Citrus Sinensis ID: 020949

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------32
Protein Sequence
MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQRM
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccHHHHHcccHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHcccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccccHHHHHcHHccccccHHHccccHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccEHHHHHHccccccHHHHcccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcc
Coil and Loop (DISEMBL)
MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQlnksditcpllVSTQLVRYLlpltehptkkIQDFASDLIVSWRDMFLEQIrdekkgsctipgdtepakiekvdkrtsEECQEISGVGIVKVqkvdqnstssssnvvRSEIveteetnsadnvnvgnsiteegeaSGIILHKlssskircndcFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFekwgrsdgpykIKYRAVlgnlkdpknpdfrrkvlfgqvkpetvvgMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQRM
Flexible Loop (DISEMBL)
MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRdekkgsctipgdtepakiekvdkrtseecqeisgvgivkvqkvdqnstssssnvvrseiveteetnsadnvnvgNSITEEGEASGIIlhklssskirCNDCFREVVREKVCDALskvsgeadeeirdevnacdSVRVAIALESAmfekwgrsdgpyKIKYRAVlgnlkdpknpdfrrkvlfgqvkpetvvgmtakemasDEMLRSYQHEDEERARLWKEHTRKYMQRM
Low Complexity Region (SEG)
MEKKVMQLCEEAKRGaeaavmaegeaekaWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQnstssssnvvrsEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQRM
Disordered region (IsUnstruct)
************************EAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIR**********************************VGIV**********************************************GIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVV**************************************
Disordered Region (DISOPRED)
**KKVMQLCEEA**********************IDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPT**IQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTS*****************************************************EGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKE********************************
Disordered Region (DISEMBL)
MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKI***********QEISGVGIVKVQKV*************SEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALS*********IRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQRM
Disordered Region (DISPRO)
****VMQLCEEAKRGAEAAVMA**E*EKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLE***************************************************************************************************RCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTR******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQRM
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	319	2.2.26 [Sep-21-2011]
P23881	347	Transcription elongation	yes	no	0.294	0.270	0.381	2e-11
Q15560	299	Transcription elongation	yes	no	0.219	0.234	0.442	9e-11
Q92576	2039	PHD finger protein 3 OS=H	no	no	0.357	0.055	0.336	1e-10
Q148K0	300	Transcription elongation	yes	no	0.206	0.22	0.469	3e-10
Q2KI09	349	Transcription elongation	no	no	0.294	0.269	0.371	4e-10
O75764	348	Transcription elongation	no	no	0.294	0.270	0.371	4e-10
P23193	301	Transcription elongation	no	no	0.711	0.754	0.268	2e-09
Q29RL9	301	Transcription elongation	no	no	0.241	0.255	0.392	3e-09
Q4KLL0	301	Transcription elongation	no	no	0.241	0.255	0.392	3e-09
P10711	301	Transcription elongation	no	no	0.241	0.255	0.392	4e-09

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

 Score = 70.1 bits (170), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 61/97 (62%), Gaps = 3/97 (3%)

Query: 197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
           VR+K  + LS  + +A++  +D    CD  ++A  +E  ++++   +D  Y+ + R+ + 
Sbjct: 186 VRDKCVEMLS-AALKAEDNFKDYGVNCD--KLASEIEDHIYQELKSTDMKYRNRVRSRIS 242

Query: 257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
           NLKDP+NP  RR VL G + PE +  MTA+EMASDE+
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|Q15560|TCEA2_HUMAN Transcription elongation factor A protein 2 OS=Homo sapiens GN=TCEA2 PE=1 SV=1

 Score = 67.8 bits (164), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 45/70 (64%)

Query: 224 DSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGM 283
           D  R++  +E  +F   G +D  YK + R+ + NLKD KNPD RR VL G + P+ +  M
Sbjct: 162 DCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVM 221

Query: 284 TAKEMASDEM 293
           T++EMASDE+
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|Q92576|PHF3_HUMAN PHD finger protein 3 OS=Homo sapiens GN=PHF3 PE=1 SV=3

 Score = 67.8 bits (164), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 40/119 (33%), Positives = 70/119 (58%), Gaps = 5/119 (4%)

Query: 176  GII-LHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALES 234
            G++ +H  +S+     D  R+ VR  + D L K   +++ ++ +E  A    +VA  +E 
Sbjct: 909  GVLNVHPAASASKPSADQIRQSVRHSLKDILMKRLTDSNLKVPEEKAA----KVATKIEK 964

Query: 235  AMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
             +F  +  +D  YK KYR+++ NLKDPKN    +KVL G+V P+ ++ M+ +E+AS E+
Sbjct: 965  ELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKEL 1023

Homo sapiens (taxid: 9606)

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

 Score = 66.2 bits (160), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 43/66 (65%)

Query: 228 VAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKE 287
           +A  +E  +F   G +D  YK + R+ L NLKD KNP  RRKVL G + P+ +  MT++E
Sbjct: 167 LAGQIEECIFRDVGNTDMKYKNRVRSRLSNLKDAKNPGLRRKVLCGAITPQQIAVMTSEE 226

Query: 288 MASDEM 293
           MASDE+
Sbjct: 227 MASDEL 232

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

 Score = 65.9 bits (159), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 60/97 (61%), Gaps = 3/97 (3%)

Query: 197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
           VR+K  + LS  + +AD++ +D    CD  ++A  +E  ++++   +D  Y+ + R+ + 
Sbjct: 188 VRDKCVEMLS-AALKADDDYKDYGVNCD--KMASEIEDHIYQELKSTDMKYRNRVRSRIS 244

Query: 257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
           NLKDP+NP  RR VL G +    +  MTA+EMASDE+
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|O75764|TCEA3_HUMAN Transcription elongation factor A protein 3 OS=Homo sapiens GN=TCEA3 PE=2 SV=2

 Score = 65.9 bits (159), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 60/97 (61%), Gaps = 3/97 (3%)

Query: 197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
           VR+K  + LS  + +AD++ +D    CD  ++A  +E  ++++   +D  Y+ + R+ + 
Sbjct: 187 VRDKCVEMLS-AALKADDDYKDYGVNCD--KMASEIEDHIYQELKSTDMKYRNRVRSRIS 243

Query: 257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
           NLKDP+NP  RR VL G +    +  MTA+EMASDE+
Sbjct: 244 NLKDPRNPGLRRNVLSGAISAGLIAKMTAEEMASDEL 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|P23193|TCEA1_HUMAN Transcription elongation factor A protein 1 OS=Homo sapiens GN=TCEA1 PE=1 SV=2

 Score = 63.9 bits (154), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 128/294 (43%), Gaps = 67/294 (22%)

Query: 27  EKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPT-KKIQDFASDLIVSWRDM 85
           +K   A  +D L +L    +T  LL ST++   +  + +  T +++   A  LI SW+ +
Sbjct: 17  QKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWKKL 76

Query: 86  F----LEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSS 141
                 E+  DEKK         EPA    +  + S E +E S               +S
Sbjct: 77  LDGPSTEKDLDEKK--------KEPA----ITSQNSPEAREES---------------TS 109

Query: 142 SSNVVRSEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKV 201
           S NV   +    +ETN+ D     +S       S        S +++C    RE++   +
Sbjct: 110 SGNVSNRK----DETNARDTY--VSSFPRAPSTS-------DSVRLKC----REMLAAAL 152

Query: 202 CDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDP 261
                 ++  ADEE            +   +E A++++   +D  YK + R+ + NLKD 
Sbjct: 153 RTGDDYIAIGADEE-----------ELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDA 201

Query: 262 KNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKY 315
           KNP+ R+ VL G + P+    MTA+EMASDE+        E R  L KE  R++
Sbjct: 202 KNPNLRKNVLCGNIPPDLFARMTAEEMASDEL-------KEMRKNLTKEAIREH 248

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

Homo sapiens (taxid: 9606)

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

 Score = 62.8 bits (151), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 50/84 (59%), Gaps = 7/84 (8%)

Query: 232 LESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASD 291
           +E A++++   +D  YK + R+ + NLKD KNP+ R+ VL G + P+    MTA+EMASD
Sbjct: 172 IEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD 231

Query: 292 EMLRSYQHEDEERARLWKEHTRKY 315
           E+        E R  L KE  R++
Sbjct: 232 EL-------KEMRKNLTKEAIREH 248

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

Bos taurus (taxid: 9913)

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

 Score = 62.8 bits (151), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 50/84 (59%), Gaps = 7/84 (8%)

Query: 232 LESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASD 291
           +E A++++   +D  YK + R+ + NLKD KNP+ R+ VL G + P+    MTA+EMASD
Sbjct: 172 IEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD 231

Query: 292 EMLRSYQHEDEERARLWKEHTRKY 315
           E+        E R  L KE  R++
Sbjct: 232 EL-------KEMRKNLTKEAIREH 248

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

Rattus norvegicus (taxid: 10116)

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

 Score = 62.4 bits (150), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 50/84 (59%), Gaps = 7/84 (8%)

Query: 232 LESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASD 291
           +E A++++   +D  YK + R+ + NLKD KNP+ R+ VL G + P+    MTA+EMASD
Sbjct: 172 IEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD 231

Query: 292 EMLRSYQHEDEERARLWKEHTRKY 315
           E+        E R  L KE  R++
Sbjct: 232 EL-------KEMRKNLTKEAIREH 248

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

Mus musculus (taxid: 10090)

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	319
224087871	352	predicted protein [Populus trichocarpa]	0.877	0.795	0.398	5e-51
225439709	367	PREDICTED: transcription elongation fact	0.815	0.708	0.422	1e-50
449441244	369	PREDICTED: transcription elongation fact	0.821	0.710	0.425	4e-49
224139382	334	predicted protein [Populus trichocarpa]	0.840	0.802	0.386	5e-49
356509090	368	PREDICTED: putative transcription elonga	0.918	0.796	0.393	1e-47
255637690	368	unknown [Glycine max]	0.918	0.796	0.390	3e-47
255575598	342	transcription elongation factor s-II, pu	0.752	0.701	0.416	2e-46
356516223	367	PREDICTED: transcription elongation fact	0.915	0.795	0.4	6e-46
255559741	330	transcription elongation factor s-II, pu	0.821	0.793	0.410	3e-45
255641093	350	unknown [Glycine max]	0.915	0.834	0.393	4e-45

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

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 120/301 (39%), Positives = 181/301 (60%), Gaps = 21/301 (6%)

Query: 1   MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYL 60
           ME + ++L +EAK+ A+A++  +  +       C+D+L QL K  +T  LLVSTQ+ + L
Sbjct: 1   MEMEFVELFDEAKKAADASLNDDVSSSGPEVTRCVDSLKQLRKFKVTSELLVSTQVGKKL 60

Query: 61  LPLTEHPTKKIQDFASDLIVSWRDMFLEQIR------DEKKGSCTIPGDTEPAKIEKVDK 114
            PL +HP +KI+  ASDL+  W+ M +++ R      D K         +E  K+EK+ K
Sbjct: 61  RPLAKHPKEKIRAVASDLLEMWKKMVIDETRKKNGSIDSKSSVKAEVSKSETVKVEKLRK 120

Query: 115 RTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGNSITEEGEA 174
            +  + +  S    VKV+K+DQ+ T     + + EI                S  ++   
Sbjct: 121 TSVVKVERASTSETVKVEKMDQDKTVKVEKMSKQEI--------------QTSSVKQPSQ 166

Query: 175 SGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALES 234
           S I   KL +  ++CND  R+ +RE + +ALSKV+ EADE+IRDEV ACD +RVA+++ES
Sbjct: 167 SPIGPPKLKTL-VKCNDALRDKIRELLAEALSKVASEADEDIRDEVEACDPIRVAVSVES 225

Query: 235 AMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEML 294
            MFEK GRS+G  K+KYR+++ N+KD  NPDFRRKVL G+V+PE +V M  +EMAS++  
Sbjct: 226 MMFEKLGRSNGAQKLKYRSIMFNIKDQNNPDFRRKVLLGEVQPERLVTMGPEEMASEQRK 285

Query: 295 R 295
           R
Sbjct: 286 R 286

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 114/270 (42%), Positives = 171/270 (63%), Gaps = 10/270 (3%)

Query: 34  CIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDE 93
           C+DAL QL    +T   L STQ+ + L  LT+HP  KIQ  ASDL+  W+ + +++ R++
Sbjct: 34  CVDALKQLKSFPVTYEALASTQVGKRLRHLTKHPKGKIQSLASDLLEMWKKVVIDETRNK 93

Query: 94  KKGSCTIPGD-------TEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVV 146
           K G     G        TE  K+E   K    + ++ S V  VK++K D+ S++   +V 
Sbjct: 94  KNGGLDNNGSAKAEVSKTETVKVEMAHKAGGVKVEKASKVETVKIEKFDRGSSTKPGSVS 153

Query: 147 RSEIVETEE-TNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDAL 205
           RSE ++ E+   + D     +S+ +  +AS     KL++  I+CND  R+ VRE + +AL
Sbjct: 154 RSETIKVEKRVENVDERKQFSSVKKPPQASNGP-PKLTAM-IKCNDALRDKVRELLAEAL 211

Query: 206 SKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPD 265
            KV+ EADE+I+DEVNACD +RVA+++ES MFEK GRS+G  K KYR+++ N+KDP NPD
Sbjct: 212 FKVASEADEDIKDEVNACDPIRVAVSVESVMFEKMGRSNGTQKFKYRSIMFNIKDPNNPD 271

Query: 266 FRRKVLFGQVKPETVVGMTAKEMASDEMLR 295
            RRKVL G+VKP+ ++ M+ +EMAS++  R
Sbjct: 272 LRRKVLLGEVKPDRLINMSPEEMASNQRQR 301

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 123/289 (42%), Positives = 174/289 (60%), Gaps = 27/289 (9%)

Query: 34  CIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDE 93
           C+DAL QL K  +T  +LVSTQ+ + L  LT+HP KKIQ+ ASDLI  W+++ +++    
Sbjct: 33  CLDALRQLKKFPVTYQILVSTQVGKRLRHLTKHPKKKIQEHASDLIEMWKEIVIKETNKN 92

Query: 94  KKGSCTIPGDT--------EPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNV 145
           KK       D+        E  K+EK  K +S + + +S     KV++ D+N  +SS   
Sbjct: 93  KKNGNASSKDSPKIGSPSAESVKVEKFQKSSSMKVERVS-----KVEQFDRNGATSSVKY 147

Query: 146 VRSEIV-------ETEETNSADNVNVGNSITEEGE-ASGIILHKLSSSKIRCNDCFREVV 197
            +SE V       + E+T+S   V V   + EE + +SG       +S I+  D  R+ +
Sbjct: 148 SKSESVVSERNSVKVEKTDSM--VKVERVVKEEKKPSSGAAAPPKLTSMIKSKDAARDKI 205

Query: 198 REKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGN 257
           RE + +A SKV GEADEE  DEVNA D +RVA+++ES MFE WG S G  K KYR+++ N
Sbjct: 206 RELLFEAFSKVPGEADEEFMDEVNASDPIRVAVSVESVMFENWGGSTGAQKAKYRSIMFN 265

Query: 258 LKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERAR 306
           LKDPKNPDFRRKVL G +KPE ++ M+  +MASD+  R    E+EE A+
Sbjct: 266 LKDPKNPDFRRKVLLGLIKPERMINMSTADMASDQRKR----ENEEIAQ 310

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  201 bits (510), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 114/295 (38%), Positives = 180/295 (61%), Gaps = 27/295 (9%)

Query: 1   MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYL 60
           MEK++++L ++AK+ A+A++  +  +     + C+D+L QL K  +T  +LVSTQ+ + L
Sbjct: 1   MEKELVELFDKAKKAADASLNDDKSSSGPEVSRCVDSLKQLRKFKVTSEILVSTQVGKKL 60

Query: 61  LPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEEC 120
            PL +HP  KI+  ASDL+ +W+ + +++   +K  +          K+EK+ K +    
Sbjct: 61  RPLAKHPKDKIRAVASDLLETWKKIVIDETMRKKNAT---------VKVEKLQKTSM--- 108

Query: 121 QEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGNSITEEGEASGIILH 180
            ++S    VKV+K+DQ+ T   +   + EI +T           G               
Sbjct: 109 VKVSTSETVKVEKMDQDKTVKVAQTCKEEI-QTSSVKKPSQAPTGPP------------- 154

Query: 181 KLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKW 240
           KL +  ++CND  R+ +RE + +ALSKV+ EADE+IRDEV ACD +RVA+++ESAMFEK 
Sbjct: 155 KLKTL-VKCNDALRDKIRELLAEALSKVASEADEDIRDEVEACDPIRVAVSVESAMFEKL 213

Query: 241 GRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLR 295
           GRS+G  K+KYR+++ N+KD  NPD RRKVL GQV+P+ +V M  +EMAS++  R
Sbjct: 214 GRSNGAQKMKYRSIMFNIKDQNNPDLRRKVLLGQVQPQRLVTMPPEEMASEQRKR 268

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 122/310 (39%), Positives = 190/310 (61%), Gaps = 17/310 (5%)

Query: 1   MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYL 60
           MEK++++L E AK+ A+AA+  +G+ E++    CIDAL+QL K  +   +LV+TQ+ ++L
Sbjct: 1   MEKELVELYEAAKKAADAAISGDGKHEESR---CIDALEQLKKFPVNYKILVNTQVGKHL 57

Query: 61  LPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEEC 120
             LT+HP  KI+ FA DLI  W+ + +++    K G      ++   +  K  K      
Sbjct: 58  KVLTKHPRLKIKAFAIDLIEIWKGIIIKETSKNKNGGSDSKVESANGEKSKAGKMQKSPS 117

Query: 121 QEISGVGIVKVQKVDQNSTSSSSNVVRSEI---VETEETNSADNVNVGNSITEEGEASGI 177
            ++     VKV+K+D+N T+ SS+    ++   V+ E+T+ + +V V     EE   SG 
Sbjct: 118 VKVEKGETVKVEKIDRNGTTKSSSENMKKVQNDVKNEKTDRSASVKVEKIAKEEKPVSG- 176

Query: 178 ILHKLSSSK---------IRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRV 228
              K+SSS          I+ ND  R+ +RE + +ALSKV+GEADE++ D VN  D +RV
Sbjct: 177 -AKKMSSSSAAPPKLKTMIKSNDATRDKIREILHEALSKVTGEADEDLVDVVNNSDPIRV 235

Query: 229 AIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEM 288
           A+ +ES +FEKWG S+G  K+KYR+++ NLKD  NPDFRRKVL G ++PE ++ M+  EM
Sbjct: 236 AVTVESVLFEKWGPSNGAQKVKYRSLMFNLKDSNNPDFRRKVLLGVIEPEQLINMSTAEM 295

Query: 289 ASDEMLRSYQ 298
           AS++  + YQ
Sbjct: 296 ASEQRKQEYQ 305

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637690|gb|ACU19168.1| unknown [Glycine max]

 Score =  195 bits (495), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 121/310 (39%), Positives = 189/310 (60%), Gaps = 17/310 (5%)

Query: 1   MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYL 60
           MEK++++L E AK+ A+AA+  +G+ E++    CIDA +QL K  +   +LV+TQ+ ++L
Sbjct: 1   MEKELVELYEAAKKAADAAISGDGKHEESR---CIDAFEQLKKFPVNYKILVNTQVGKHL 57

Query: 61  LPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEEC 120
             LT+HP  KI+ FA DLI  W+ + +++    K G      ++   +  K  K      
Sbjct: 58  KVLTKHPRLKIKAFAIDLIEIWKGIIIKETSKNKNGGSDSKVESANGEKSKAGKMQKSPS 117

Query: 121 QEISGVGIVKVQKVDQNSTSSSSNVVRSEI---VETEETNSADNVNVGNSITEEGEASGI 177
            ++     VKV+K+D+N T+ SS+    ++   V+ E+T+ + +V V     EE   SG 
Sbjct: 118 VKVEKGETVKVEKIDRNGTTKSSSENMKKVQNDVKNEKTDRSASVKVEKIAKEEKPVSG- 176

Query: 178 ILHKLSSSK---------IRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRV 228
              K+SSS          I+ ND  R+ +RE + +ALSKV+GEADE++ D VN  D +RV
Sbjct: 177 -AKKMSSSSAAPPKLKTMIKSNDATRDKIREILHEALSKVTGEADEDLVDVVNNSDPIRV 235

Query: 229 AIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEM 288
           A+ +ES +FEKWG S+G  K+KYR+++ NLKD  NPDFRRKVL G ++PE ++ M+  EM
Sbjct: 236 AVTVESVLFEKWGPSNGAQKVKYRSLMFNLKDSNNPDFRRKVLLGVIEPEQLINMSTAEM 295

Query: 289 ASDEMLRSYQ 298
           AS++  + YQ
Sbjct: 296 ASEQRKQEYQ 305

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 108/259 (41%), Positives = 164/259 (63%), Gaps = 19/259 (7%)

Query: 34  CIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDE 93
           C+DAL QL    I+  +LVS+Q+ + L PLT+HP +KIQ  ASDL+  W+ + +++   +
Sbjct: 34  CVDALKQLKIFPISYDILVSSQVGKRLRPLTKHPREKIQTVASDLLEMWKKIVIDETTRK 93

Query: 94  KKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVET 153
           K G+              VD ++S +  E+S V  +KV+KV + ST     + R   V+ 
Sbjct: 94  KNGT--------------VDNKSSVKA-EVSKVETIKVEKVQKASTVKVEKIDRERTVKV 138

Query: 154 EETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEAD 213
           E+ +      +   + +  +AS +   KL++  ++CND  R+ +RE + +ALSKV  EA+
Sbjct: 139 EKKSEEKQQAI--DVKKPSQAS-VTPPKLTAI-VKCNDALRDKIRELLVEALSKVVSEAN 194

Query: 214 EEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFG 273
           E+ RDE++ CD +RVA+++ESAMFEK GRS+G  K KYR+++ NLKDP NPD RRKVL G
Sbjct: 195 EDGRDEISKCDPIRVAVSVESAMFEKMGRSNGAQKFKYRSIMFNLKDPNNPDLRRKVLLG 254

Query: 274 QVKPETVVGMTAKEMASDE 292
           +VKPE ++ MT +EMAS E
Sbjct: 255 EVKPERLISMTPEEMASKE 273

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516223|ref|XP_003526795.1| PREDICTED: transcription elongation factor A protein 2-like [Glycine max]

 Score =  190 bits (483), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 124/310 (40%), Positives = 188/310 (60%), Gaps = 18/310 (5%)

Query: 1   MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYL 60
           MEK++++L E AK+ A+AA+  +GE E++    CIDAL+QL K  +   +LV+TQ+ ++L
Sbjct: 1   MEKELVELYEAAKKAADAAISGDGEHEESR---CIDALEQLKKFPVNYKILVNTQVGKHL 57

Query: 61  LPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEEC 120
             LT+HP +KI+ FA DLI  W+ + +++    K G      ++   +  K  K      
Sbjct: 58  KVLTKHPRQKIKSFAIDLIEIWKGIIIKETSKNKNGGSDSKDESANREKSKAGKMQKSPS 117

Query: 121 QEISGVGIVKVQKVDQNSTSSSSNVVRSEI---VETEETNSADNVNVGNSITEEGEASGI 177
            +I     VKV+K+++N TS SS     ++   V+ E T+ A +V +   I EE   SG 
Sbjct: 118 VKIEKGETVKVEKIERNGTSKSSFENMKKVQNDVKNERTDRAASVKM-EKIAEEKPISG- 175

Query: 178 ILHKLSSSK---------IRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRV 228
              K+SSS          I+ ND  R+ +RE + +ALSKV+ EADE++   VN  D +RV
Sbjct: 176 -AKKMSSSSTAPPKLKTMIKSNDATRDKIREILHEALSKVTREADEDLVAVVNDSDPIRV 234

Query: 229 AIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEM 288
           A+ +ES +FEKWG S+G  K+KYR+++ NLKD  NPDFRRKVL G V+PE ++ M+  EM
Sbjct: 235 AVTVESVLFEKWGPSNGAQKVKYRSLMFNLKDSNNPDFRRKVLLGVVEPEQLINMSTAEM 294

Query: 289 ASDEMLRSYQ 298
           AS++  + YQ
Sbjct: 295 ASEQRKQEYQ 304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  188 bits (478), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 128/312 (41%), Positives = 175/312 (56%), Gaps = 50/312 (16%)

Query: 2   EKKVMQLCEEAKRGAEAAVMAE-GEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYL 60
           EK++++L E AK+ A A  + E G AE++    C+DAL QL    +T  LLVSTQ+ + L
Sbjct: 8   EKELVELFEVAKKAAGATELEEKGGAEESR---CLDALAQLKAFPVTAQLLVSTQVGKLL 64

Query: 61  LPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSC----TIPGDTEPAKIEKVDKRT 116
            PLT+H  K IQD ASD+   W+  FLEQ    KK       T    TE  KIEK   RT
Sbjct: 65  RPLTKHSRKNIQDLASDVFPLWKKKFLEQTSSTKKNGMLEDKTSVKSTENIKIEKT--RT 122

Query: 117 SEECQEISGVGIVKVQ-KVDQNSTSSSSNVVRSEIVETEETNSADNVNVGNSITEEGEAS 175
                       +KV+ K +      S+ VV SE                          
Sbjct: 123 ------------IKVEAKTEHKGEPRSAKVVESEC------------------------- 145

Query: 176 GIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESA 235
            ++      S  +CND  R+ +RE++ +AL KVS EA+EEI+ EVNACD++ VA+A+ESA
Sbjct: 146 -LLRSPRMKSIPKCNDPSRDNIREQLYEALCKVSSEANEEIQKEVNACDAIGVAVAVESA 204

Query: 236 MFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLR 295
           +F  WG S+G  +IKYR+++ N +D KNPDFRRKVL GQVKPE +  ++++EMASDE  R
Sbjct: 205 LFSNWGPSNGSDRIKYRSLIFNTRDAKNPDFRRKVLLGQVKPERIAELSSEEMASDER-R 263

Query: 296 SYQHEDEERARL 307
               E +E+A L
Sbjct: 264 KKNKEIKEKALL 275

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255641093|gb|ACU20825.1| unknown [Glycine max]

 Score =  187 bits (476), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 122/310 (39%), Positives = 188/310 (60%), Gaps = 18/310 (5%)

Query: 1   MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYL 60
           MEK++++L E AK+ A+AA+  +GE E++    CIDAL+QL K  +   +LV+TQ+ ++L
Sbjct: 1   MEKELVELYEAAKKAADAAISGDGEHEESR---CIDALEQLKKFPVNYKILVNTQVGKHL 57

Query: 61  LPLTEHPTKKIQDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEEC 120
             LT+HP +KI+ FA DLI  W+ + +++    K G      ++   +  K  K      
Sbjct: 58  KVLTKHPRQKIKSFAIDLIEIWKGIIIKETGKNKNGGSDSKDESANREKSKAGKMQKSPS 117

Query: 121 QEISGVGIVKVQKVDQNSTSSSSNVVRSEI---VETEETNSADNVNVGNSITEEGEASGI 177
            +I     VKV+K+++N TS SS     ++   V+ E T+ A +V +   I EE   SG 
Sbjct: 118 VKIEKGETVKVEKIERNGTSKSSFENMKKVQNDVKNERTDRAASVKM-EKIAEEKPISGA 176

Query: 178 ILHKLSSSK---------IRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRV 228
              K+SSS          I+ +D  R+ ++E + +ALSKV+ EADE++   VN  D +RV
Sbjct: 177 --KKMSSSSTAPPKLKTMIKSSDATRDKIKEILHEALSKVTREADEDLVAVVNDSDPIRV 234

Query: 229 AIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEM 288
           A+ +ES +FEKWG S+G  K+KYR+++ NLKD  NPDFRRKVL G V+PE ++ M+  EM
Sbjct: 235 AVTVESVLFEKWGPSNGAQKVKYRSLMFNLKDSNNPDFRRKVLLGVVEPEQLINMSTAEM 294

Query: 289 ASDEMLRSYQ 298
           AS++  + YQ
Sbjct: 295 ASEQRKQEYQ 304

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	319
TAIR|locus:2064195	378	TFIIS "transcript elongation f	0.601	0.507	0.370	5.7e-27
TAIR|locus:2052351	737	AT2G42730 [Arabidopsis thalian	0.416	0.180	0.422	4.6e-20
TAIR|locus:2124097	266	AT4G18720 [Arabidopsis thalian	0.322	0.387	0.451	9.5e-18
MGI|MGI:1196908	347	Tcea3 "transcription elongatio	0.341	0.314	0.365	5.6e-13
ZFIN|ZDB-GENE-030131-8049	309	tcea1 "transcription elongatio	0.335	0.346	0.372	8.2e-13
RGD|1311369	348	Tcea3 "transcription elongatio	0.836	0.767	0.250	9.4e-13
ZFIN|ZDB-GENE-040426-985	301	tcea2 "transcription elongatio	0.341	0.362	0.361	4e-12
UNIPROTKB|O75764	348	TCEA3 "Transcription elongatio	0.836	0.767	0.257	5.3e-12
ZFIN|ZDB-GENE-040426-1860	409	tcea3 "transcription elongatio	0.294	0.229	0.340	2.1e-11
UNIPROTKB|F1N0P7	348	TCEA3 "Transcription elongatio	0.836	0.767	0.236	8.8e-11

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

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 76/205 (37%), Positives = 128/205 (62%)

Query:   102 GDTEPAKIEKVDKRTSEECQEISGVGIVKVQKV-DQXXXXXXXXXXXXEIVETEETNSAD 160
             GD+  AK  KV+++  +  + ++GV I +  KV D             + V+ E+  S D
Sbjct:   129 GDS--AKSIKVERKEPDN-KVVTGVKIER--KVPDIKVTNGTKIDYRGQAVKDEKV-SKD 182

Query:   161 NVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEV 220
             N +   S+    +A+     KL++  ++CND  R+ +RE + +AL +V+GEAD+  R+ V
Sbjct:   183 NQS---SMKAPAKAANAP-PKLTAM-LKCNDPVRDKIRELLVEALCRVAGEADDYERESV 237

Query:   221 NACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETV 280
             NA D +RVA+++ES MFEK GRS G  K+KYR+++ NL+D  NPD RR+VL G++ PE +
Sbjct:   238 NASDPLRVAVSVESLMFEKLGRSTGAQKLKYRSIMFNLRDSNNPDLRRRVLTGEISPEKL 297

Query:   281 VGMTAKEMASDEMLRSYQHEDEERA 305
             + ++A++MASD+  +   ++ +E+A
Sbjct:   298 ITLSAEDMASDKR-KQENNQIKEKA 321

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 = 248 (92.4 bits), Expect = 4.6e-20, P = 4.6e-20
 Identities = 57/135 (42%), Positives = 83/135 (61%)

Query:   184 SSKIRCNDCFREVVREKVCDALSKVSGE-ADEEIRDEVNACDSVRVAIALESAMFEKWGR 242
             S+  +  D  R+ VRE +  +L KV+ E  D E++  V ACD   VA+++ESAMFEK G 
Sbjct:   597 STMKKTGDSKRDKVREILQTSLVKVASEIVDTEMKTRVTACDPSVVAVSVESAMFEKLGC 656

Query:   243 SDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDE 302
               GP+K KYR++L N+ D  NPD RRKVL G++  E +V M  +EM S+++ +  Q   +
Sbjct:   657 FMGPHKAKYRSILFNMGDSNNPDLRRKVLIGEINGERLVTMERQEMGSEKIQKEVQRI-K 715

Query:   303 ERARLWKEHTRKYMQ 317
             E AR  +E   K +Q
Sbjct:   716 ENARFKEESRMKILQ 730

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 = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 47/104 (45%), Positives = 66/104 (63%)

Query:   188 RCNDCFREVVREKVCDALSKVSGEA-DEEIRDEVNACDSVRVAIALESAMFEKWGRSDGP 246
             +  D  R+ VRE +  +L+KV+ E  D E++  V ACD   VA+++E+AMFE  G   GP
Sbjct:   112 KTGDSKRDKVREILQTSLAKVASEVVDTEMKTRVTACDPWVVAVSVETAMFENLGCFMGP 171

Query:   247 YKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMAS 290
              K KYR++L N+ D  NPD RRKVL G++  E +V M  +EM S
Sbjct:   172 QKAKYRSILFNMGDSNNPDLRRKVLLGEISGERLVKMEKEEMGS 215

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

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

 Score = 173 (66.0 bits), Expect = 5.6e-13, Sum P(2) = 5.6e-13
 Identities = 42/115 (36%), Positives = 68/115 (59%)

Query:   197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
             VR+K  + LS    +A++  +D    CD  ++A  +E  ++++   +D  Y+ + R+ + 
Sbjct:   186 VRDKCVEMLSAAL-KAEDNFKDYGVNCD--KLASEIEDHIYQELKSTDMKYRNRVRSRIS 242

Query:   257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEH 311
             NLKDP+NP  RR VL G + PE +  MTA+EMASDE LR  ++   + A   +EH
Sbjct:   243 NLKDPRNPGLRRNVLSGAISPELIAKMTAEEMASDE-LRELRNAMTQEAI--REH 294

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

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

 Score = 160 (61.4 bits), Expect = 8.2e-13, Sum P(2) = 8.2e-13
 Identities = 41/110 (37%), Positives = 60/110 (54%)

Query:   197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
             VR K  + LS      D+ I    + CD +   I  E  +F ++  +D  YK + R+ + 
Sbjct:   148 VRIKCREMLSNALQTGDDYITIGSD-CDELGAQI--EECIFLEFKNTDMKYKNRVRSRIS 204

Query:   257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERAR 306
             NLKD KNP+ RR VL G V P+ +  MTA+EMASDE+    ++  +E  R
Sbjct:   205 NLKDAKNPNLRRNVLCGNVSPDRIAKMTAEEMASDELKEMRKNLTKEAIR 254

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006414 "translational elongation" evidence=IEA

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

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

 Score = 188 (71.2 bits), Expect = 9.4e-13, P = 9.4e-13
 Identities = 72/287 (25%), Positives = 134/287 (46%)

Query:    31 TAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPT-KKIQDFASDLIVSWRDMFLEQ 89
             T   +D L +LN   ++  LL +T++   +  + +H + K++   A  LI +W+ + L+ 
Sbjct:    23 TEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRL-LDS 81

Query:    90 IRDEKKGSCTIPGDTEPA-KIEKVDKRT-SEECQEISGVGIVKVQKVDQXXXXXXXXXXX 147
              R  K       G+ E   K +K +K   S   +  +G+   + ++  +           
Sbjct:    82 PRTTK-------GEREAREKAKKKEKGLGSSGWKPEAGLSPPRKKEGGEPKTRRDSVDSR 134

Query:   148 XEIVETEETNSADNVNVGNSITEEGEA-SGIILHKLSSSKIRCNDCFR--EVVREKVCDA 204
                  + +  S +  N   S  E  +  S       + +      C+   + VR+K  + 
Sbjct:   135 SSTTSSPKRPSLERSNSSRSKVETPKTPSSPSTPTFAPAVCLLASCYLTGDSVRDKCVEM 194

Query:   205 LSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNP 264
             LS    +A+++ +D    CD  ++A  +E  ++++   +D  Y+ + R+ + NLKDP+NP
Sbjct:   195 LSAAL-KAEDDFKDYGVNCD--KLASEIEDHIYQELKSTDMKYRNRVRSRISNLKDPRNP 251

Query:   265 DFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEH 311
               RR VL G + PE +  MTA+EMASDE LR  ++   + A   +EH
Sbjct:   252 GLRRNVLSGTISPELIAKMTAEEMASDE-LRELRNAMTQEAI--REH 295

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

ZFIN|ZDB-GENE-040426-985 tcea2 "transcription elongation factor A (SII), 2" [Danio rerio (taxid:7955)]

 Score = 162 (62.1 bits), Expect = 4.0e-12, Sum P(2) = 4.0e-12
 Identities = 43/119 (36%), Positives = 64/119 (53%)

Query:   197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
             VR K C  L   + + D +    + A D   +A  +E  +++++  +D  YK + R+ + 
Sbjct:   140 VRTK-CRELLVAALQTDGD-HQTIGA-DCEHMAAQIEDYIYQEFKSTDMKYKTRLRSRIS 196

Query:   257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKY 315
             NLKD KNPD RR VL G + PE +  MTA+EMAS E+        E R  L KE  R++
Sbjct:   197 NLKDQKNPDLRRNVLCGNISPERIASMTAEEMASPEL-------KEIRKALTKESIREH 248

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:0003746 "translation elongation factor activity" evidence=IEA

GO:0006414 "translational elongation" evidence=IEA

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

 Score = 182 (69.1 bits), Expect = 5.3e-12, P = 5.3e-12
 Identities = 74/287 (25%), Positives = 133/287 (46%)

Query:    31 TAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPT-KKIQDFASDLIVSWRDMFLEQ 89
             T   +D L +L+   ++  LL +T++   +  + +H + K++   A  LI +W+ + L+ 
Sbjct:    23 TEGALDLLKKLHSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRL-LDS 81

Query:    90 IRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISG-VGIVKVQKV-DQXXXXXXXXXXX 147
                  KG     G+ E  K +K +K    EC +     G+   +K  +            
Sbjct:    82 -PGPPKGE---KGE-EREKAKKKEKGL--ECSDWKPEAGLSPPRKKREDPKTRRDSVDSK 134

Query:   148 XEIVETEETNSADNVNVGNSITEEGEA-SGIILHKLSSSKIRCNDCFR--EVVREKVCDA 204
                  + +  S +  N   S  E  +  S  +    +SS      C+   + VR+K  + 
Sbjct:   135 SSASSSPKRPSVERSNSSKSKAESPKTPSSPLTPTFASSMCLLAPCYLTGDSVRDKCVEM 194

Query:   205 LSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNP 264
             LS    +AD++ +D    CD  ++A  +E  ++++   +D  Y+ + R+ + NLKDP+NP
Sbjct:   195 LSAAL-KADDDYKDYGVNCD--KMASEIEDHIYQELKSTDMKYRNRVRSRISNLKDPRNP 251

Query:   265 DFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEH 311
               RR VL G +    +  MTA+EMASDE LR  ++   + A   +EH
Sbjct:   252 GLRRNVLSGAISAGLIAKMTAEEMASDE-LRELRNAMTQEAI--REH 295

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

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

 Score = 157 (60.3 bits), Expect = 2.1e-11, Sum P(2) = 2.1e-11
 Identities = 33/97 (34%), Positives = 58/97 (59%)

Query:   197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
             +R+K  + L+      D++ +D    C+++   I  E  ++++   +D  YK + R+ + 
Sbjct:   248 IRDKCIEMLTAAL-RTDDDYKDYGTNCEAMGAEI--EDYIYQETKATDMKYKNRVRSRIS 304

Query:   257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
             NLKDPKNP+ R+ VL G ++   +  MTA+EMASDE+
Sbjct:   305 NLKDPKNPNLRKNVLAGAIELSRIASMTAEEMASDEL 341

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

 Score = 172 (65.6 bits), Expect = 8.8e-11, P = 8.8e-11
 Identities = 68/288 (23%), Positives = 128/288 (44%)

Query:    31 TAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEH-PTKKIQDFASDLIVSWRDMFLEQ 89
             T   +D L +L    ++  LL +T++   +  + +H   K++   A  LI +W+     Q
Sbjct:    23 TEGALDLLKKLGSWQMSIQLLQTTRIGVAVNGVRKHCSNKEVVALAKVLIRNWK-----Q 77

Query:    90 IRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEI---SGVGIVKVQKVDQXXXXXXXXXX 146
             + D      T  G+    +++   K    +C +    + +   + ++V++          
Sbjct:    78 LLDSP---ATPKGEKGEERVKAKKKEKGLDCSDWKPETSLSPPRKKRVEEPKDRRDSVDS 134

Query:   147 XXEIVETEETNSADNVNVGNSITEEGEA-SGIILHKLSSSKIRCNDCFR--EVVREKVCD 203
                   + +  S +  N   S  E     S       + S      C+   + VR+K  +
Sbjct:   135 KSSATSSPKRPSMERSNSSKSKAETPRTPSSPSSPTFAPSVCLLAPCYLTGDSVRDKCVE 194

Query:   204 ALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKN 263
              LS    +AD++ +D    CD  ++A  +E  ++++   +D  Y+ + R+ + NLKDP+N
Sbjct:   195 MLSAAL-KADDDYKDYGVNCD--KMASEIEDHIYQELKSTDMKYRNRVRSRISNLKDPRN 251

Query:   264 PDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEH 311
             P  RR VL G +    +  MTA+EMASDE LR  ++   + A   +EH
Sbjct:   252 PGLRRNVLSGAISAGLIAKMTAEEMASDE-LRELRNAMTQEAI--REH 296

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

---

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: eugene3.00060955 hypothetical protein (353 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	319
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	6e-26
smart00510	102	smart00510, TFS2M, Domain in the central regions o	7e-25
pfam07500	115	pfam07500, TFIIS_M, Transcription factor S-II (TFI	9e-25
cd00183	76	cd00183, TFIIS_I, N-terminal domain (domain I) of	4e-06
smart00509	75	smart00509, TFS2N, Domain in the N-terminus of tra	9e-05
pfam08711	51	pfam08711, Med26, TFIIS helical bundle-like domain	4e-04

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

 Score =  104 bits (261), Expect = 6e-26
 Identities = 76/299 (25%), Positives = 111/299 (37%), Gaps = 61/299 (20%)

Query: 15  GAEAAVMA---EGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKI 71
            AE A  A   +          C+D L QL +   T  LL  T++   +  L +HP + I
Sbjct: 1   SAEVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDI 60

Query: 72  QDFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKV 131
              A  +I SW+ +      D+ K              +K      E    +      + 
Sbjct: 61  SKLAKKIIKSWKKVV-----DKNK-----SDHPGGNPEDK--TTVGESVNSVKQEAKSQS 108

Query: 132 QKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCND 191
            K++Q    SSS                D V                           ND
Sbjct: 109 DKIEQPKYVSSS----------PRNAKNDFVPT----------------------AVTND 136

Query: 192 CFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKY 251
             R+  RE + DAL+K S            + D    AI +E   F   G ++  YK +Y
Sbjct: 137 KVRDKCRELLYDALAKDSDHP-------PQSIDPEAKAIQIEELKFNNLGTTEAAYKARY 189

Query: 252 RAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKE 310
           R++  NL+D  NPD R  VL G++ PE +  MTA+EMAS E+        +ER  + KE
Sbjct: 190 RSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAEL-------KQEREEITKE 241

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

 Score = 95.8 bits (239), Expect = 7e-25
 Identities = 41/97 (42%), Positives = 59/97 (60%), Gaps = 3/97 (3%)

Query: 197 VREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLG 256
           VR+K  + L K      +    E    D   +A+ +E+ MF ++G +D  YK KYR++  
Sbjct: 3   VRDKCQEMLYKA---LQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYF 59

Query: 257 NLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
           NLKD KNPD RRKVL G++ PE +  MTA+E+AS E+
Sbjct: 60  NLKDKKNPDLRRKVLNGEITPEKLATMTAEELASAEL 96

Length = 102

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

 Score = 96.2 bits (240), Expect = 9e-25
 Identities = 48/118 (40%), Positives = 72/118 (61%), Gaps = 11/118 (9%)

Query: 189 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYK 248
            ND  R+  RE + DAL+K S        D ++  +  R+A  +E  +F+ +G +   YK
Sbjct: 1   TNDKVRDKCRELLYDALAKGSE-------DSMSEEEVERLAAEIEEELFKLYGNTGKKYK 53

Query: 249 IKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERAR 306
            KYR+++ NLKDPKNPD RRKVL G++ PE +V M+ +E+ASDE+    + E EE  +
Sbjct: 54  NKYRSLMFNLKDPKNPDLRRKVLNGEISPERLVNMSPEELASDEL----KKEREEIEK 107

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|238107 cd00183, TFIIS_I, N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 16/53 (30%), Positives = 28/53 (52%)

Query: 34 CIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMF 86
           +D L  L K  +T  +L  T++ + +  L +H  +KI+  A  LI SW+ + 
Sbjct: 23 LLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLV 75

Length = 76

>gnl|CDD|197766 smart00509, TFS2N, Domain in the N-terminus of transcription elongation factor S-II (and elsewhere)

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 18/55 (32%), Positives = 30/55 (54%)

Query: 34 CIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLE 88
          C+D L +L K  IT  LL  T++ + +  L +H  ++I+  A  LI SW+ +   
Sbjct: 21 CLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVYS 75

Length = 75

>gnl|CDD|204037 pfam08711, Med26, TFIIS helical bundle-like domain

 Score = 37.1 bits (87), Expect = 4e-04
 Identities = 14/50 (28%), Positives = 26/50 (52%)

Query: 36 DALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDM 85
          + L +L K  IT  LL  T + + +  L +H  ++++  A  LI  W+ +
Sbjct: 1  ELLKELKKLPITEELLRETGIGKAVNKLRKHENEEVKKLAKKLIKKWKRL 50

Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5. Length = 51

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	319
TIGR01385	299	TFSII transcription elongation factor S-II. This m	100.0
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	100.0
smart00510	102	TFS2M Domain in the central regions of transcripti	99.97
PF07500	115	TFIIS_M: Transcription factor S-II (TFIIS), centra	99.95
smart00509	75	TFS2N Domain in the N-terminus of transcription el	99.7
cd00183	76	TFIIS_I N-terminal domain (domain I) of transcript	99.59
KOG1634	778	consensus Predicted transcription factor DATF1, co	99.51
PF08711	53	Med26: TFIIS helical bundle-like domain; InterPro:	99.38
PF11467	106	LEDGF: Lens epithelium-derived growth factor (LEDG	96.18
KOG2821	433	consensus RNA polymerase II transcription elongati	95.97
KOG1793	417	consensus Uncharacterized conserved protein [Funct	95.92
COG5139	397	Uncharacterized conserved protein [Function unknow	94.88
PLN02976	1713	amine oxidase	86.04

>TIGR01385 TFSII transcription elongation factor S-II

Probab=100.00  E-value=4.5e-48  Score=366.38  Aligned_cols=246  Identities=27%  Similarity=0.404  Sum_probs=176.0

Q ss_pred             HHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHH
Q 020949            7 QLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMF   86 (319)
Q Consensus         7 ~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v   86 (319)
                      |+...++ ++++++.+++      .+.|+++|++|+.++||.++|++|+||++||+||+|++++|+.+|+.||.+||++|
T Consensus         3 ei~~~~k-~L~k~~~~~~------~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v   75 (299)
T TIGR01385         3 EVASHAK-ALDKNKSSKN------VEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVV   75 (299)
T ss_pred             HHHHHHH-HhhhhccCCC------HHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence            3444444 5788776432      45899999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcccccCCCCCCCCCCCCCcccccccCCchhhhhhccccccccccccCCCCCCCCccccchhhhhhcccccCCcccCC
Q 020949           87 LEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGN  166 (319)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~  166 (319)
                      ..++..+....+  +....  .  ++++            ...+   ++.  .+.+   .              ......
T Consensus        76 ~~~k~~~~~~~~--~~~~~--~--~~~~------------~~~~---~~~--~~~~---~--------------~~~~~~  115 (299)
T TIGR01385        76 DKNKSDHPGGNP--EDKTT--V--GESV------------NSVK---QEA--KSQS---D--------------KIEQPK  115 (299)
T ss_pred             hhhcccCccccc--ccccc--c--CCCC------------CCCC---ccc--cCCc---c--------------cccCCC
Confidence            876332111100  00000  0  0000            0000   000  0000   0              000000


Q ss_pred             CcccCCCCcccccccccCCCCCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChh
Q 020949          167 SITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGP  246 (319)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~  246 (319)
                      .....++..  +.+.+  ..+.++|++|++||++||+||.....+.+       ..+++..+|.+||.+||..|+.++.+
T Consensus       116 ~~~~~~~~~--~~~~~--~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~-------~~~~~~~lA~~iE~~~f~~~~~~~~~  184 (299)
T TIGR01385       116 YVSSSPRNA--KNDFV--PTAVTNDKVRDKCRELLYDALAKDSDHPP-------QSIDPEAKAIQIEELKFNNLGTTEAA  184 (299)
T ss_pred             CCCCccccc--CCCCC--CCccCCcHHHHHHHHHHHHHHhhcCCCCc-------cccCHHHHHHHHHHHHHHHcCCCcHH
Confidence            000011111  11222  23589999999999999999997543222       23467789999999999999988899


Q ss_pred             hhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 020949          247 YKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHT  312 (319)
Q Consensus       247 Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e~r~~l~ke~~  312 (319)
                      |+++||||+|||||++||+||++||+|+|+|++||.||++||||+++|+++++|.+  ++|+...+
T Consensus       185 Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~k--e~l~~~~~  248 (299)
T TIGR01385       185 YKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITK--ENLFEAQG  248 (299)
T ss_pred             HHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHH--HHHHHHHh
Confidence            99999999999999999999999999999999999999999999999998888888  88876543

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

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

Probab=100.00  E-value=2.3e-44  Score=337.01  Aligned_cols=243  Identities=31%  Similarity=0.440  Sum_probs=178.9

Q ss_pred             HHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecc-cccCCCCHHHHHHHHHHHHHHHHHH
Q 020949            8 LCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLL-PLTEHPTKKIQDFASDLIVSWRDMF   86 (319)
Q Consensus         8 l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~-~Lrkh~~~~I~~~Ak~Lv~~WK~~v   86 (319)
                      +||.+.++|++.....+.+.   ++.++++|.+|++++||.++|++|+||+.|| .|++|+|++|.++|+.||+.||++|
T Consensus         2 ~~e~~~r~ak~l~~~~~~~n---~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~   78 (296)
T KOG1105|consen    2 LEEEALRAAKALEKDKQSKN---VEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLV   78 (296)
T ss_pred             ccHHHHHHHHHHHhhccccc---HHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence            57777777777644334456   8899999999999999999999999999999 7888999999999999999999999


Q ss_pred             HhhcccccCCCCCCCCCCCCCcccccccCCchhhhhhccccccccccccCCCCCCCCccccchhhhhhcccccCCcccCC
Q 020949           87 LEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGN  166 (319)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~  166 (319)
                      +.. +....... .+...| ...+..+.         ++          +.++.++.               .+..    
T Consensus        79 ~~~-~~~~k~~~-~~~~~p-~~~~~~~~---------s~----------~~~~~ks~---------------~~~~----  117 (296)
T KOG1105|consen   79 DKS-PGREKSGD-NKSHDP-GEASSKSP---------SG----------AKQPEKSR---------------GDSK----  117 (296)
T ss_pred             hcc-cccccCcc-ccCCCC-CcCCcCCc---------cC----------CCCccccc---------------cccc----
Confidence            864 11111000 000000 00000000         00          00000000               0000    


Q ss_pred             CcccCCCCcccccccccCCCCCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChh
Q 020949          167 SITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGP  246 (319)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~  246 (319)
                        .. +..+..      ...+.++|++|++|++|||+||....    +.   ....+++..+|.+||.+||..++.++++
T Consensus       118 --~~-~~~~~~------~~~~~~~d~~r~k~~e~l~~al~~~~----~~---~~~~~~~~~~a~~iE~~~~~~~g~~~~k  181 (296)
T KOG1105|consen  118 --RD-KHSGSK------DPVPITNDPVRDKCRELLYAALTTED----DS---RVTGADPLELAVQIEEAIFEKLGNTDSK  181 (296)
T ss_pred             --cc-cccCcC------CCCCCCCchHHHHHHHHHHHHhcccc----cc---cccCCCHHHHHHHHHHHHHHHhCCCcHH
Confidence              00 000000      11235689999999999999998321    11   1235677899999999999999999999


Q ss_pred             hhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020949          247 YKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQ  317 (319)
Q Consensus       247 Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e~r~~l~ke~~r~~~~  317 (319)
                      |+++|||++|||+|++||+||++||+|+|+|++|+.||++||||+++|+       +|++|++|+|++|+-
T Consensus       182 yK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~-------~~~k~~keal~~~q~  245 (296)
T KOG1105|consen  182 YKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKE-------ERQKLTKEALREHQM  245 (296)
T ss_pred             HHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHH-------HHHHHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999       999999999999974

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

Probab=99.97  E-value=9.7e-31  Score=212.21  Aligned_cols=101  Identities=42%  Similarity=0.654  Sum_probs=91.0

Q ss_pred             hHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhHHhhh
Q 020949          191 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKV  270 (319)
Q Consensus       191 d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~V  270 (319)
                      |++|++|+++||++|.......+.       .+++..+|.+||.+||..|+.++.+|++++|||+|||||++||+||++|
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            679999999999999976543321       2356789999999999999988889999999999999999999999999


Q ss_pred             hcCCcCccccccCChhhcCCHHHHHHHH
Q 020949          271 LFGQVKPETVVGMTAKEMASDEMLRSYQ  298 (319)
Q Consensus       271 l~G~I~p~~lv~Mt~eEMASdelk~e~~  298 (319)
                      |+|+|+|++||.||++||||+|+|++++
T Consensus        74 l~G~i~p~~lv~Ms~~ElAs~elk~~~e  101 (102)
T smart00510       74 LNGEITPEKLATMTAEELASAELKEKRE  101 (102)
T ss_pred             HcCCCCHHHHhcCCHHHcCCHHHHHHHh
Confidence            9999999999999999999999999664

>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=1.8e-28  Score=202.77  Aligned_cols=110  Identities=38%  Similarity=0.648  Sum_probs=97.2

Q ss_pred             CChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhHHh
Q 020949          189 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRR  268 (319)
Q Consensus       189 t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~  268 (319)
                      |++++|++|+++|+++|.....+ .+      ...++..+|.+||.+||..|+.++..|++++|+|+|||||++||+||.
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            57999999999999999987544 11      123567999999999999998888999999999999999999999999


Q ss_pred             hhhcCCcCccccccCChhhcCCHHHHHHHHHHHHHHHHH
Q 020949          269 KVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARL  307 (319)
Q Consensus       269 ~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e~r~~l  307 (319)
                      +||+|+|+|.+||.||++||||+++|++++++.+  +++
T Consensus        74 ~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~--~~l  110 (115)
T PF07500_consen   74 RILSGEISPEELVTMSPEELASEELKEEREKIRK--ESL  110 (115)
T ss_dssp             HHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHH--HHH
T ss_pred             HHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHH--HHH
Confidence            9999999999999999999999999997777776  554

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.

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

Probab=99.70  E-value=1.6e-17  Score=127.75  Aligned_cols=74  Identities=31%  Similarity=0.468  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 020949            8 LCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFL   87 (319)
Q Consensus         8 l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~   87 (319)
                      ||+.+++..+.+..   +++   ++.|+++|++|+.++||.++|++|+||+.|+.||+|++++|+.+|+.||+.||++|+
T Consensus         1 ~~~~~k~~~k~~~~---~~~---~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~   74 (75)
T smart00509        1 LLRAAKKLDKVANN---GKE---VSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY   74 (75)
T ss_pred             ChHHHHHHHHHhcC---CCC---HHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence            46777775555532   235   678999999999999999999999999999999999999999999999999999985

>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme

Probab=99.59  E-value=1.4e-15  Score=117.06  Aligned_cols=72  Identities=28%  Similarity=0.380  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 020949           10 EEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFL   87 (319)
Q Consensus        10 ~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~   87 (319)
                      ..++++++....+   ++   .+.|+++|+.|+.++||.++|++|+||+.||+||+|++++|+.+|+.||.+||+.|+
T Consensus         5 ~r~~~~l~~~~~~---~~---~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~   76 (76)
T cd00183           5 LRAKKKLEKKDSN---EE---VSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD   76 (76)
T ss_pred             HHHHHHhhccccC---CC---HHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence            3445556665532   24   678999999999999999999999999999999999999999999999999999873

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

Probab=99.51  E-value=8.2e-15  Score=151.73  Aligned_cols=85  Identities=33%  Similarity=0.504  Sum_probs=75.6

Q ss_pred             chHHHHHHHHHHHHHHhc-CCChhhhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHH
Q 020949          224 DSVRVAIALESAMFEKWG-RSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDE  302 (319)
Q Consensus       224 ~~~~lA~~IE~~lf~~~~-~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e  302 (319)
                      ++.-++..||..+|..|| +.+.+|++|+|||+|||||++||.||.+|+.|+|+|++||.|+++||||.++.+.+++..+
T Consensus       268 d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rEek~e  347 (778)
T KOG1634|consen  268 DPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWREEKAE  347 (778)
T ss_pred             chhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHHHHHH
Confidence            445677799999999999 7889999999999999999999999999999999999999999999999999997777666


Q ss_pred             HHHHHH
Q 020949          303 ERARLW  308 (319)
Q Consensus       303 ~r~~l~  308 (319)
                      +=..|+
T Consensus       348 e~~~mv  353 (778)
T KOG1634|consen  348 EMNEMV  353 (778)
T ss_pred             HHHhhh
Confidence            333333

>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=99.38  E-value=1.9e-13  Score=98.00  Aligned_cols=52  Identities=31%  Similarity=0.455  Sum_probs=47.4

Q ss_pred             HHHHHhhcCCCChhhhhcCCcceecccccCC-CCHHHHHHHHHHHHHHHHHHH
Q 020949           36 DALDQLNKSDITCPLLVSTQLVRYLLPLTEH-PTKKIQDFASDLIVSWRDMFL   87 (319)
Q Consensus        36 ~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh-~~~~I~~~Ak~Lv~~WK~~v~   87 (319)
                      ++|+.|..+|||.++|++|+||++|+.|++| .+++|++.|+.||.+||+.|+
T Consensus         1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~   53 (53)
T PF08711_consen    1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD   53 (53)
T ss_dssp             HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred             CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence            5899999999999999999999999999999 999999999999999999874

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.

>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis

Probab=96.18  E-value=0.0045  Score=50.76  Aligned_cols=78  Identities=23%  Similarity=0.442  Sum_probs=55.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhh-cCCcceecccccCC-CCHHHHHHHHHHH
Q 020949            2 EKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLV-STQLVRYLLPLTEH-PTKKIQDFASDLI   79 (319)
Q Consensus         2 e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~-~T~iGk~V~~Lrkh-~~~~I~~~Ak~Lv   79 (319)
                      |..|.+|.-.    +..+-.-+ .|.   +.+|+++|.+|..++||.-+|+ .+.+-.++.+||+. .|..|.+.|..|.
T Consensus         1 E~~L~~l~~~----Ik~~L~~~-~~D---v~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lY   72 (106)
T PF11467_consen    1 ERRLQELHSE----IKSSLKVD-NPD---VKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELY   72 (106)
T ss_dssp             HHHHHHHHHH----HHHTCETT-EE----HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHH
T ss_pred             ChhHHHHHHH----HHHHHcCC-CCC---HHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence            4566666653    33332111 235   7899999999999999986655 67788888999998 5588999999999


Q ss_pred             HHHHHHHH
Q 020949           80 VSWRDMFL   87 (319)
Q Consensus        80 ~~WK~~v~   87 (319)
                      .+.|.++.
T Consensus        73 nkfK~~f~   80 (106)
T PF11467_consen   73 NKFKSLFL   80 (106)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhC
Confidence            99999986

It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.

>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]

Probab=95.97  E-value=0.0032  Score=62.83  Aligned_cols=57  Identities=19%  Similarity=0.295  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHHHhh
Q 020949           31 TAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQ   89 (319)
Q Consensus        31 ~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~~~   89 (319)
                      ..+.+..|..|.++|++.++|.+|.+|+.|+.|++|.  .+..+|..|+..||+.|...
T Consensus        24 pkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~d   80 (433)
T KOG2821|consen   24 PKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLVD   80 (433)
T ss_pred             HHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcccc
Confidence            3489999999999999999999999999999999999  69999999999999999543

>KOG1793 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.92  E-value=0.009  Score=58.85  Aligned_cols=56  Identities=25%  Similarity=0.328  Sum_probs=49.4

Q ss_pred             HHHHHHHhhcCCCCh-hhhhcCCcceecccccCCCC--HHHHHHHHHHHHHHHHHHHhh
Q 020949           34 CIDALDQLNKSDITC-PLLVSTQLVRYLLPLTEHPT--KKIQDFASDLIVSWRDMFLEQ   89 (319)
Q Consensus        34 ~l~~L~~L~~~~it~-~lL~~T~iGk~V~~Lrkh~~--~~I~~~Ak~Lv~~WK~~v~~~   89 (319)
                      =..+|..|.+++|-. +.|...+||++|=.|.+|+.  ..++.+|..||..|-.-|+..
T Consensus       235 r~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~~  293 (417)
T KOG1793|consen  235 RKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFKL  293 (417)
T ss_pred             HHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccCC
Confidence            345778888899998 99999999999999999966  779999999999999988643

>COG5139 Uncharacterized conserved protein [Function unknown]

Probab=94.88  E-value=0.035  Score=52.91  Aligned_cols=54  Identities=22%  Similarity=0.280  Sum_probs=45.9

Q ss_pred             HHHHHHhhcCCCChhhhhcCCcceecccccCC--CCHHHHHHHHHHHHHHHHHHHh
Q 020949           35 IDALDQLNKSDITCPLLVSTQLVRYLLPLTEH--PTKKIQDFASDLIVSWRDMFLE   88 (319)
Q Consensus        35 l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh--~~~~I~~~Ak~Lv~~WK~~v~~   88 (319)
                      -.+|..|+.+||-.++|.+.+||+.|=+....  ..++|+..|+.||..|-.-|..
T Consensus       233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIik  288 (397)
T COG5139         233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIK  288 (397)
T ss_pred             HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhccccC
Confidence            34677888899999999999999999766554  6688999999999999988753

>PLN02976 amine oxidase

Probab=86.04  E-value=0.93  Score=52.21  Aligned_cols=56  Identities=14%  Similarity=0.233  Sum_probs=46.5

Q ss_pred             HHHHHhhcCCCChhhhhcCCcceec-ccccCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 020949           36 DALDQLNKSDITCPLLVSTQLVRYL-LPLTEHPTKKIQDFASDLIVSWRDMFLEQIR   91 (319)
Q Consensus        36 ~~L~~L~~~~it~~lL~~T~iGk~V-~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~~~~~   91 (319)
                      .+|+-|=-++..+..|+..+||++| +++--|.+++|+.+|.+|+..|...+..++.
T Consensus      1305 ~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~ 1361 (1713)
T PLN02976       1305 HCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKA 1361 (1713)
T ss_pred             HHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3444444456667778899999999 9999999999999999999999999977644

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	319
2lw4_A	113	Solution Nmr Structure Of Human Transcription Elong		2e-12
2dme_A	120	Solution Structure Of The Tfiis Domain Ii Of Human		5e-11
3ndq_A	108	Structure Of Human Tfiis Domain Ii Length = 108		3e-09
3po3_S	178	Arrested Rna Polymerase Ii Reactivation Intermediat		2e-04
1y1v_S	179	Refined Rna Polymerase Ii-tfiis Complex Length = 17		2e-04
1pqv_S	309	Rna Polymerase Ii-Tfiis Complex Length = 309		2e-04
1enw_A	114	Elongation Factor Tfiis Domain Ii Length = 114		3e-04
3gtm_S	173	Co-Complex Of Backtracked Rna Polymerase Ii With Tf		5e-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 = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 45/70 (64%)
Query: 224 DSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGM 283
           D  R++  +E  +F   G +D  YK + R+ + NLKD KNPD RR VL G + P+ +  M
Sbjct: 36  DCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVM 95
Query: 284 TAKEMASDEM 293
           T++EMASDE+
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 = 65.1 bits (157), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 62/103 (60%), Gaps = 4/103 (3%)
Query: 191 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIK 250
           D  R+ VR  + D L K   +++ ++ +E  A    +VA  +E  +F  +  +D  YK K
Sbjct: 10  DQIRQSVRHSLKDILMKRLTDSNLKVPEEKAA----KVATKIEKELFSFFRDTDAKYKNK 65
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
           YR+++ NLKDPKN    +KVL G+V P+ ++ M+ +E+AS E+
Sbjct: 66  YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKEL 108

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 41/61 (67%)
Query: 232 LESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASD 291
           +E A++++   +D  YK + R+ + NLKD KNP+ R+ VL G + P+    MTA+EMASD
Sbjct: 48  IEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD 107
Query: 292 E 292
           E
Sbjct: 108 E 108

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
           +   +R++V  AL  V  +  E     +     +  A A+ES M        ++  YK +
Sbjct: 13  YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 67
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
           YR +  N+    NPD + K+  G + PE +    AK++A
Sbjct: 68  YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 106

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
           +   +R++V  AL  V  +  E     +     +  A A+ES M        ++  YK +
Sbjct: 14  YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 68
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
           YR +  N+    NPD + K+  G + PE +    AK++A
Sbjct: 69  YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 107

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/224 (23%), Positives = 81/224 (36%), Gaps = 52/224 (23%)
Query: 71  IQDFASDLIVSWRDMFLEQIRD---EKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVG 127
           I      +I SW+D   +  R    ++      PG+ E       DK T  E        
Sbjct: 61  ISKLVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAE-------DKTTVGES------- 106
Query: 128 IVKVQKVDQXXXXXXXXXXXXEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKI 187
              V  V Q            + V T+  NS +          +G  + I  HKL     
Sbjct: 107 ---VNGVQQPASSQSDAMKQDKYVSTKPRNSKN----------DGVDTAIYHHKL----- 148
Query: 188 RCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDG 245
                 R+ V + + D L+K S    + I         +  A A+ES M        ++ 
Sbjct: 149 ------RDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDTNEA 193
Query: 246 PYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
            YK +YR +  N+    NPD + K+  G + PE +    AK++A
Sbjct: 194 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 237

>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii Length = 114

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
           +   +R++V  AL  V  +  E     +     +  A A+ES M        ++  YK +
Sbjct: 18  YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 72
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
           YR +  N+    NPD + K+  G + PE +    AK++A
Sbjct: 73  YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 11/99 (11%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
            R+ V + + D L+K S    + I         +  A A+ES M        ++  YK +
Sbjct: 12  LRDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDTNEAAYKAR 62
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
           YR +  N+    NPD + K+  G + PE +    AK++A
Sbjct: 63  YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 101
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	319
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	5e-24
3ndq_A	108	Transcription elongation factor A protein 1; helix	2e-23
3po3_S	178	Transcription elongation factor S-II; RNA polymera	1e-16
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	3e-16
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

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

 Score = 93.9 bits (233), Expect = 5e-24
 Identities = 38/121 (31%), Positives = 65/121 (53%), Gaps = 4/121 (3%)

Query: 183 SSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGR 242
           SS      D  R+ VR  + D L K   +++ ++ +E     + +VA  +E  +F  +  
Sbjct: 2   SSGSSGSADQIRQSVRHSLKDILMKRLTDSNLKVPEE----KAAKVATKIEKELFSFFRD 57

Query: 243 SDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDE 302
           +D  YK KYR+++ NLKDPKN    +KVL G+V P+ ++ M+ +E+AS E+    +    
Sbjct: 58  TDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRRSGP 117

Query: 303 E 303
            
Sbjct: 118 S 118

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

 Score = 92.0 bits (228), Expect = 2e-23
 Identities = 34/114 (29%), Positives = 53/114 (46%), Gaps = 7/114 (6%)

Query: 179 LHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFE 238
           +   +      +D  R   RE +  AL                  D   +   +E A+++
Sbjct: 2   IDPFTPRAPSTSDSVRLKCREMLAAALRTGDDYIAIG-------ADEEELGSQIEEAIYQ 54

Query: 239 KWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDE 292
           +   +D  YK + R+ + NLKD KNP+ R+ VL G + P+    MTA+EMASDE
Sbjct: 55  EIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 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 = 75.6 bits (185), Expect = 1e-16
 Identities = 28/136 (20%), Positives = 55/136 (40%), Gaps = 11/136 (8%)

Query: 185 SKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFE--KWGR 242
                +   R+ V + + D L+K S    + I         +  A A+ES M +      
Sbjct: 9   DTAIYHHKLRDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDT 59

Query: 243 SDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDE 302
           ++  YK +YR +  N+    NPD + K+  G + PE +    AK++A   + +  +   +
Sbjct: 60  NEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAK 119

Query: 303 ERARLWKEHTRKYMQR 318
           +     +  T +    
Sbjct: 120 QNLYNAQGATIERSVT 135

>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 = 77.1 bits (188), Expect = 3e-16
 Identities = 39/286 (13%), Positives = 83/286 (29%), Gaps = 43/286 (15%)

Query: 34  CIDALDQLNKS-DITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQIRD 92
            ++ L  L+K    T  LL  T++   +    +    +I      +I SW+D        
Sbjct: 23  VLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAI------ 76

Query: 93  EKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVE 152
                                 +   +                 N     ++     + +
Sbjct: 77  -------------NKNKRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAMKQ 123

Query: 153 TEETNSADNVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEA 212
            +  ++    +                          +   R+ V + + D L+K S   
Sbjct: 124 DKYVSTKPRNS----------------KNDGVDTAIYHHKLRDQVLKALYDVLAKESEHP 167

Query: 213 DEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLF 272
            + I            AI  E         ++  YK +YR +  N+    NPD + K+  
Sbjct: 168 PQSILHTA-------KAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIAN 220

Query: 273 GQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQR 318
           G + PE +    AK++A   + +  +   ++     +  T +    
Sbjct: 221 GDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVT 266

>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 = 45.2 bits (106), Expect = 2e-05
 Identities = 42/304 (13%), Positives = 87/304 (28%), Gaps = 108/304 (35%)

Query: 30  WTAWCIDALDQLNKSDITCPLLVSTQ-----------------LVRYLLPLTEHPTKKIQ 72
             A   +A +      ++C +L++T+                 L  + + LT    K + 
Sbjct: 254 QNAKAWNAFN------LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL- 306

Query: 73  DFASDLIVSWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQ 132
                    + D   + +  E     T      P ++  +    +E  ++    G+    
Sbjct: 307 -LL-----KYLDCRPQDLPRE---VLTT----NPRRLSII----AESIRD----GLATWD 345

Query: 133 KVDQNSTSSSSNVVRS--EIVETEETNSA--------DNVNV---------GNSITEEGE 173
                +    + ++ S   ++E  E             + ++          + I  +  
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405

Query: 174 ASGIILHKLS-------SSKIRCNDCFREVVREKVCDALSKVSGEAD--EEIRDEVNACD 224
                LHK S        S I     +         +   K+  E      I D  N   
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPSIY--------LELKVKLENEYALHRSIVDHYNIPK 457

Query: 225 SVRVAIALESAMFEKWGRS----DGPYKIKYRAVLG-NLKDPKNPD----FRRKVL---F 272
           +           F+         D  Y   +   +G +LK+ ++P+    FR   L   F
Sbjct: 458 T-----------FDSDDLIPPYLDQ-YFYSH---IGHHLKNIEHPERMTLFRMVFLDFRF 502

Query: 273 GQVK 276
            + K
Sbjct: 503 LEQK 506

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	319
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	100.0
2lw4_A	113	Transcription elongation factor A protein 2; struc	99.98
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	99.96
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	99.72
2xpp_A	145	IWS1, ECU08_0440; transcription, elongation, histo	97.69
3nfq_A	170	Transcription factor IWS1; SPN1, RNA polymerase II	97.46
2b4j_C	98	PC4 and SFRS1 interacting protein; HIV, integratio	96.29
1z9e_A	127	PC4 and SFRS1 interacting protein 2; heat repeat-l	96.09

>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=2.4e-44  Score=342.39  Aligned_cols=250  Identities=18%  Similarity=0.261  Sum_probs=171.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHh-hcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHH
Q 020949            2 EKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQL-NKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIV   80 (319)
Q Consensus         2 e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L-~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~   80 (319)
                      |+||+++++...+    .   ...     .+.|+++|++| +.++||.++|++|+||++||+||+|++++|+.+|+.||.
T Consensus         3 ~~el~~~~~~L~k----~---~~~-----~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~   70 (309)
T 1pqv_S            3 SKEVLVHVKNLEK----N---KSN-----DAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMIS   70 (309)
T ss_pred             HHHHHHHHHHHhc----c---CCC-----HHHHHHHHHHHHhcCCCCHHHHHhCChhHHHHHHHcCCCHHHHHHHHHHHH
Confidence            7889999986666    1   222     34799999999 899999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcccccCCCCCCCCCCCCCcccccccCCchhhhhhccccccccccccCCCCCCCCccccchhhhhhcccccC
Q 020949           81 SWRDMFLEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSAD  160 (319)
Q Consensus        81 ~WK~~v~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~i~~~~~~~~~  160 (319)
                      +||++|..+...+...... ....+.....++++     .+   .        +.. .++.. ++..+.        ...
T Consensus        71 ~WK~~v~~~~~~~~~~~~~-~~~~~~~~~~~~~~-----~~---~--------~~~-~~~~~-~~~~~~--------~~~  123 (309)
T 1pqv_S           71 SWKDAINKNKRSRQAQQHH-QDHAPGNAEDKTTV-----GE---S--------VNG-VQQPA-SSQSDA--------MKQ  123 (309)
T ss_pred             HHHHHHHHhccCCcccccc-cccccccccCCCCC-----CC---C--------cCC-CCCCc-cccccc--------ccC
Confidence            9999998765432211100 00000000000000     00   0        000 00000 000000        000


Q ss_pred             CcccCCCcccCCCCcccccccccCCCCCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHh
Q 020949          161 NVNVGNSITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKW  240 (319)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~  240 (319)
                      ...    ....++.+  ..+.+  ....++|.+|++||++|+++|.....+.+.         ++..+|.+||.+||..|
T Consensus       124 ~~~----~~~~~~~~--~~~~~--~~~~~~d~~R~k~r~~L~~aL~~~~~~~~~---------~~~~~A~~IE~al~~~~  186 (309)
T 1pqv_S          124 DKY----VSTKPRNS--KNDGV--DTAIYHHKLRDQVLKALYDVLAKESEHPPQ---------SILHTAKAIESEMNKVN  186 (309)
T ss_pred             CCC----CCCCCCCC--CCCCC--CcCcCChHHHHHHHHHHHHHHhcCCCccch---------hHHHHHHHHHHHHHHHh
Confidence            000    00001111  11222  134788999999999999999865332221         35689999999999999


Q ss_pred             cCCChh--hhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHHHHHHHHH
Q 020949          241 GRSDGP--YKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWK  309 (319)
Q Consensus       241 ~~~~~~--Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e~r~~l~k  309 (319)
                      ++++.+  |++++|||+|||||++||.||++||.|+|+|++||.||++||||+|+|++++++.+  ++|++
T Consensus       187 ~~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr~~vl~g~i~p~~lv~Ms~eElasde~k~~~~~~~~--e~l~~  255 (309)
T 1pqv_S          187 NCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAK--QNLYN  255 (309)
T ss_pred             CCCchhHHHHHHHHHHHHHcCcCCChHHHHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHH--HHHHH
Confidence            888877  99999999999999999999999999999999999999999999999996666666  55543

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

Probab=99.98  E-value=3.7e-34  Score=234.96  Aligned_cols=105  Identities=35%  Similarity=0.519  Sum_probs=93.4

Q ss_pred             CCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhH
Q 020949          187 IRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDF  266 (319)
Q Consensus       187 ~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~L  266 (319)
                      +.|+|++|++||++||+||...     .+..  ...+++..+|.+||.++|..|++++.+|++++|||+|||||++||+|
T Consensus         6 p~t~D~vRdk~~e~L~~aL~~~-----~~~~--~~~~~~~~~A~~IE~~~f~~~~~~~~~Yk~k~Rsl~~NLkd~~Np~L   78 (113)
T 2lw4_A            6 PVTCDAVRNKCREMLTAALQTD-----HDHV--AIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDL   78 (113)
T ss_dssp             CCCCSTTHHHHHHHHHHHHHSS-----THHH--HHTCCHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHCSSSSHH
T ss_pred             CCCCcHHHHHHHHHHHHHHHcC-----CCcc--cccchHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHH
Confidence            5789999999999999999842     1211  12346789999999999999999999999999999999999999999


Q ss_pred             HhhhhcCCcCccccccCChhhcCCHHHHHHHH
Q 020949          267 RRKVLFGQVKPETVVGMTAKEMASDEMLRSYQ  298 (319)
Q Consensus       267 r~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~  298 (319)
                      |++||+|+|+|++||.||++||||+|+|++++
T Consensus        79 r~~vl~G~i~p~~l~~Ms~eEmAs~elk~~r~  110 (113)
T 2lw4_A           79 RRNVLCGAITPQQIAVMTSEEMASDELKEIRK  110 (113)
T ss_dssp             HHHHHTTSSCHHHHHHSCHHHHHCTTTTTCSS
T ss_pred             HHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHH
Confidence            99999999999999999999999999999443

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

Probab=99.97  E-value=3.6e-32  Score=221.51  Aligned_cols=99  Identities=34%  Similarity=0.509  Sum_probs=85.7

Q ss_pred             CCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhH
Q 020949          187 IRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDF  266 (319)
Q Consensus       187 ~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~L  266 (319)
                      +.|+|++|++|+++||+||+...     +...  ..+++..+|.+||.+||..|+.++.+||+++|||+|||||++||+|
T Consensus        10 ~~t~d~vR~k~~~lL~~aL~~~~-----d~~~--~~~~~~~lA~~IE~~if~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~L   82 (108)
T 3ndq_A           10 PSTSDSVRLKCREMLAAALRTGD-----DYIA--IGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNL   82 (108)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTGGG-----HHHH--HTCCHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHTCTTCHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHcCC-----CCCc--ccccHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHHH
Confidence            57999999999999999998642     2221  2356789999999999999998889999999999999999999999


Q ss_pred             HhhhhcCCcCccccccCChhhcCCHH
Q 020949          267 RRKVLFGQVKPETVVGMTAKEMASDE  292 (319)
Q Consensus       267 r~~Vl~G~I~p~~lv~Mt~eEMASde  292 (319)
                      |++||+|+|+|++||+||++||||+|
T Consensus        83 r~~vl~G~isp~~lv~Ms~eEmAS~E  108 (108)
T 3ndq_A           83 RKNVLCGNIPPDLFARMTAEEMASDE  108 (108)
T ss_dssp             HHHHHHTSSCHHHHHHCCTTTC----
T ss_pred             HHHHHcCCcCHHHHhCCCHHHccCCC
Confidence            99999999999999999999999997

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

Probab=99.97  E-value=1.7e-32  Score=227.28  Aligned_cols=110  Identities=32%  Similarity=0.483  Sum_probs=96.2

Q ss_pred             CCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhHH
Q 020949          188 RCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFR  267 (319)
Q Consensus       188 ~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr  267 (319)
                      .++|.+|++|+++|+++|...+.+.+...    ..+++..+|.+||.+||..|+.++.+|++++|||+|||||++||+||
T Consensus         7 ~~~d~~Rd~~r~~L~eaL~~~~~~~~~~~----~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~Lr   82 (120)
T 2dme_A            7 GSADQIRQSVRHSLKDILMKRLTDSNLKV----PEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILF   82 (120)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHTTTTCCC----CHHHHHHHHHHHHHHHHHHHCSCSHHHHHHHHHHTHHHHSSSCCSHH
T ss_pred             CCCchHHHHHHHHHHHHHHHhcccccccc----chhHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHH
Confidence            45699999999999999998765433211    12345789999999999999988899999999999999999999999


Q ss_pred             hhhhcCCcCccccccCChhhcCCHHHHHHHHHHH
Q 020949          268 RKVLFGQVKPETVVGMTAKEMASDEMLRSYQHED  301 (319)
Q Consensus       268 ~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~  301 (319)
                      ++||+|+|+|++||.||++||||+|+|++++++.
T Consensus        83 ~~vl~G~i~p~~lv~Ms~eEmAS~elk~~r~~~~  116 (120)
T 2dme_A           83 KKVLKGEVTPDHLIRMSPEELASKELAAWRRRSG  116 (120)
T ss_dssp             HHHHHTSSCTTHHHHSCTTTTTTCCSTTTCTTCC
T ss_pred             HHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHh
Confidence            9999999999999999999999999999776653

>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=99.96  E-value=2e-30  Score=228.54  Aligned_cols=112  Identities=23%  Similarity=0.369  Sum_probs=91.8

Q ss_pred             ccccCCCCCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcC-CCh-hhhhhhhhHhhc
Q 020949          180 HKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGR-SDG-PYKIKYRAVLGN  257 (319)
Q Consensus       180 ~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~-~~~-~Yk~k~RSl~fN  257 (319)
                      +++  +.+.++|++|++|+++||+||....++.+.         ++..+|.+||.+||..|++ ++. +|++++|||+||
T Consensus         6 d~v--~~~~~~d~vRdk~~~lL~~aL~~~~~~~~~---------~~~~~A~~IE~~if~~~~~~~~~k~Yk~k~Rsl~~N   74 (178)
T 3po3_S            6 DGV--DTAIYHHKLRDQVLKALYDVLAKESEHPPQ---------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSN   74 (178)
T ss_dssp             -----------CHHHHHHHHHHHHHTTSSSSCSTT---------HHHHHHHHHHHHHHHHTSCSSSSTHHHHHHHHHHHH
T ss_pred             CCc--CcCcCCChHHHHHHHHHHHHHhcCCCCchh---------hHHHHHHHHHHHHHHHhcCCCchhhhhhhhhHHHHH
Confidence            444  446899999999999999999976554433         2458999999999999987 565 899999999999


Q ss_pred             cCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHH
Q 020949          258 LKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDE  302 (319)
Q Consensus       258 LKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e  302 (319)
                      |||++||+||++|++|+|+|.+||.|+++||||+|+|++++++.+
T Consensus        75 LKd~~N~~Lr~~vl~g~isp~~lv~Ms~eElas~elk~~~e~~~~  119 (178)
T 3po3_S           75 VISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAK  119 (178)
T ss_dssp             HHSSSCSHHHHHHHHCCCTTHHHHCCTTTTSSCSHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHhcCCCCHHHHHhcCchhhCCHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999995555554

>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=99.72  E-value=3.4e-18  Score=137.80  Aligned_cols=79  Identities=19%  Similarity=0.381  Sum_probs=68.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCC-CCHHHHHHHHHHH
Q 020949            1 MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEH-PTKKIQDFASDLI   79 (319)
Q Consensus         1 ~e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh-~~~~I~~~Ak~Lv   79 (319)
                      +|.|++++++...++++    ..++ +     .|+++|++|+.++||.++|++|+||++||+|||| ++++|+.+|+.||
T Consensus        10 ~e~ev~~i~k~L~k~~~----~~~~-~-----~~l~~L~~L~~~~iT~e~L~~T~IGk~Vn~LrKh~~~~~V~~lAk~Lv   79 (103)
T 1wjt_A           10 LEEELLRIAKKLEKMVS----RKKT-E-----GALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLI   79 (103)
T ss_dssp             SHHHHHHHHHHHHHHHH----TTCC-S-----SHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHh----cCCH-H-----HHHHHHHHHhCCCCCHHHHHHcchhHHHHHHHccCCcHHHHHHHHHHH
Confidence            47899999996666544    2222 3     6999999999999999999999999999999998 8899999999999


Q ss_pred             HHHHHHHHhh
Q 020949           80 VSWRDMFLEQ   89 (319)
Q Consensus        80 ~~WK~~v~~~   89 (319)
                      .+||++|...
T Consensus        80 ~~WK~~v~~~   89 (103)
T 1wjt_A           80 KNWKRLLDSP   89 (103)
T ss_dssp             HHHHHHTCCS
T ss_pred             HHHHHHHHHh
Confidence            9999999653

>2xpp_A IWS1, ECU08_0440; transcription, elongation, histone chaperone, RNA polymerase mRNA export; 1.74A {Encephalitozoon cuniculi} PDB: 2xpo_A 2xpn_A 2xpl_A

Probab=97.69  E-value=1.6e-05  Score=67.37  Aligned_cols=56  Identities=20%  Similarity=0.293  Sum_probs=49.8

Q ss_pred             HHHHHHHHhhcCCCChhhhhcCCcceecccccCCCC--HHHHHHHHHHHHHHHHHHHh
Q 020949           33 WCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPT--KKIQDFASDLIVSWRDMFLE   88 (319)
Q Consensus        33 ~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~--~~I~~~Ak~Lv~~WK~~v~~   88 (319)
                      ---.+|+.|..+||+.+.|.+++||++|..|.+|+.  ++++.+|..||.+|..-+..
T Consensus        83 Ir~~lL~~L~~lPI~~e~Lk~SglGkvv~~l~k~~~et~~nk~la~~Li~~WsRpi~~  140 (145)
T 2xpp_A           83 IRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVFK  140 (145)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHCCCCHHHhhcCCCCcchhhhhcCCccCHHHHHHHHHHHHHHHHHHhC
Confidence            344678888889999999999999999999999966  78999999999999998853

>3nfq_A Transcription factor IWS1; SPN1, RNA polymerase II; 1.85A {Saccharomyces cerevisiae} PDB: 3o8z_A 3oak_A

Probab=97.46  E-value=3.9e-05  Score=66.53  Aligned_cols=54  Identities=19%  Similarity=0.278  Sum_probs=47.8

Q ss_pred             HHHHHHHhhcCCCChhhhhcCCcceecccccCCCC--HHHHHHHHHHHHHHHHHHH
Q 020949           34 CIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPT--KKIQDFASDLIVSWRDMFL   87 (319)
Q Consensus        34 ~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~--~~I~~~Ak~Lv~~WK~~v~   87 (319)
                      =-.+|+.|..+||+.+.|..++||++|..|.+|+.  ++++.+|..||.+|-.-+.
T Consensus        99 r~~lL~~L~~lPI~~e~Lk~SglGkvV~~l~k~~~et~~nkrla~~Li~~WsRpI~  154 (170)
T 3nfq_A           99 QKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWTRPII  154 (170)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHSHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHHCCCCHHHHhhCCCCceeeehhcCCcccHHHHHHHHHHHHHHHHHHh
Confidence            34677888889999999999999999999999966  8899999999999977663

>2b4j_C PC4 and SFRS1 interacting protein; HIV, integration, transcription, viral protein, recombinatio; 2.02A {Homo sapiens} SCOP: a.48.4.1 PDB: 3f9k_C 3hpg_G 3u88_C* 3hph_E

Probab=96.29  E-value=0.0024  Score=50.42  Aligned_cols=79  Identities=22%  Similarity=0.389  Sum_probs=62.2

Q ss_pred             ChhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChh-hhhcCCcceecccccCC-CCHHHHHHHHHH
Q 020949            1 MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCP-LLVSTQLVRYLLPLTEH-PTKKIQDFASDL   78 (319)
Q Consensus         1 ~e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~-lL~~T~iGk~V~~Lrkh-~~~~I~~~Ak~L   78 (319)
                      ||..|++|.-.-+-++...     -+.   +.+|+++|.+|+++++|.- +++.+.+--++.+||+. .+..|.+.|..|
T Consensus         4 ~E~~l~~L~~~ik~~L~~~-----~~D---v~kcl~~L~~l~~l~~T~~mL~rnpe~V~t~kklRry~g~q~Ir~kA~~i   75 (98)
T 2b4j_C            4 MDSRLQRIHAEIKNSLKID-----NLD---VNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTML   75 (98)
T ss_dssp             HHHHHHHHHHHHHHHTCTT-----SCC---HHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHccC-----CCC---HHHHHHHHHHHhcccccHHHHhhChHHHHHHHHHHHHhchHHHHHHHHHH
Confidence            5788899887555444331     224   7789999999999999986 55577888899999887 568899999999


Q ss_pred             HHHHHHHHH
Q 020949           79 IVSWRDMFL   87 (319)
Q Consensus        79 v~~WK~~v~   87 (319)
                      ..+.|.++.
T Consensus        76 Y~kfK~~f~   84 (98)
T 2b4j_C           76 YNKFKNMFL   84 (98)
T ss_dssp             HHHHHHC--
T ss_pred             HHHHHHHHh
Confidence            999999984

>1z9e_A PC4 and SFRS1 interacting protein 2; heat repeat-like, ledgf, protein binding/transcription complex; NMR {Homo sapiens} SCOP: a.48.4.1

Probab=96.09  E-value=0.0036  Score=51.51  Aligned_cols=79  Identities=22%  Similarity=0.384  Sum_probs=63.7

Q ss_pred             ChhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChh-hhhcCCcceecccccCC-CCHHHHHHHHHH
Q 020949            1 MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCP-LLVSTQLVRYLLPLTEH-PTKKIQDFASDL   78 (319)
Q Consensus         1 ~e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~-lL~~T~iGk~V~~Lrkh-~~~~I~~~Ak~L   78 (319)
                      ||..|++|.-.-+-++...  .   +.   +.+|+++|..|.++++|.- +++.+.|--++.+||+. .+..|.+.|..|
T Consensus         4 ~E~~L~~L~~~Ik~~L~v~--~---~D---v~kCl~~Leel~~l~vT~~mL~Rnpe~V~TlkklRrY~gnq~Ir~kA~~i   75 (127)
T 1z9e_A            4 MDSRLQRIHAEIKNSLKID--N---LD---VNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTML   75 (127)
T ss_dssp             HHHHHHHHHHHHHHHTCGG--G---CC---HHHHHHHHHHHHHSCCCHHHHGGGHHHHHHHHHHTTCTTCSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHccC--C---CC---HHHHHHHHHHHccccccHHHHhhChHHHHHHHHHHHHhccHHHHHHHHHH
Confidence            5788888887555444331  2   24   7789999999999999986 55578888899999887 557899999999


Q ss_pred             HHHHHHHHH
Q 020949           79 IVSWRDMFL   87 (319)
Q Consensus        79 v~~WK~~v~   87 (319)
                      ..+.|.++.
T Consensus        76 Y~kFK~lf~   84 (127)
T 1z9e_A           76 YNKFKNMFL   84 (127)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999995

---

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	319
d1enwa_	114	a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak	5e-20
d1eo0a_	77	a.48.3.1 (A:) Transcription elongation factor TFII	2e-04
d1wjta_	103	a.48.3.1 (A:) Transcription elongation factor S-II	8e-04

>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 = 81.8 bits (202), Expect = 5e-20
 Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 11/102 (10%)

Query: 190 NDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRS--DGPY 247
           +   R+ V + + D L+K S    + I         +  A A+ES M +       +  Y
Sbjct: 19  HHKLRDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDTNEAAY 69

Query: 248 KIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
           K +YR +  N+    NPD + K+  G + PE +    AK++A
Sbjct: 70  KARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111

>d1eo0a_ a.48.3.1 (A:) Transcription elongation factor TFIIS N-domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 77

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 TFIIS N-domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 34 CIDALDQLNKS-DITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDM 85
           ++ L  L+K    T  LL  T++   +    +    +I      +I SW+D 
Sbjct: 23 VLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDA 75

>d1wjta_ a.48.3.1 (A:) Transcription elongation factor S-II protein 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 103

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]

 Score = 36.0 bits (83), Expect = 8e-04
 Identities = 13/63 (20%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 34 CIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPT-KKIQDFASDLIVSWRDMFLEQIRD 92
           +D L +LN   ++  LL +T++   +  + +H + K++   A  LI +W+ +       
Sbjct: 33 ALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLLDSPRTT 92

Query: 93 EKK 95
          + +
Sbjct: 93 KGE 95

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	319
d1enwa_	114	Elongation factor TFIIS domain 2 {Baker's yeast (S	99.91
d1wjta_	103	Transcription elongation factor S-II protein 3 {Mo	99.62
d1eo0a_	77	Transcription elongation factor TFIIS N-domain {Ba	99.61
d2b4jc1	81	PC4 and SFRS1-interacting protein, PSIP1 {Human (H	97.44

>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=99.91  E-value=1.2e-25  Score=182.68  Aligned_cols=95  Identities=27%  Similarity=0.426  Sum_probs=84.5

Q ss_pred             CCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCC--ChhhhhhhhhHhhccCCCCCh
Q 020949          187 IRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRS--DGPYKIKYRAVLGNLKDPKNP  264 (319)
Q Consensus       187 ~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~--~~~Yk~k~RSl~fNLKD~kNp  264 (319)
                      ..++|++|++|+++|+++|.....+..+.         ...+|.+||++||..|+..  +..|++|+|||+|||||++||
T Consensus        16 ~~~~d~~R~~~~~~L~~aL~~~~~~~~~~---------~~~la~~IE~~lf~~~~~~~~~~~Y~~k~rsi~~NLkd~~N~   86 (114)
T d1enwa_          16 AIYHHKLRDQVLKALYDVLAKESEHPPQS---------ILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNP   86 (114)
T ss_dssp             CSSTTTTHHHHHHHHHHHHHHHCSSSCSC---------HHHHHHHHTTTTTSSCTTTTTHHHHHHHHHHHHHHHTTSCCC
T ss_pred             ccCCcHHHHHHHHHHHHHHhCcCccchhH---------HHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHcCccchH
Confidence            57899999999999999999765544333         3589999999999999743  367999999999999999999


Q ss_pred             hHHhhhhcCCcCccccccCChhhcCC
Q 020949          265 DFRRKVLFGQVKPETVVGMTAKEMAS  290 (319)
Q Consensus       265 ~Lr~~Vl~G~I~p~~lv~Mt~eEMAS  290 (319)
                      +||.+|++|+|+|.+||.|+++|||.
T Consensus        87 ~L~~~v~~g~i~p~~l~~M~~~ElaP  112 (114)
T d1enwa_          87 DLKHKIANGDITPEFLATCDAKDLAP  112 (114)
T ss_dssp             CTTTHHHHCSSCCSSHHHHTTTTTCS
T ss_pred             HHHHHHHcCCCCHHHHhCCCHHHcCC
Confidence            99999999999999999999999996

>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=99.62  E-value=1.1e-16  Score=127.00  Aligned_cols=79  Identities=20%  Similarity=0.357  Sum_probs=67.0

Q ss_pred             ChhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCC-CHHHHHHHHHHH
Q 020949            1 MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHP-TKKIQDFASDLI   79 (319)
Q Consensus         1 ~e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~-~~~I~~~Ak~Lv   79 (319)
                      +|.|++.+..    .+++++...+.+      .++++|+.|+.++||.++|++|+||++||+||||. +++|+.+|+.||
T Consensus        10 ~eeei~~i~k----~L~~~~~~~~~~------~vl~~L~~L~~~~it~e~L~~T~IGk~Vn~LrK~~~~~~v~~lAk~Lv   79 (103)
T d1wjta_          10 LEEELLRIAK----KLEKMVSRKKTE------GALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLI   79 (103)
T ss_dssp             SHHHHHHHHH----HHHHHHHTTCCS------SHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHH
T ss_pred             HHHHHHHHHH----HHHHHHccCCHH------HHHHHHHHHHcCCCCHHHHHhCCccHhHHHHHccCCCHHHHHHHHHHH
Confidence            3566666555    788776655532      59999999999999999999999999999999985 699999999999


Q ss_pred             HHHHHHHHhh
Q 020949           80 VSWRDMFLEQ   89 (319)
Q Consensus        80 ~~WK~~v~~~   89 (319)
                      ++||++|..+
T Consensus        80 ~~WK~~v~~~   89 (103)
T d1wjta_          80 KNWKRLLDSP   89 (103)
T ss_dssp             HHHHHHTCCS
T ss_pred             HHHHHHHHhh
Confidence            9999998554

>d1eo0a_ a.48.3.1 (A:) Transcription elongation factor TFIIS N-domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

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 TFIIS N-domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.61  E-value=1.6e-16  Score=119.46  Aligned_cols=66  Identities=20%  Similarity=0.250  Sum_probs=58.2

Q ss_pred             HHHHHHHHhccChhhHhhHHHHHHHHHHhhc-CCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHH
Q 020949           13 KRGAEAAVMAEGEAEKAWTAWCIDALDQLNK-SDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMF   86 (319)
Q Consensus        13 ~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~-~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v   86 (319)
                      +++++++.   ..++     .++++|+.|++ ++||.++|++|+||++||+||+|++++|+.+|+.||.+||+.|
T Consensus        10 ~k~Lek~~---~~~~-----~~l~~L~~L~~~~~it~d~L~~T~iG~~Vn~LRkh~~~~v~~lAk~Lv~~WK~~V   76 (77)
T d1eo0a_          10 VKNLEKNK---SNDA-----AVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAI   76 (77)
T ss_dssp             HHHHHHHC---SSSH-----HHHHHHHHHTTTCSCSTTHHHHHHHHHHHHHCCSSSCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccc---CCHH-----HHHHHHHHHHhcCCCcHHHHHHCCccHHHHHHhcCCcHHHHHHHHHHHHHHHHhc
Confidence            34677753   2223     79999999996 9999999999999999999999999999999999999999987

>d2b4jc1 a.48.4.1 (C:346-426) PC4 and SFRS1-interacting protein, PSIP1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: N-cbl like
superfamily: HIV integrase-binding domain
family: HIV integrase-binding domain
domain: PC4 and SFRS1-interacting protein, PSIP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.44  E-value=3.4e-05  Score=57.24  Aligned_cols=76  Identities=18%  Similarity=0.350  Sum_probs=60.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhh-hcCCcceecccccCC-CCHHHHHHHHHH
Q 020949            1 MEKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLL-VSTQLVRYLLPLTEH-PTKKIQDFASDL   78 (319)
Q Consensus         1 ~e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL-~~T~iGk~V~~Lrkh-~~~~I~~~Ak~L   78 (319)
                      ||..|.+|.-.-+-++..    . -|.   +..|+++|.+|.++++|.-+| +.+.+--++.++|++ .|.+|...|..|
T Consensus         3 ~E~~l~~L~~~ik~sL~~----~-~~d---v~kcL~~L~~l~~l~vt~~mL~kn~e~V~tikklRry~gn~~Ir~kA~~l   74 (81)
T d2b4jc1           3 MDSRLQRIHAEIKNSLKI----D-NLD---VNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTML   74 (81)
T ss_dssp             HHHHHHHHHHHHHHHTCT----T-SCC---HHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc----C-CCC---HHHHHHHHHHHHcCCCCHHHHHHChHHHHHHHHHHHHhccHHHHHHHHHH
Confidence            578888887744433321    1 124   778999999999999998555 477888999999999 779999999999


Q ss_pred             HHHHHH
Q 020949           79 IVSWRD   84 (319)
Q Consensus        79 v~~WK~   84 (319)
                      ..+||.
T Consensus        75 y~kfKs   80 (81)
T d2b4jc1          75 YNKFKN   80 (81)
T ss_dssp             HHHHHH
T ss_pred             HHHhcc
Confidence            999996