQFDRNGATSSVKYSKSESVVSERNSVKVEKTDSMVKVERVVKEEKKP 181

Query: 103 -----------SMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALE 151
                      SMI+  D  R+ +RE + +A SKV GEADEE  DEVNA D +RVA+++E
Sbjct: 182 SSGAAAPPKLTSMIKSKDAARDKIRELLFEAFSKVPGEADEEFMDEVNASDPIRVAVSVE 241

Query: 152 SAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDK 210
           S MFE W    G  K KY++++ NLKDPKNPDFRR V LG +KPE ++ M+  +MA D+
Sbjct: 242 SVMFENWGGSTGAQKAKYRSIMFNLKDPKNPDFRRKVLLGLIKPERMINMSTADMASDQ 300

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 82/206 (39%), Positives = 128/206 (62%), Gaps = 25/206 (12%)

Query: 8   KIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEP---AKIEKVDKRTSEECQEISGV 64
           KIQ  ASDL+  W+ + +++ R+++ G     G  +    +K+E V+KR           
Sbjct: 70  KIQSLASDLLEMWKKVVIDETRNKKNGGLDNNGSAKAEKASKVETVEKR----------- 118

Query: 65  GIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCDALS 124
               V+ VD+      S+V +P     + +N    L+ +MI+CND  R+ VRE + +AL 
Sbjct: 119 ----VENVDERKQF--SSVKKP----PQASNGPPKLT-AMIKCNDALRDKVRELLAEALF 167

Query: 125 KVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDF 184
           KV+ EADE+I+DEVNACD +RVA+++ES MFEK  R +G  K KY++++ N+KDP NPD 
Sbjct: 168 KVASEADEDIKDEVNACDPIRVAVSVESVMFEKMGRSNGTQKFKYRSIMFNIKDPNNPDL 227

Query: 185 RRNVHLGQVKPETIVGMTAKEMAGDK 210
           RR V LG+VKP+ ++ M+ +EMA ++
Sbjct: 228 RRKVLLGEVKPDRLINMSPEEMASNQ 253

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 81/208 (38%), Positives = 131/208 (62%), Gaps = 17/208 (8%)

Query: 8   KIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGVGIV 67
           KI+  ASDL+ +W+ + +++    RK + T+       K+EK+ K +     ++S    V
Sbjct: 70  KIRAVASDLLETWKKIVIDETM--RKKNATV-------KVEKLQKTSM---VKVSTSETV 117

Query: 68  KVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLS-----RSMIRCNDCFREVVREKVCDA 122
           KV+K+DQ+ T   +   + E   +     S   +     +++++CND  R+ +RE + +A
Sbjct: 118 KVEKMDQDKTVKVAQTCKEEIQTSSVKKPSQAPTGPPKLKTLVKCNDALRDKIRELLAEA 177

Query: 123 LSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNP 182
           LSKV+ EADE+IRDEV ACD +RVA+++ESAMFEK  R +G  K+KY++++ N+KD  NP
Sbjct: 178 LSKVASEADEDIRDEVEACDPIRVAVSVESAMFEKLGRSNGAQKMKYRSIMFNIKDQNNP 237

Query: 183 DFRRNVHLGQVKPETIVGMTAKEMAGDK 210
           D RR V LGQV+P+ +V M  +EMA ++
Sbjct: 238 DLRRKVLLGQVQPQRLVTMPPEEMASEQ 265

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  144 bits (363), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 80/210 (38%), Positives = 135/210 (64%), Gaps = 13/210 (6%)

Query: 6   RKKIQDFASDLIVSWRNMSLEQMRDERKGSY----TIPGDI---EPAKIEKVDKRTSEEC 58
           R+KIQ  ASDL+  W+ + +++   ++ G+     ++  ++   E  K+EKV K ++ + 
Sbjct: 68  REKIQTVASDLLEMWKKIVIDETTRKKNGTVDNKSSVKAEVSKVETIKVEKVQKASTVKV 127

Query: 59  QEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREK 118
           ++I     VKV+K  +     + +V +P    ++ + +   L+ ++++CND  R+ +RE 
Sbjct: 128 EKIDRERTVKVEKKSEEKQQ-AIDVKKP----SQASVTPPKLT-AIVKCNDALRDKIREL 181

Query: 119 VCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKD 178
           + +ALSKV  EA+E+ RDE++ CD +RVA+++ESAMFEK  R +G  K KY++++ NLKD
Sbjct: 182 LVEALSKVVSEANEDGRDEISKCDPIRVAVSVESAMFEKMGRSNGAQKFKYRSIMFNLKD 241

Query: 179 PKNPDFRRNVHLGQVKPETIVGMTAKEMAG 208
           P NPD RR V LG+VKPE ++ MT +EMA 
Sbjct: 242 PNNPDLRRKVLLGEVKPERLISMTPEEMAS 271

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 83/206 (40%), Positives = 124/206 (60%), Gaps = 17/206 (8%)

Query: 5   SRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGV 64
           SRK IQD ASD+   W+   LEQ    +K      G +E    +K   +++E  + I   
Sbjct: 71  SRKNIQDLASDVFPLWKKKFLEQTSSTKKN-----GMLE----DKTSVKSTENIK-IEKT 120

Query: 65  GIVKVQ-KVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCDAL 123
             +KV+ K +      S+ VV  E ++           +S+ +CND  R+ +RE++ +AL
Sbjct: 121 RTIKVEAKTEHKGEPRSAKVVESECLL------RSPRMKSIPKCNDPSRDNIREQLYEAL 174

Query: 124 SKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPD 183
            KVS EA+EEI+ EVNACD++ VA+A+ESA+F  W   +G  +IKY++++ N +D KNPD
Sbjct: 175 CKVSSEANEEIQKEVNACDAIGVAVAVESALFSNWGPSNGSDRIKYRSLIFNTRDAKNPD 234

Query: 184 FRRNVHLGQVKPETIVGMTAKEMAGD 209
           FRR V LGQVKPE I  ++++EMA D
Sbjct: 235 FRRKVLLGQVKPERIAELSSEEMASD 260

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388514187|gb|AFK45155.1| unknown [Medicago truncatula]

 Score =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 87/234 (37%), Positives = 135/234 (57%), Gaps = 32/234 (13%)

Query: 6   RKKIQDFASDLIVSWRNMSLEQMRDERKG---SYTIPGDIEPAKIEKVDKRTSEECQEIS 62
           R+ I+ FA DLI  W+++ +++    + G   S     + E AK  K+ K  S + ++  
Sbjct: 70  RENIRTFAVDLIAIWKDVIIKETSKNKNGASDSKVESTNGERAKAGKLQKSPSVKVEKGE 129

Query: 63  GVGIVKVQKVDQNATS-LSSNVVRPESV--VTEKTNSSDNLS------------------ 101
                KV+KV+ N +S LSS  VR ++V    EKT+ + N+                   
Sbjct: 130 SA---KVEKVNGNGSSKLSSGNVRAQNVDVKIEKTDRTSNIKAKEEKPVSAAKKISSSAA 186

Query: 102 -----RSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFE 156
                ++MI+ ND  R+ +RE + DAL+KV  EADE++ DEVNACD +RVA+ +ES +FE
Sbjct: 187 APPKLKTMIKSNDSARDKIRELLRDALAKVFEEADEDMMDEVNACDPIRVAVTVESVLFE 246

Query: 157 KWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDK 210
            W   +G  K+KY++++ NLKD KNPDFRR V LG V+P+ +  M++ EMA ++
Sbjct: 247 NWGPSNGAQKVKYRSLMFNLKDQKNPDFRRKVLLGTVEPQRLAVMSSAEMASEQ 300

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  135 bits (339), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 79/194 (40%), Positives = 111/194 (57%), Gaps = 31/194 (15%)

Query: 43  EPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTE-------KTN 95
           E  K+EK  K +S + + +S     KV++ D+N  + S    + ESVV+E       KT+
Sbjct: 33  ESVKVEKFQKSSSMKVERVS-----KVEQFDRNGATSSVKYSKSESVVSERNSVKVEKTD 87

Query: 96  SSDNLSR-------------------SMIRCNDCFREVVREKVCDALSKVSGEADEEIRD 136
           S   + R                   SMI+  D  R+ +RE + +A SKV GEADEE  D
Sbjct: 88  SMVKVERVVKEEKKPSSGAAAPPKLTSMIKSKDAARDKIRELLFEAFSKVPGEADEEFMD 147

Query: 137 EVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPE 196
           EVNA D +RVA+++ES MFE W    G  K KY++++ NLKDPKNPDFRR V LG +KPE
Sbjct: 148 EVNASDPIRVAVSVESVMFENWGGSTGAQKAKYRSIMFNLKDPKNPDFRRKVLLGLIKPE 207

Query: 197 TIVGMTAKEMAGDK 210
            ++ M+  +MA D+
Sbjct: 208 RMINMSTADMASDQ 221

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509090|ref|XP_003523285.1| PREDICTED: putative transcription elongation factor S-II-like [Glycine max]

 Score =  133 bits (334), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 86/245 (35%), Positives = 138/245 (56%), Gaps = 36/245 (14%)

Query: 6   RKKIQDFASDLIVSWRNMSLEQMRDERKG---SYTIPGDIEPAKIEKVDKRTSEECQEIS 62
           R KI+ FA DLI  W+ + +++    + G   S     + E +K  K+ K  S + ++  
Sbjct: 65  RLKIKAFAIDLIEIWKGIIIKETSKNKNGGSDSKVESANGEKSKAGKMQKSPSVKVEKGE 124

Query: 63  GVGIVKVQKVDQNATSLSS--NVVRPES-VVTEKTNSSDNLS------------------ 101
               VKV+K+D+N T+ SS  N+ + ++ V  EKT+ S ++                   
Sbjct: 125 ---TVKVEKIDRNGTTKSSSENMKKVQNDVKNEKTDRSASVKVEKIAKEEKPVSGAKKMS 181

Query: 102 ---------RSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALES 152
                    ++MI+ ND  R+ +RE + +ALSKV+GEADE++ D VN  D +RVA+ +ES
Sbjct: 182 SSSAAPPKLKTMIKSNDATRDKIREILHEALSKVTGEADEDLVDVVNNSDPIRVAVTVES 241

Query: 153 AMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKML 212
            +FEKW   +G  K+KY++++ NLKD  NPDFRR V LG ++PE ++ M+  EMA ++  
Sbjct: 242 VLFEKWGPSNGAQKVKYRSLMFNLKDSNNPDFRRKVLLGVIEPEQLINMSTAEMASEQRK 301

Query: 213 SCYQR 217
             YQ+
Sbjct: 302 QEYQK 306

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	217
TAIR|locus:2064195	378	TFIIS "transcript elongation f	0.764	0.439	0.357	5.9e-25
TAIR|locus:2052351	737	AT2G42730 [Arabidopsis thalian	0.529	0.156	0.413	3.7e-17
TAIR|locus:2124097	266	AT4G18720 [Arabidopsis thalian	0.479	0.390	0.419	2.3e-16
RGD|1311369	348	Tcea3 "transcription elongatio	0.585	0.364	0.330	6.9e-12
MGI|MGI:1196908	347	Tcea3 "transcription elongatio	0.594	0.371	0.298	8.9e-12
UNIPROTKB|F1N0P7	348	TCEA3 "Transcription elongatio	0.718	0.448	0.289	1.9e-11
UNIPROTKB|O75764	348	TCEA3 "Transcription elongatio	0.751	0.468	0.275	1.9e-11
UNIPROTKB|Q2KI09	349	TCEA3 "Transcription elongatio	0.718	0.446	0.289	1.9e-11
UNIPROTKB|Q5JRI7	246	TCEA2 "Transcription elongatio	0.442	0.390	0.343	5.7e-10
ZFIN|ZDB-GENE-030131-8049	309	tcea1 "transcription elongatio	0.728	0.511	0.305	8.5e-10

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

 Score = 284 (105.0 bits), Expect = 5.9e-25, P = 5.9e-25
 Identities = 65/182 (35%), Positives = 111/182 (60%)

Query:    43 EPAKIEKVDKRTSEECQEISGVGI------VKVQ---KVDQNATSLSSNVVRPESVVTEK 93
             + AK  KV+++  +  + ++GV I      +KV    K+D    ++    V  ++  + K
Sbjct:   130 DSAKSIKVERKEPDN-KVVTGVKIERKVPDIKVTNGTKIDYRGQAVKDEKVSKDNQSSMK 188

Query:    94 T-----NSSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAI 148
                   N+   L+ +M++CND  R+ +RE + +AL +V+GEAD+  R+ VNA D +RVA+
Sbjct:   189 APAKAANAPPKLT-AMLKCNDPVRDKIRELLVEALCRVAGEADDYERESVNASDPLRVAV 247

Query:   149 ALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAG 208
             ++ES MFEK  R  G  K+KY++++ NL+D  NPD RR V  G++ PE ++ ++A++MA 
Sbjct:   248 SVESLMFEKLGRSTGAQKLKYRSIMFNLRDSNNPDLRRRVLTGEISPEKLITLSAEDMAS 307

Query:   209 DK 210
             DK
Sbjct:   308 DK 309

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

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

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

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

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

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

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

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

GO:0005829 "cytosol" evidence=RCA

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

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

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

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

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

GO:0009880 "embryonic pattern specification" evidence=RCA

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

GO:0009933 "meristem structural organization" evidence=RCA

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

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

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

GO:0010431 "seed maturation" evidence=RCA

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

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

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

GO:0048366 "leaf development" evidence=RCA

GO:0048825 "cotyledon development" evidence=RCA

GO:0050826 "response to freezing" evidence=RCA

GO:0051301 "cell division" evidence=RCA

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

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

 Score = 221 (82.9 bits), Expect = 3.7e-17, P = 3.7e-17
 Identities = 48/116 (41%), Positives = 72/116 (62%)

Query:   103 SMIRCNDCFREVVREKVCDALSKVSGE-ADEEIRDEVNACDSVRVAIALESAMFEKWDRY 161
             +M +  D  R+ VRE +  +L KV+ E  D E++  V ACD   VA+++ESAMFEK   +
Sbjct:   598 TMKKTGDSKRDKVREILQTSLVKVASEIVDTEMKTRVTACDPSVVAVSVESAMFEKLGCF 657

Query:   162 DGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR 217
              GP+K KY+++L N+ D  NPD RR V +G++  E +V M  +EM  +K+    QR
Sbjct:   658 MGPHKAKYRSILFNMGDSNNPDLRRKVLIGEINGERLVTMERQEMGSEKIQKEVQR 713

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 203 (76.5 bits), Expect = 2.3e-16, P = 2.3e-16
 Identities = 44/105 (41%), Positives = 66/105 (62%)

Query:   103 SMIRCNDCFREVVREKVCDALSKVSGEA-DEEIRDEVNACDSVRVAIALESAMFEKWDRY 161
             +M +  D  R+ VRE +  +L+KV+ E  D E++  V ACD   VA+++E+AMFE    +
Sbjct:   109 TMKKTGDSKRDKVREILQTSLAKVASEVVDTEMKTRVTACDPWVVAVSVETAMFENLGCF 168

Query:   162 DGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEM 206
              GP K KY+++L N+ D  NPD RR V LG++  E +V M  +EM
Sbjct:   169 MGPQKAKYRSILFNMGDSNNPDLRRKVLLGEISGERLVKMEKEEM 213

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

RGD|1311369 Tcea3 "transcription elongation factor A (SII), 3" [Rattus norvegicus (taxid:10116)]

 Score = 166 (63.5 bits), Expect = 6.9e-12, P = 6.9e-12
 Identities = 45/136 (33%), Positives = 76/136 (55%)

Query:    81 SNVVRPESVVTEKTNSSDN---LSRSMIRCNDCFR--EVVREKVCDALSKVSGEADEEIR 135
             SN  R + V T KT SS +    + ++     C+   + VR+K  + LS    +A+++ +
Sbjct:   149 SNSSRSK-VETPKTPSSPSTPTFAPAVCLLASCYLTGDSVRDKCVEMLSAAL-KAEDDFK 206

Query:   136 DEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKP 195
             D    CD  ++A  +E  ++++    D  Y+ + ++ + NLKDP+NP  RRNV  G + P
Sbjct:   207 DYGVNCD--KLASEIEDHIYQELKSTDMKYRNRVRSRISNLKDPRNPGLRRNVLSGTISP 264

Query:   196 ETIVGMTAKEMAGDKM 211
             E I  MTA+EMA D++
Sbjct:   265 ELIAKMTAEEMASDEL 280

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA;ISO

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

MGI|MGI:1196908 Tcea3 "transcription elongation factor A (SII), 3" [Mus musculus (taxid:10090)]

 Score = 165 (63.1 bits), Expect = 8.9e-12, P = 8.9e-12
 Identities = 40/134 (29%), Positives = 74/134 (55%)

Query:    80 SSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFR--EVVREKVCDALSKVSGEADEEIRDE 137
             +S+  + E+  T  + S+   + ++     C+   + VR+K  + LS    +A++  +D 
Sbjct:   149 NSSKSKVETPTTPSSPSTPTFAPAVCLLAPCYLTGDSVRDKCVEMLSAAL-KAEDNFKDY 207

Query:   138 VNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPET 197
                CD  ++A  +E  ++++    D  Y+ + ++ + NLKDP+NP  RRNV  G + PE 
Sbjct:   208 GVNCD--KLASEIEDHIYQELKSTDMKYRNRVRSRISNLKDPRNPGLRRNVLSGAISPEL 265

Query:   198 IVGMTAKEMAGDKM 211
             I  MTA+EMA D++
Sbjct:   266 IAKMTAEEMASDEL 279

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" 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:0006414 "translational elongation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F1N0P7 TCEA3 "Transcription elongation factor A protein 3" [Bos taurus (taxid:9913)]

 Score = 162 (62.1 bits), Expect = 1.9e-11, P = 1.9e-11
 Identities = 48/166 (28%), Positives = 86/166 (51%)

Query:    48 EKVDKRTSEECQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRC 107
             E  D+R S + +  S     K   ++++ +S S    + E+  T  + SS   + S+   
Sbjct:   124 EPKDRRDSVDSKS-SATSSPKRPSMERSNSSKS----KAETPRTPSSPSSPTFAPSVCLL 178

Query:   108 NDCFR--EVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPY 165
               C+   + VR+K  + LS    +AD++ +D    CD  ++A  +E  ++++    D  Y
Sbjct:   179 APCYLTGDSVRDKCVEMLSAAL-KADDDYKDYGVNCD--KMASEIEDHIYQELKSTDMKY 235

Query:   166 KIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
             + + ++ + NLKDP+NP  RRNV  G +    I  MTA+EMA D++
Sbjct:   236 RNRVRSRISNLKDPRNPGLRRNVLSGAISAGLIAKMTAEEMASDEL 281

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|O75764 TCEA3 "Transcription elongation factor A protein 3" [Homo sapiens (taxid:9606)]

 Score = 162 (62.1 bits), Expect = 1.9e-11, P = 1.9e-11
 Identities = 48/174 (27%), Positives = 88/174 (50%)

Query:    42 IEPAKIEKVDKRTSEEC--QEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDN 99
             + P + ++ D +T  +    + S     K   V+++ +S S    + ES  T  +  +  
Sbjct:   114 LSPPRKKREDPKTRRDSVDSKSSASSSPKRPSVERSNSSKS----KAESPKTPSSPLTPT 169

Query:   100 LSRSMIRCNDCFR--EVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEK 157
              + SM     C+   + VR+K  + LS    +AD++ +D    CD  ++A  +E  ++++
Sbjct:   170 FASSMCLLAPCYLTGDSVRDKCVEMLSAAL-KADDDYKDYGVNCD--KMASEIEDHIYQE 226

Query:   158 WDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
                 D  Y+ + ++ + NLKDP+NP  RRNV  G +    I  MTA+EMA D++
Sbjct:   227 LKSTDMKYRNRVRSRISNLKDPRNPGLRRNVLSGAISAGLIAKMTAEEMASDEL 280

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q2KI09 TCEA3 "Transcription elongation factor A protein 3" [Bos taurus (taxid:9913)]

 Score = 162 (62.1 bits), Expect = 1.9e-11, P = 1.9e-11
 Identities = 48/166 (28%), Positives = 86/166 (51%)

Query:    48 EKVDKRTSEECQEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRC 107
             E  D+R S + +  S     K   ++++ +S S    + E+  T  + SS   + S+   
Sbjct:   124 EPKDRRDSVDSKS-SATSSPKRPSMERSNSSKS----KAETPRTPSSPSSPTFAPSVCLL 178

Query:   108 NDCFR--EVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPY 165
               C+   + VR+K  + LS    +AD++ +D    CD  ++A  +E  ++++    D  Y
Sbjct:   179 APCYLTGDSVRDKCVEMLSAAL-KADDDYKDYGVNCD--KMASEIEDHIYQELKSTDMKY 235

Query:   166 KIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
             + + ++ + NLKDP+NP  RRNV  G +    I  MTA+EMA D++
Sbjct:   236 RNRVRSRISNLKDPRNPGLRRNVLSGAISAGLIAKMTAEEMASDEL 281

GO:0005634 "nucleus" 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

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

UNIPROTKB|Q5JRI7 TCEA2 "Transcription elongation factor A protein 2" [Homo sapiens (taxid:9606)]

 Score = 144 (55.7 bits), Expect = 5.7e-10, Sum P(2) = 5.7e-10
 Identities = 34/99 (34%), Positives = 54/99 (54%)

Query:   113 EVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAV 172
             + VR K C  +   + + D +    + A D  R++  +E  +F      D  YK + ++ 
Sbjct:   109 DAVRNK-CREMLTAALQTDHD-HVAIGA-DCERLSAQIEECIFRDVGNTDMKYKNRVRSR 165

Query:   173 LGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
             + NLKD KNPD RRNV  G + P+ I  MT++EMA D++
Sbjct:   166 ISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDEL 204

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

 Score = 154 (59.3 bits), Expect = 8.5e-10, P = 8.5e-10
 Identities = 52/170 (30%), Positives = 86/170 (50%)

Query:    43 EPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSSNVVRPESV-VTEKTNSSDNLS 101
             EPA  +  +++  E    +        +  +++++S SS+  + ESV VT  T  +    
Sbjct:    83 EPAADKNSEEKKKERTTPVVSPSETSPEPREESSSSNSSS--KSESVDVTPNTLIA-TFP 139

Query:   102 RSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRY 161
             R+    +D  R   RE + +AL   +G+    I  +   CD +   I  E  +F ++   
Sbjct:   140 RAP-GTSDSVRIKCREMLSNALQ--TGDDYITIGSD---CDELGAQI--EECIFLEFKNT 191

Query:   162 DGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
             D  YK + ++ + NLKD KNP+ RRNV  G V P+ I  MTA+EMA D++
Sbjct:   192 DMKYKNRVRSRISNLKDAKNPNLRRNVLCGNVSPDRIAKMTAEEMASDEL 241

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	217
smart00510	102	smart00510, TFS2M, Domain in the central regions o	4e-22
pfam07500	115	pfam07500, TFIIS_M, Transcription factor S-II (TFI	3e-21
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	1e-16

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

 Score = 86.6 bits (215), Expect = 4e-22
 Identities = 35/97 (36%), Positives = 54/97 (55%), Gaps = 3/97 (3%)

Query: 115 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLG 174
           VR+K  + L K      +    E    D   +A+ +E+ MF ++   D  YK KY+++  
Sbjct: 3   VRDKCQEMLYKA---LQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYF 59

Query: 175 NLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
           NLKD KNPD RR V  G++ PE +  MTA+E+A  ++
Sbjct: 60  NLKDKKNPDLRRKVLNGEITPEKLATMTAEELASAEL 96

Length = 102

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

 Score = 84.6 bits (210), Expect = 3e-21
 Identities = 39/105 (37%), Positives = 62/105 (59%), Gaps = 7/105 (6%)

Query: 107 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYK 166
            ND  R+  RE + DAL+K S        D ++  +  R+A  +E  +F+ +      YK
Sbjct: 1   TNDKVRDKCRELLYDALAKGSE-------DSMSEEEVERLAAEIEEELFKLYGNTGKKYK 53

Query: 167 IKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
            KY++++ NLKDPKNPD RR V  G++ PE +V M+ +E+A D++
Sbjct: 54  NKYRSLMFNLKDPKNPDLRRKVLNGEISPERLVNMSPEELASDEL 98

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|233390 TIGR01385, TFSII, transcription elongation factor S-II

 Score = 76.4 bits (188), Expect = 1e-16
 Identities = 51/209 (24%), Positives = 80/209 (38%), Gaps = 31/209 (14%)

Query: 2   KASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEI 61
           +    + I   A  +I SW+ +  +   D        PG     K         E    +
Sbjct: 53  RKHPNEDISKLAKKIIKSWKKVVDKNKSDH-------PGGNPEDK-----TTVGESVNSV 100

Query: 62  SGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCD 121
                 +  K++Q     SS           +   +D +       ND  R+  RE + D
Sbjct: 101 KQEAKSQSDKIEQPKYVSSS----------PRNAKNDFVP--TAVTNDKVRDKCRELLYD 148

Query: 122 ALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKN 181
           AL+K S            + D    AI +E   F      +  YK +Y+++  NL+D  N
Sbjct: 149 ALAKDSDHP-------PQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNN 201

Query: 182 PDFRRNVHLGQVKPETIVGMTAKEMAGDK 210
           PD R NV  G++ PE +  MTA+EMA  +
Sbjct: 202 PDLRHNVLTGEITPEKLATMTAEEMASAE 230

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	217
TIGR01385	299	TFSII transcription elongation factor S-II. This m	100.0
smart00510	102	TFS2M Domain in the central regions of transcripti	99.97
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	99.97
PF07500	115	TFIIS_M: Transcription factor S-II (TFIIS), centra	99.95
KOG1634	778	consensus Predicted transcription factor DATF1, co	99.45
smart00509	75	TFS2N Domain in the N-terminus of transcription el	96.69
PF08711	53	Med26: TFIIS helical bundle-like domain; InterPro:	95.37

>TIGR01385 TFSII transcription elongation factor S-II

Probab=100.00  E-value=4.5e-36  Score=270.36  Aligned_cols=181  Identities=28%  Similarity=0.385  Sum_probs=129.3

Q ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHhhhccCCCccCCCCCCcchhhccccccccccccccccccccccccccccccCCC
Q 038232            2 KASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSS   81 (217)
Q Consensus         2 ~~~~~~~i~~~A~~l~~~WKkvv~~e~~~~~~~~~~~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~   81 (217)
                      ++||+++|+++|++||..||++|.++..++...       .++.+...++.....              +.+..+++.  
T Consensus        53 rkh~~~~I~~lAk~li~~WK~~v~~~k~~~~~~-------~~~~~~~~~~~~~~~--------------~~~~~~~~~--  109 (299)
T TIGR01385        53 RKHPNEDISKLAKKIIKSWKKVVDKNKSDHPGG-------NPEDKTTVGESVNSV--------------KQEAKSQSD--  109 (299)
T ss_pred             HcCCcHHHHHHHHHHHHHHHHHHhhhcccCccc-------ccccccccCCCCCCC--------------CccccCCcc--
Confidence            589999999999999999999999984332211       011110000000000              000000000  


Q ss_pred             CCCCCCccccccCCCCC---CCCccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhh
Q 038232           82 NVVRPESVVTEKTNSSD---NLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKW  158 (217)
Q Consensus        82 ~~~~~~~v~~e~~ss~~---~~~~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~  158 (217)
                         .....+. .+++..   +.+.+++.++|++|++|+++||+||.....+.+       ..+++..+|.+||.+||..|
T Consensus       110 ---~~~~~~~-~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~-------~~~~~~~lA~~iE~~~f~~~  178 (299)
T TIGR01385       110 ---KIEQPKY-VSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP-------QSIDPEAKAIQIEELKFNNL  178 (299)
T ss_pred             ---cccCCCC-CCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCCc-------cccCHHHHHHHHHHHHHHHc
Confidence               0000000 011111   225566789999999999999999997543332       23567799999999999999


Q ss_pred             cCCChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232          159 DRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ  216 (217)
Q Consensus       159 ~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q  216 (217)
                      +.++..|+++||||+|||||++||+||++||+|+|+|++||.|+++||||+++|++++
T Consensus       179 ~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e  236 (299)
T TIGR01385       179 GTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQERE  236 (299)
T ss_pred             CCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHH
Confidence            9888899999999999999999999999999999999999999999999999999875

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.

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

Probab=99.97  E-value=2.9e-31  Score=205.56  Aligned_cols=102  Identities=35%  Similarity=0.570  Sum_probs=93.0

Q ss_pred             hHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCCChhhHhhh
Q 038232          109 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNV  188 (217)
Q Consensus       109 d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~V  188 (217)
                      |++|++|+++|+++|...+...+.       .+++..+|.+||.+||..|+..++.|++++|||+|||||++||+||++|
T Consensus         1 d~~R~~~~~~L~~al~~~~~~~~~-------~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~v   73 (102)
T smart00510        1 DKVRDKCQEMLYKALQKISDPEEI-------ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKV   73 (102)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCcc-------cccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            689999999999999986554432       2456799999999999999988889999999999999999999999999


Q ss_pred             hcCCCCccccccCCcccCCCHHHHhhhhC
Q 038232          189 HLGQVKPETIVGMTAKEMAGDKMLSCYQR  217 (217)
Q Consensus       189 L~G~isp~~Lv~Ms~eEMASdelk~e~q~  217 (217)
                      |+|+|+|++||.||++||||+++|+++++
T Consensus        74 l~G~i~p~~lv~Ms~~ElAs~elk~~~e~  102 (102)
T smart00510       74 LNGEITPEKLATMTAEELASAELKEKREK  102 (102)
T ss_pred             HcCCCCHHHHhcCCHHHcCCHHHHHHHhC
Confidence            99999999999999999999999999875

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

Probab=99.97  E-value=2.7e-30  Score=231.60  Aligned_cols=176  Identities=30%  Similarity=0.487  Sum_probs=125.8

Q ss_pred             cccchHHHHHHHHHHHHHHHHHHHHH-hhhccCCC-ccCCCCCCcchhhccccccccccccccccccccccccccccccC
Q 038232            2 KASSRKKIQDFASDLIVSWRNMSLEQ-MRDERKGS-YTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSL   79 (217)
Q Consensus         2 ~~~~~~~i~~~A~~l~~~WKkvv~~e-~~~~~~~~-~~~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~   79 (217)
                      |+||+++|.++|+.||..||++|.+. ...+.+.. ...|+..     ...++         +..  ..|.         
T Consensus        56 Kk~~n~ev~~~ak~Lik~Wkk~~~~~~~~~k~~~~~~~~p~~~-----~~~~~---------s~~--~~~~---------  110 (296)
T KOG1105|consen   56 KKHKNEEVRSLAKKLIKSWKKLVDKSPGREKSGDNKSHDPGEA-----SSKSP---------SGA--KQPE---------  110 (296)
T ss_pred             HhCCCHHHHHHHHHHHHHHHHHhhcccccccCccccCCCCCcC-----CcCCc---------cCC--CCcc---------
Confidence            79999999999999999999999985 11111110 1111111     00000         000  0000         


Q ss_pred             CCCCCCCCccccccCCCCCCCCccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhc
Q 038232           80 SSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWD  159 (217)
Q Consensus        80 ~~~~~~~~~v~~e~~ss~~~~~~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~  159 (217)
                         .++.+....+-+++    ....+.++|++|++|+++||+||.....       +....+++..+|.+||.+||..++
T Consensus       111 ---ks~~~~~~~~~~~~----~~~~~~~~d~~r~k~~e~l~~al~~~~~-------~~~~~~~~~~~a~~iE~~~~~~~g  176 (296)
T KOG1105|consen  111 ---KSRGDSKRDKHSGS----KDPVPITNDPVRDKCRELLYAALTTEDD-------SRVTGADPLELAVQIEEAIFEKLG  176 (296)
T ss_pred             ---ccccccccccccCc----CCCCCCCCchHHHHHHHHHHHHhccccc-------ccccCCCHHHHHHHHHHHHHHHhC
Confidence               01111111110111    1334456999999999999999984211       122346778999999999999999


Q ss_pred             CCChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232          160 RYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ  216 (217)
Q Consensus       160 ~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q  216 (217)
                      .+...|+.+|||++|||+|++||+||++||+|+|+|++|+.|+++||||+++|+.++
T Consensus       177 ~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~  233 (296)
T KOG1105|consen  177 NTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKEERQ  233 (296)
T ss_pred             CCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999886

>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=99.95  E-value=2.2e-28  Score=191.62  Aligned_cols=104  Identities=35%  Similarity=0.602  Sum_probs=93.3

Q ss_pred             CChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCCChhhHh
Q 038232          107 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRR  186 (217)
Q Consensus       107 ~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~  186 (217)
                      |++++|++++++|+++|.....+ .+      ....+..+|.+||.+||..|+..+..|++++|+|+|||||++||+||.
T Consensus         1 ~~~~~R~k~~~~L~~~l~~~~~~-~~------~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~   73 (115)
T PF07500_consen    1 TNDKVRDKARKLLYKALQKRSDE-QD------DPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRR   73 (115)
T ss_dssp             -TCHHHHHHHHHHHHHHHHCCCC-CC------CTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHH
T ss_pred             CCcHHHHHHHHHHHHHHHhcCcc-cc------chhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHH
Confidence            68999999999999999986544 11      234667999999999999998888999999999999999999999999


Q ss_pred             hhhcCCCCccccccCCcccCCCHHHHhhhhC
Q 038232          187 NVHLGQVKPETIVGMTAKEMAGDKMLSCYQR  217 (217)
Q Consensus       187 ~VL~G~isp~~Lv~Ms~eEMASdelk~e~q~  217 (217)
                      +||+|+|+|.+||.|+++||||+++|+++++
T Consensus        74 ~il~g~i~p~~lv~ms~~Elas~e~k~~~e~  104 (115)
T PF07500_consen   74 RILSGEISPEELVTMSPEELASEELKEEREK  104 (115)
T ss_dssp             HHHHSSSTTCHHHHCTTTTTTTSCCCCCHCC
T ss_pred             HHHcCCCCHHHHhcCCHHHhCCHHHHHHHHH
Confidence            9999999999999999999999999988753

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

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

Probab=99.45  E-value=3e-14  Score=140.80  Aligned_cols=76  Identities=29%  Similarity=0.454  Sum_probs=70.7

Q ss_pred             cchHHHHHHHHHHHHHhhc-CCChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232          141 CDSVRVAIALESAMFEKWD-RYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ  216 (217)
Q Consensus       141 ~~~~~lA~~IE~alf~~~~-~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q  216 (217)
                      .++.-++..||..||..|+ +.+..|+.|+|+|+|||||++||.||.+|+.|+|++++||.|+++|||+.++.+.++
T Consensus       267 ~d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rE  343 (778)
T KOG1634|consen  267 QDPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWRE  343 (778)
T ss_pred             cchhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHH
Confidence            3555778899999999999 778999999999999999999999999999999999999999999999999988765

>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere)

Probab=96.69  E-value=0.0014  Score=48.08  Aligned_cols=24  Identities=25%  Similarity=0.610  Sum_probs=22.3

Q ss_pred             cccchHHHHHHHHHHHHHHHHHHH
Q 038232            2 KASSRKKIQDFASDLIVSWRNMSL   25 (217)
Q Consensus         2 ~~~~~~~i~~~A~~l~~~WKkvv~   25 (217)
                      .+|++++|+.+|++||..||++|.
T Consensus        51 rkh~~~~I~~~A~~Li~~WK~~v~   74 (75)
T smart00509       51 RKHKNEEIRKLAKKLIKSWKKLVY   74 (75)
T ss_pred             HcCCcHHHHHHHHHHHHHHHHHhc
Confidence            579999999999999999999984

>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription

Probab=95.37  E-value=0.017  Score=39.02  Aligned_cols=22  Identities=23%  Similarity=0.588  Sum_probs=19.6

Q ss_pred             cc-chHHHHHHHHHHHHHHHHHH
Q 038232            3 AS-SRKKIQDFASDLIVSWRNMS   24 (217)
Q Consensus         3 ~~-~~~~i~~~A~~l~~~WKkvv   24 (217)
                      +| ++.+|+..|++||..||++|
T Consensus        30 k~~~~~~i~~~A~~Li~~Wk~~v   52 (53)
T PF08711_consen   30 KHSENPEIRKLAKELIKKWKRIV   52 (53)
T ss_dssp             HCTS-HHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHhHhc
Confidence            56 99999999999999999987

The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	217
2lw4_A	113	Solution Nmr Structure Of Human Transcription Elong		7e-10
2dme_A	120	Solution Structure Of The Tfiis Domain Ii Of Human		1e-08
3ndq_A	108	Structure Of Human Tfiis Domain Ii Length = 108		1e-07
1pqv_S	309	Rna Polymerase Ii-Tfiis Complex Length = 309		5e-05
1y1v_S	179	Refined Rna Polymerase Ii-tfiis Complex Length = 17		7e-04
3po3_S	178	Arrested Rna Polymerase Ii Reactivation Intermediat		8e-04

>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 = 60.5 bits (145), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 42/70 (60%)
Query: 142 DSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGM 201
           D  R++  +E  +F      D  YK + ++ + NLKD KNPD RRNV  G + P+ I  M
Sbjct: 36  DCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVM 95
Query: 202 TAKEMAGDKM 211
           T++EMA D++
Sbjct: 96  TSEEMASDEL 105

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 62/109 (56%), Gaps = 5/109 (4%)
Query: 109 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIK 168
           D  R+ VR  + D L K   +++ ++ +E  A    +VA  +E  +F  +   D  YK K
Sbjct: 10  DQIRQSVRHSLKDILMKRLTDSNLKVPEEKAA----KVATKIEKELFSFFRDTDAKYKNK 65
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR 217
           Y++++ NLKDPKN    + V  G+V P+ ++ M+ +E+A  K L+ ++R
Sbjct: 66  YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELAS-KELAAWRR 113

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 150 LESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGD 209
           +E A++++    D  YK + ++ + NLKD KNP+ R+NV  G + P+    MTA+EMA D
Sbjct: 48  IEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD 107
Query: 210 K 210
           +
Sbjct: 108 E 108

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 50/211 (23%), Positives = 86/211 (40%), Gaps = 32/211 (15%)
Query: 2   KASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYT---IPGDIEPAKIEKVDKRTSEEC 58
           K S+  +I      +I SW++   +  R  +   +     PG+ E       DK T  E 
Sbjct: 54  KKSTNVEISKLVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAE-------DKTTVGES 106
Query: 59  QEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREK 118
                     V  V Q A+S S  + + + V T+  NS ++   + I     +   +R++
Sbjct: 107 ----------VNGVQQPASSQSDAMKQDKYVSTKPRNSKNDGVDTAI-----YHHKLRDQ 151
Query: 119 VCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIKYKAVLGNL 176
           V  AL  V  +  E     +     +  A A+ES M      D  +  YK +Y+ +  N+
Sbjct: 152 VLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNV 206
Query: 177 KDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
               NPD +  +  G + PE +    AK++A
Sbjct: 207 ISKNNPDLKHKIANGDITPEFLATCDAKDLA 237

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 111 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIK 168
           +   +R++V  AL  V  +  E     +     +  A A+ES M      D  +  YK +
Sbjct: 14  YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 68
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
           Y+ +  N+    NPD +  +  G + PE +    AK++A
Sbjct: 69  YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 107

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 111 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIK 168
           +   +R++V  AL  V  +  E     +     +  A A+ES M      D  +  YK +
Sbjct: 13  YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 67
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
           Y+ +  N+    NPD +  +  G + PE +    AK++A
Sbjct: 68  YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 106

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	217
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	1e-20
3ndq_A	108	Transcription elongation factor A protein 1; helix	9e-20
3po3_S	178	Transcription elongation factor S-II; RNA polymera	7e-15
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	7e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05

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

 Score = 82.7 bits (204), Expect = 1e-20
 Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 4/104 (3%)

Query: 108 NDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKI 167
            D  R+ VR  + D L K   +++ ++ +E     + +VA  +E  +F  +   D  YK 
Sbjct: 9   ADQIRQSVRHSLKDILMKRLTDSNLKVPEE----KAAKVATKIEKELFSFFRDTDAKYKN 64

Query: 168 KYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
           KY++++ NLKDPKN    + V  G+V P+ ++ M+ +E+A  ++
Sbjct: 65  KYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKEL 108

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

 Score = 80.0 bits (197), Expect = 9e-20
 Identities = 31/105 (29%), Positives = 49/105 (46%), Gaps = 7/105 (6%)

Query: 106 RCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPY 165
             +D  R   RE +  AL                  D   +   +E A++++    D  Y
Sbjct: 11  STSDSVRLKCREMLAAALRTGDDYIAIG-------ADEEELGSQIEEAIYQEIRNTDMKY 63

Query: 166 KIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDK 210
           K + ++ + NLKD KNP+ R+NV  G + P+    MTA+EMA D+
Sbjct: 64  KNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 108

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

 Score = 68.7 bits (167), Expect = 7e-15
 Identities = 28/118 (23%), Positives = 50/118 (42%), Gaps = 11/118 (9%)

Query: 96  SSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMF 155
           +S N        +   R+ V + + D L+K S    + I         +  A A+ES M 
Sbjct: 2   NSKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMN 52

Query: 156 E--KWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
           +    D  +  YK +Y+ +  N+    NPD +  +  G + PE +    AK++A   +
Sbjct: 53  KVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPL 110

>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 = 62.5 bits (150), Expect = 7e-12
 Identities = 39/210 (18%), Positives = 75/210 (35%), Gaps = 22/210 (10%)

Query: 2   KASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEI 61
           K S+  +I      +I SW++   +  R  +   +        A+ +     +    Q+ 
Sbjct: 54  KKSTNVEISKLVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQ- 112

Query: 62  SGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCD 121
                           S  S+ ++ +  V+ K  +S N        +   R+ V + + D
Sbjct: 113 --------------PASSQSDAMKQDKYVSTKPRNSKNDGVDTAIYHHKLRDQVLKALYD 158

Query: 122 ALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKN 181
            L+K S    + I            AI  E       D  +  YK +Y+ +  N+    N
Sbjct: 159 VLAKESEHPPQSILHTA-------KAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNN 211

Query: 182 PDFRRNVHLGQVKPETIVGMTAKEMAGDKM 211
           PD +  +  G + PE +    AK++A   +
Sbjct: 212 PDLKHKIANGDITPEFLATCDAKDLAPAPL 241

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

 Score = 42.5 bits (99), Expect = 5e-05
 Identities = 29/243 (11%), Positives = 67/243 (27%), Gaps = 61/243 (25%)

Query: 1   CKASSRKKIQDFASDLIVSWRNMS--------LEQMRD-----------ERKGSYTIPGD 41
           C +   +   DF     + W N+         LE ++                S  I   
Sbjct: 171 CLSYKVQCKMDFK----IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226

Query: 42  IEPAKIEKVD---KRTSEEC----QEISGVGIVKVQKVDQNATSLSSNVV-RPESVVTEK 93
           I   + E       +  E C      +           + +   L   +  R + V    
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA--FNLSCKIL---LTTRFKQV---- 277

Query: 94  TNSSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESA 153
           T+     + + I  +     +  ++V   L K      +++  E     +    +++ + 
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE--VLTTNPRRLSIIAE 335

Query: 154 MFEK----WDRYDGPYKIKYKAVLGNLKDPKNPD-----------FRRNVHLGQVKPETI 198
                   WD +      K   ++ +  +   P            F  + H+    P  +
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI----PTIL 391

Query: 199 VGM 201
           + +
Sbjct: 392 LSL 394

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	217
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.98
2lw4_A	113	Transcription elongation factor A protein 2; struc	99.97
3ndq_A	108	Transcription elongation factor A protein 1; helix	99.97
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	99.97
3po3_S	178	Transcription elongation factor S-II; RNA polymera	99.95
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	97.0

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

Probab=99.98  E-value=7.3e-32  Score=242.45  Aligned_cols=189  Identities=19%  Similarity=0.257  Sum_probs=126.9

Q ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHhhhccCCCccCCCCCCcchhhccccccccccccccccccccccccccccccCCC
Q 038232            2 KASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSS   81 (217)
Q Consensus         2 ~~~~~~~i~~~A~~l~~~WKkvv~~e~~~~~~~~~~~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~   81 (217)
                      .+|++.+|+++|++||..||++|.+++.++.+......++ +..+.+.+++...     ++. . ..+. +...++.   
T Consensus        54 rkh~~~~v~~~Ak~Li~~WK~~v~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-----~~~-~-~~~~-~~~~~~~---  121 (309)
T 1pqv_S           54 KKSTNVEISKLVKKMISSWKDAINKNKRSRQAQQHHQDHA-PGNAEDKTTVGES-----VNG-V-QQPA-SSQSDAM---  121 (309)
T ss_pred             HcCCCHHHHHHHHHHHHHHHHHHHHhccCCcccccccccc-cccccCCCCCCCC-----cCC-C-CCCc-ccccccc---
Confidence            5899999999999999999999999977554322111010 0000011111000     000 0 0000 0000000   


Q ss_pred             CCCCCCccccccCCCCCCC--CccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhc
Q 038232           82 NVVRPESVVTEKTNSSDNL--SRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWD  159 (217)
Q Consensus        82 ~~~~~~~v~~e~~ss~~~~--~~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~  159 (217)
                        +   +...+.+++.+..  ...+..++|++|++|+++|+++|.....+.+.         ++..+|.+||.+||+.|+
T Consensus       122 --~---~~~~~~~~~~~~~~~~~~~~~~~d~~R~k~r~~L~~aL~~~~~~~~~---------~~~~~A~~IE~al~~~~~  187 (309)
T 1pqv_S          122 --K---QDKYVSTKPRNSKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ---------SILHTAKAIESEMNKVNN  187 (309)
T ss_pred             --c---CCCCCCCCCCCCCCCCCCcCcCChHHHHHHHHHHHHHHhcCCCccch---------hHHHHHHHHHHHHHHHhC
Confidence              0   0000001111111  22255789999999999999999874332221         456999999999999998


Q ss_pred             CCChh--hHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232          160 RYDGP--YKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ  216 (217)
Q Consensus       160 ~~~~~--Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q  216 (217)
                      +++..  |++++|+|+|||||++||.||++||.|+|+|++||.|+++||||+++|++++
T Consensus       188 ~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr~~vl~g~i~p~~lv~Ms~eElasde~k~~~~  246 (309)
T 1pqv_S          188 CDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIE  246 (309)
T ss_pred             CCchhHHHHHHHHHHHHHcCcCCChHHHHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHH
Confidence            87777  9999999999999999999999999999999999999999999999998875

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

Probab=99.97  E-value=1.5e-33  Score=220.90  Aligned_cols=107  Identities=32%  Similarity=0.481  Sum_probs=95.6

Q ss_pred             cccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCCCh
Q 038232          103 SMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNP  182 (217)
Q Consensus       103 s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp  182 (217)
                      +.+.++|++|++|+++|+++|....    +..   ....++..+|.+||.+||..|+.++..|++++|||+|||||++||
T Consensus         4 p~p~t~D~vRdk~~e~L~~aL~~~~----~~~---~~~~~~~~~A~~IE~~~f~~~~~~~~~Yk~k~Rsl~~NLkd~~Np   76 (113)
T 2lw4_A            4 PVPVTCDAVRNKCREMLTAALQTDH----DHV---AIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNP   76 (113)
T ss_dssp             CSCCCCSTTHHHHHHHHHHHHHSST----HHH---HHTCCHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHCSSSS
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCC----Ccc---cccchHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCH
Confidence            4677999999999999999998521    111   123567799999999999999998999999999999999999999


Q ss_pred             hhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232          183 DFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ  216 (217)
Q Consensus       183 ~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q  216 (217)
                      +||++||+|+|+|++||.||++||||+|+|+.++
T Consensus        77 ~Lr~~vl~G~i~p~~l~~Ms~eEmAs~elk~~r~  110 (113)
T 2lw4_A           77 DLRRNVLCGAITPQQIAVMTSEEMASDELKEIRK  110 (113)
T ss_dssp             HHHHHHHTTSSCHHHHHHSCHHHHHCTTTTTCSS
T ss_pred             HHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHH
Confidence            9999999999999999999999999999999876

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

Probab=99.97  E-value=5.1e-32  Score=210.68  Aligned_cols=103  Identities=30%  Similarity=0.452  Sum_probs=87.4

Q ss_pred             CccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCC
Q 038232          101 SRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPK  180 (217)
Q Consensus       101 ~~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~k  180 (217)
                      +.+.+.++|++|++|+++|+++|....     +..+.  .+++..+|.+||.+||+.|+.++..|++++|||+|||||++
T Consensus         6 ~~~~~~t~d~vR~k~~~lL~~aL~~~~-----d~~~~--~~~~~~lA~~IE~~if~~~~~~~~~Yk~k~Rsl~fNLKd~k   78 (108)
T 3ndq_A            6 TPRAPSTSDSVRLKCREMLAAALRTGD-----DYIAI--GADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAK   78 (108)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHTTGGG-----HHHHH--TCCHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHTCTT
T ss_pred             CCCCCCCCChHHHHHHHHHHHHHHcCC-----CCCcc--cccHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCC
Confidence            456678999999999999999999732     22211  25677999999999999999888999999999999999999


Q ss_pred             ChhhHhhhhcCCCCccccccCCcccCCCHH
Q 038232          181 NPDFRRNVHLGQVKPETIVGMTAKEMAGDK  210 (217)
Q Consensus       181 Np~Lr~~VL~G~isp~~Lv~Ms~eEMASde  210 (217)
                      ||+||++||+|+|+|++||+||++||||+|
T Consensus        79 Np~Lr~~vl~G~isp~~lv~Ms~eEmAS~E  108 (108)
T 3ndq_A           79 NPNLRKNVLCGNIPPDLFARMTAEEMASDE  108 (108)
T ss_dssp             CHHHHHHHHHTSSCHHHHHHCCTTTC----
T ss_pred             CHHHHHHHHcCCcCHHHHhCCCHHHccCCC
Confidence            999999999999999999999999999987

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

Probab=99.97  E-value=5.6e-32  Score=213.97  Aligned_cols=107  Identities=29%  Similarity=0.478  Sum_probs=95.2

Q ss_pred             CChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCCChhhHh
Q 038232          107 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRR  186 (217)
Q Consensus       107 ~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~  186 (217)
                      ++|++|++|+++|+++|.....+.+...    ..+++..+|.+||.+||+.|+.++..|++++|||+|||||++||+||+
T Consensus         8 ~~d~~Rd~~r~~L~eaL~~~~~~~~~~~----~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~Lr~   83 (120)
T 2dme_A            8 SADQIRQSVRHSLKDILMKRLTDSNLKV----PEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFK   83 (120)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTTTCCC----CHHHHHHHHHHHHHHHHHHHCSCSHHHHHHHHHHTHHHHSSSCCSHHH
T ss_pred             CCchHHHHHHHHHHHHHHHhcccccccc----chhHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            5689999999999999998766543211    123567999999999999999888999999999999999999999999


Q ss_pred             hhhcCCCCccccccCCcccCCCHHHHhhhhC
Q 038232          187 NVHLGQVKPETIVGMTAKEMAGDKMLSCYQR  217 (217)
Q Consensus       187 ~VL~G~isp~~Lv~Ms~eEMASdelk~e~q~  217 (217)
                      +||+|+|+|++||.||++||||+|+|+++++
T Consensus        84 ~vl~G~i~p~~lv~Ms~eEmAS~elk~~r~~  114 (120)
T 2dme_A           84 KVLKGEVTPDHLIRMSPEELASKELAAWRRR  114 (120)
T ss_dssp             HHHHTSSCTTHHHHSCTTTTTTCCSTTTCTT
T ss_pred             HHHcCCCCHHHHhcCCHHHcCCHHHHHHHHH
Confidence            9999999999999999999999999999874

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

Probab=99.95  E-value=1e-28  Score=206.85  Aligned_cols=107  Identities=22%  Similarity=0.346  Sum_probs=90.3

Q ss_pred             CccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcC-CCh-hhHHHHHHHHhhcCC
Q 038232          101 SRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDR-YDG-PYKIKYKAVLGNLKD  178 (217)
Q Consensus       101 ~~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~-~~~-~Yk~k~RSl~fNLKD  178 (217)
                      ...++.++|++|++|+++|++||.....+.+.         ++..+|.+||.+||+.|++ ++. .|++++|||+|||||
T Consensus         7 ~v~~~~~~d~vRdk~~~lL~~aL~~~~~~~~~---------~~~~~A~~IE~~if~~~~~~~~~k~Yk~k~Rsl~~NLKd   77 (178)
T 3po3_S            7 GVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ---------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVIS   77 (178)
T ss_dssp             --------CHHHHHHHHHHHHHTTSSSSCSTT---------HHHHHHHHHHHHHHHHTSCSSSSTHHHHHHHHHHHHHHS
T ss_pred             CcCcCcCCChHHHHHHHHHHHHHhcCCCCchh---------hHHHHHHHHHHHHHHHhcCCCchhhhhhhhhHHHHHcCC
Confidence            35667899999999999999999986655443         3458999999999999986 455 899999999999999


Q ss_pred             CCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232          179 PKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ  216 (217)
Q Consensus       179 ~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q  216 (217)
                      ++||+||++||+|+|+|++||.|+++||||+|+|++++
T Consensus        78 ~~N~~Lr~~vl~g~isp~~lv~Ms~eElas~elk~~~e  115 (178)
T 3po3_S           78 KNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIE  115 (178)
T ss_dssp             SSCSHHHHHHHHCCCTTHHHHCCTTTTSSCSHHHHHHH
T ss_pred             CCCHHHHHHHhcCCCCHHHHHhcCchhhCCHHHHHHHH
Confidence            99999999999999999999999999999999999875

>1wjt_A Transcription elongation factor S-II protein 3; four-helix bundle, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.48.3.1

Probab=97.00  E-value=0.00014  Score=55.56  Aligned_cols=28  Identities=21%  Similarity=0.374  Sum_probs=24.5

Q ss_pred             ccc-chHHHHHHHHHHHHHHHHHHHHHhh
Q 038232            2 KAS-SRKKIQDFASDLIVSWRNMSLEQMR   29 (217)
Q Consensus         2 ~~~-~~~~i~~~A~~l~~~WKkvv~~e~~   29 (217)
                      ++| |+++|+.+|++||..||++|.++..
T Consensus        63 rKh~~~~~V~~lAk~Lv~~WK~~v~~~~~   91 (103)
T 1wjt_A           63 RKHCSDKEVVSLAKVLIKNWKRLLDSPRT   91 (103)
T ss_dssp             HHHCCCSHHHHHHHHHHHHHHHHTCCSCC
T ss_pred             HccCCcHHHHHHHHHHHHHHHHHHHHhcc
Confidence            356 9999999999999999999988643

---

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	217
d1enwa_	114	a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak	1e-18

>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 = 76.0 bits (187), Expect = 1e-18
 Identities = 25/102 (24%), Positives = 46/102 (45%), Gaps = 11/102 (10%)

Query: 108 NDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDR--YDGPY 165
           +   R+ V + + D L+K S    + I         +  A A+ES M +  +    +  Y
Sbjct: 19  HHKLRDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDTNEAAY 69

Query: 166 KIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
           K +Y+ +  N+    NPD +  +  G + PE +    AK++A
Sbjct: 70  KARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	217
d1enwa_	114	Elongation factor TFIIS domain 2 {Baker's yeast (S	99.92
d1wjta_	103	Transcription elongation factor S-II protein 3 {Mo	95.87

>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=99.92  E-value=2e-26  Score=178.80  Aligned_cols=98  Identities=24%  Similarity=0.386  Sum_probs=86.6

Q ss_pred             ccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCC--ChhhHHHHHHHHhhcCCC
Q 038232          102 RSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRY--DGPYKIKYKAVLGNLKDP  179 (217)
Q Consensus       102 ~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~--~~~Yk~k~RSl~fNLKD~  179 (217)
                      .....++|++|++|+++|+++|.....+.++         ....+|.+||.+||..|+..  +..|++|+|||+|||||+
T Consensus        13 v~~~~~~d~~R~~~~~~L~~aL~~~~~~~~~---------~~~~la~~IE~~lf~~~~~~~~~~~Y~~k~rsi~~NLkd~   83 (114)
T d1enwa_          13 VDTAIYHHKLRDQVLKALYDVLAKESEHPPQ---------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISK   83 (114)
T ss_dssp             CCCCSSTTTTHHHHHHHHHHHHHHHCSSSCS---------CHHHHHHHHTTTTTSSCTTTTTHHHHHHHHHHHHHHHTTS
T ss_pred             CCCccCCcHHHHHHHHHHHHHHhCcCccchh---------HHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHcCcc
Confidence            4456789999999999999999976554443         34589999999999999743  368999999999999999


Q ss_pred             CChhhHhhhhcCCCCccccccCCcccCCC
Q 038232          180 KNPDFRRNVHLGQVKPETIVGMTAKEMAG  208 (217)
Q Consensus       180 kNp~Lr~~VL~G~isp~~Lv~Ms~eEMAS  208 (217)
                      +||+||++|++|+|+|++||.|+++|||+
T Consensus        84 ~N~~L~~~v~~g~i~p~~l~~M~~~ElaP  112 (114)
T d1enwa_          84 NNPDLKHKIANGDITPEFLATCDAKDLAP  112 (114)
T ss_dssp             CCCCTTTHHHHCSSCCSSHHHHTTTTTCS
T ss_pred             chHHHHHHHHcCCCCHHHHhCCCHHHcCC
Confidence            99999999999999999999999999997

>d1wjta_ a.48.3.1 (A:) Transcription elongation factor S-II protein 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: N-cbl like
superfamily: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
family: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
domain: Transcription elongation factor S-II protein 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.87  E-value=0.00098  Score=48.90  Aligned_cols=27  Identities=22%  Similarity=0.354  Sum_probs=22.9

Q ss_pred             cc-chHHHHHHHHHHHHHHHHHHHHHhh
Q 038232            3 AS-SRKKIQDFASDLIVSWRNMSLEQMR   29 (217)
Q Consensus         3 ~~-~~~~i~~~A~~l~~~WKkvv~~e~~   29 (217)
                      +| ++++|+.+|+.||..||++|..+..
T Consensus        64 K~~~~~~v~~lAk~Lv~~WK~~v~~~~~   91 (103)
T d1wjta_          64 KHCSDKEVVSLAKVLIKNWKRLLDSPRT   91 (103)
T ss_dssp             HHCCCSHHHHHHHHHHHHHHHHTCCSCC
T ss_pred             ccCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            45 4689999999999999999977644