Citrus Sinensis ID: 023203

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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------
Protein Sequence
MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDFGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDPYGGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPAAPHSVQVSSS
Secondary Structure (PSIPRED)
ccHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccHHHHHHccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASrcrncdfgngvvdvnkeisrgqhdevkaaqqaspstphsvngdddidiendndiidpygglfdDEQKRILEIKehledpdqsEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKlnqpgelassammdgdspqqkipqngnhqvpdfayspnphngssgsdknnseperkskqaplprkealssrppqsaspaaphsvqvsss
Flexible Loop (DISEMBL)
MDLDDFRSILKtagvdvwtfIDTAILVASLDYATELKERRDKIVERLYATCIasrcrncdfgNGVVDVNKEISRGQHDEvkaaqqaspstphsvngdDDIDIENDNDIIDPYGGLFDDEQKRILEIKehledpdqsEDALIDLLQSLADMDITFKALKetdigrhvnqlrkhssndvrkLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPNPHNGssgsdknnseperkskqaplprkealssrppqsaspaaphsvqvsss
Low Complexity Region (SEG)
MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDFGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGdddidiendndiidPYGGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEalssrppqsaspaaphsvqvsss
Disordered region (IsUnstruct)
*****FRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDFGNGVVDVN************************************NDIIDPYGGLFDDEQKRILEI************ALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLN***************************************************************************************
Disordered Region (DISOPRED)
*DLDDFRSILKTAGVDVWTFIDTAILVASL*************VERLYATCIA******************************************************************QKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKD************************************************************************************************
Disordered Region (DISEMBL)
MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDFGNGVVDVNKEISRGQ******************NGDDDIDIENDNDIIDPYGGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPN***************************************************
Disordered Region (DISPRO)
*DLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDFG***************************************************GLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKL****************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDFGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDPYGGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPAAPHSVQVSSS
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	286	2.2.26 [Sep-21-2011]
F4KFC7	353	Probable mediator of RNA	yes	no	0.961	0.779	0.569	2e-84
Q9FHK9	436	Probable mediator of RNA	no	no	0.667	0.438	0.339	1e-20
F4J4Y5	580	Probable mediator of RNA	no	no	0.646	0.318	0.298	2e-17
Q2KI09	349	Transcription elongation	yes	no	0.517	0.424	0.267	4e-06
A5PKE4	208	Transcription elongation	no	no	0.318	0.437	0.310	3e-05
Q96MN5	208	Transcription elongation	yes	no	0.237	0.326	0.367	3e-05
Q15560	299	Transcription elongation	no	no	0.206	0.197	0.416	4e-05
Q148K0	300	Transcription elongation	no	no	0.206	0.196	0.4	5e-05
P10711	301	Transcription elongation	no	no	0.269	0.255	0.354	0.0001
Q9QVN7	299	Transcription elongation	no	no	0.265	0.254	0.358	0.0001

>sp|F4KFC7|MD26C_ARATH Probable mediator of RNA polymerase II transcription subunit 26c OS=Arabidopsis thaliana GN=MED26C PE=2 SV=1

 Score =  312 bits (800), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 163/286 (56%), Positives = 205/286 (71%), Gaps = 11/286 (3%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCD 60
           MDLDDFRS++  AGVDVWTFIDTAILVASLDY  ELK RRD IVERLYAT +A++CRNCD
Sbjct: 1   MDLDDFRSVMDNAGVDVWTFIDTAILVASLDYGQELKRRRDNIVERLYATSMANKCRNCD 60

Query: 61  FGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDI-----DIENDNDIIDPYGGL 115
           FG G       I R  +  V    +       +   ++++     ++E+D+D  DP+ GL
Sbjct: 61  FGGGGNVTEAAIGRVNNGRVHEETEEEDEEGVTAAAEEEVREKSVNVEDDDDF-DPFAGL 119

Query: 116 FDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN 175
           FDDEQK I+EIKE LEDPD SE++L++LLQ+L DMDITF+AL+ETDIGRHVN++RKH SN
Sbjct: 120 FDDEQKSIVEIKEKLEDPDLSEESLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSN 179

Query: 176 DVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMM-DGDSPQQKIPQNGN-HQVPDFAYS 233
           +VR+L K LV+KWK+ VDEWVK NQPG+L   +++ D DSP QK   NG+  QVPDF YS
Sbjct: 180 NVRRLAKQLVKKWKETVDEWVKFNQPGDLEPPSLIADEDSPVQKALHNGSRQQVPDFGYS 239

Query: 234 PNPHNGSSGSDKNN--SEPERKSKQ-APLPRKEALSSRPPQSASPA 276
           P P NG S S KN+  +EPERK +  AP PR+E+ S   P   SP+
Sbjct: 240 PVPQNGYSSSSKNSNITEPERKPRPVAPQPRRESPSPAKPSRPSPS 285

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). May play a role in transcription elongation (By similarity).
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHK9|MD26B_ARATH Probable mediator of RNA polymerase II transcription subunit 26b OS=Arabidopsis thaliana GN=MED26B PE=2 SV=1

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/212 (33%), Positives = 109/212 (51%), Gaps = 21/212 (9%)

Query: 3   LDDFRSILKTAG-VDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDF 61
           LD +R   +  G  D++  ID AI+VA+ D   + K RRDKI E L+ +C  +RC  CD 
Sbjct: 7   LDSWREYFRRRGDSDIFGIIDHAIMVAATDCPNKFKSRRDKIAELLF-SCRVNRCVGCDH 65

Query: 62  GNGVVDVNKEISRGQH----------DEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDP 111
               V  + E +RG            ++ + A  +  S  +S  GD++  +   N   D 
Sbjct: 66  LELSVPGDDEANRGTTGNGGGGTAVDEDYEVAGGSKESKANSSRGDNNQIV--SNYTFDE 123

Query: 112 YGGLFDDEQ------KRILEIKE-HLEDPDQSEDALIDLLQSLADMDITFKALKETDIGR 164
              L D+ +      K +  IKE  L   D+    L+D L+ L  M +    LK T+IG+
Sbjct: 124 AEALSDEIEEFSVVSKEVARIKEILLNKEDEPNSVLLDSLRHLKLMSLNVDILKSTEIGK 183

Query: 165 HVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWV 196
            VN LRKHSS+ +R+L K L+ +WK++VD+WV
Sbjct: 184 AVNGLRKHSSDKIRQLAKTLIAEWKELVDQWV 215

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). May play a role in transcription elongation (By similarity).

Arabidopsis thaliana (taxid: 3702)

>sp|F4J4Y5|MD26A_ARATH Probable mediator of RNA polymerase II transcription subunit 26a OS=Arabidopsis thaliana GN=MED26A PE=2 SV=1

 Score = 90.1 bits (222), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 104/208 (50%), Gaps = 23/208 (11%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCD 60
           + LD +R   +    D++  ID AI+VA+ D+  E K R D+I E L+ +C  SRC  CD
Sbjct: 8   VSLDTWREYFRRGDSDIFGIIDHAIMVAAADWPKEFKSRSDRIAELLF-SCKVSRCIGCD 66

Query: 61  FGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDPYGGLFDDEQ 120
                   + E+S    +                +G    + E  +  +D          
Sbjct: 67  --------HLELSIAGDEAAVEIVGVGGGGDRGDSGVATGEGEEASVSVD---------- 108

Query: 121 KRILEIKEHLEDPDQSEDA-LIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRK 179
             ++ I++ L + D  +D+ L++ L+ L  M ++   LK+T+IG+ VN LR+HSS+ + K
Sbjct: 109 -EVMRIRDILSNKDDEKDSVLLESLRKLESMSMSVDILKDTEIGKAVNGLRRHSSDKISK 167

Query: 180 LVKHLVRKWKDIVDEWVKLNQPGELASS 207
           L K L  +WK +VD+W  +N P E+A +
Sbjct: 168 LAKTLFAEWKRLVDQW--MNTPEEMAGT 193

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). May play a role in transcription elongation (By similarity).

Arabidopsis thaliana (taxid: 3702)

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

 Score = 52.0 bits (123), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 83/172 (48%), Gaps = 24/172 (13%)

Query: 117 DDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN- 175
           ++E  RI +  E +    ++E AL DLL+ L    ++ + L+ T IG  VN +RKH SN 
Sbjct: 4   EEELLRIAKKLEKMVARKKTEGAL-DLLKKLGSWQMSIQLLQTTRIGVAVNGVRKHCSNK 62

Query: 176 DVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFA-YSP 234
           +V  L K L+R WK ++D            S A   G+  ++++      +  D + + P
Sbjct: 63  EVVALAKVLIRNWKQLLD------------SPATPKGEKGEERVKAKKKEKGLDCSDWKP 110

Query: 235 NPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPAAPHSVQVSSS 286
                    + + S P +K  + P  R++++ S+   ++SP  P   + +SS
Sbjct: 111 ---------ETSLSPPRKKRVEEPKDRRDSVDSKSSATSSPKRPSMERSNSS 153

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|A5PKE4|TEAN2_BOVIN Transcription elongation factor A N-terminal and central domain-containing protein 2 OS=Bos taurus GN=TCEANC2 PE=2 SV=1

 Score = 49.7 bits (117), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/103 (31%), Positives = 57/103 (55%), Gaps = 12/103 (11%)

Query: 110 DPYGGLFD----DEQKRILEI------KEHLEDPDQSEDALIDLLQSLADMDITFKALKE 159
           DP G ++     +  KR++ I      K  LE PDQS++ L++ L+ L     + + LK 
Sbjct: 19  DPGGKIYKQATIESLKRVVVIEDIKRWKTMLELPDQSKENLVEALRELKKKIPSREVLKS 78

Query: 160 TDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPG 202
           T IG  VN++R+HS ++V  L + +  +W+  +++ V  N+P 
Sbjct: 79  TKIGHTVNKMRQHSDSEVACLAREVYTEWRTFIEKHV--NRPS 119

Bos taurus (taxid: 9913)

>sp|Q96MN5|TEAN2_HUMAN Transcription elongation factor A N-terminal and central domain-containing protein 2 OS=Homo sapiens GN=TCEANC2 PE=1 SV=1

 Score = 49.3 bits (116), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 41/68 (60%)

Query: 127 KEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVR 186
           K  LE PDQ+++ L++ LQ L     + + LK T IG  VN++RKHS ++V  L + +  
Sbjct: 46  KTMLELPDQTKENLVEALQELKKKIPSREVLKSTRIGHTVNKMRKHSDSEVASLAREVYT 105

Query: 187 KWKDIVDE 194
           +WK   ++
Sbjct: 106 EWKTFTEK 113

Homo sapiens (taxid: 9606)

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

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 1/60 (1%)

Query: 135 QSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN-DVRKLVKHLVRKWKDIVD 193
           +S +  +DLL+ L  M IT   L+ T +G  VN LRK SS+ +V  L K L++ WK ++D
Sbjct: 22  KSAEGAMDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLLD 81

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

Homo sapiens (taxid: 9606)

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

 Score = 48.5 bits (114), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 1/60 (1%)

Query: 135 QSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN-DVRKLVKHLVRKWKDIVD 193
           +S +  +DLL+ L  M +T   L+ T +G  VN LRK SS+ +V  L K L++ WK ++D
Sbjct: 22  KSAEGAMDLLRELKAMPVTLHLLQSTRVGMSVNALRKQSSDEEVVTLAKSLIKSWKKLLD 81

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

 Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 116 FDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN 175
            +DE  RI +  + +     +  AL DLL+ L ++ +T + L+ T IG  VN LRK S++
Sbjct: 1   MEDEVVRIAKKMDKMVQKKNAAGAL-DLLKELKNIPMTLELLQSTRIGMSVNALRKQSTD 59

Query: 176 -DVRKLVKHLVRKWKDIVD 193
            +V  L K L++ WK ++D
Sbjct: 60  EEVTSLAKSLIKSWKKLLD 78

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

 Score = 47.0 bits (110), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 117 DDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN- 175
           ++E  RI    + +     +E A+ DLL+ L +M IT   L+ T +G  VN LRK SS+ 
Sbjct: 4   EEEIARIARRLDKMVTRKNAEGAM-DLLRELKNMPITLHLLQSTRVGMSVNALRKQSSDE 62

Query: 176 DVRKLVKHLVRKWKDIVD 193
           ++  L K L++ WK ++D
Sbjct: 63  ELIALAKSLIKSWKKLLD 80

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	286
255578426	362	conserved hypothetical protein [Ricinus	0.965	0.762	0.672	1e-99
449448454	345	PREDICTED: probable mediator of RNA poly	0.891	0.739	0.672	4e-96
224060453	361	predicted protein [Populus trichocarpa]	0.961	0.761	0.638	1e-94
224126771	357	predicted protein [Populus trichocarpa]	0.961	0.770	0.628	1e-93
359476965	331	PREDICTED: uncharacterized protein LOC10	0.902	0.779	0.608	4e-84
356525574	314	PREDICTED: uncharacterized protein LOC10	0.860	0.783	0.594	6e-83
296088637	332	unnamed protein product [Vitis vinifera]	0.902	0.777	0.605	7e-83
356516327	361	PREDICTED: uncharacterized protein LOC10	0.958	0.759	0.602	1e-82
18416107	353	Transcription elongation factor (TFIIS)	0.961	0.779	0.569	1e-82
356509008	356	PREDICTED: uncharacterized protein LOC10	0.933	0.75	0.614	2e-82

>gi|255578426|ref|XP_002530078.1| conserved hypothetical protein [Ricinus communis] gi|223530431|gb|EEF32318.1| conserved hypothetical protein [Ricinus communis]

 Score =  368 bits (945), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 199/296 (67%), Positives = 233/296 (78%), Gaps = 20/296 (6%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCD 60
           MD+DDFRSIL+++GVDVWTFIDTAI+VASLD+  ELK+RRDKIVE LY++  + RCRNCD
Sbjct: 1   MDVDDFRSILESSGVDVWTFIDTAIVVASLDFGNELKQRRDKIVEMLYSS--SGRCRNCD 58

Query: 61  FGNGVVDVNKEISRGQHDEVKAAQQASPSTP----HSVNGDDDIDIENDNDI-------I 109
              G ++   EI    H E K        +P     S++GD+D+D+ ND+D        +
Sbjct: 59  LDVGRINNGHEIKERSHLESKGGGGGGSGSPSTTPRSIHGDEDVDVVNDDDDDDDDDDGL 118

Query: 110 DPYGGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQL 169
           DPY GLFDDEQK+ILEIK+HLEDPDQSED+L+DLLQSLADMDITFKALKETDIGRHVNQL
Sbjct: 119 DPYAGLFDDEQKKILEIKQHLEDPDQSEDSLVDLLQSLADMDITFKALKETDIGRHVNQL 178

Query: 170 RKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMM-DGDSPQQKIPQNGNHQVP 228
           RKH+SNDVR+LVK LVRKWKDIVDEWVKLN PG+ ASS +M DGDSP+QK PQNG+HQVP
Sbjct: 179 RKHTSNDVRRLVKQLVRKWKDIVDEWVKLNPPGQHASSGLMADGDSPRQKFPQNGHHQVP 238

Query: 229 DFAYSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPAAPHSVQVS 284
           DFAYSPNPHNGSSGSDKNNSEPER+ K  P+PRKEA    PP+ A  + P S   S
Sbjct: 239 DFAYSPNPHNGSSGSDKNNSEPERRPK--PVPRKEA----PPRPAQQSVPVSASAS 288

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448454|ref|XP_004141981.1| PREDICTED: probable mediator of RNA polymerase II transcription subunit 26c-like [Cucumis sativus] gi|449528150|ref|XP_004171069.1| PREDICTED: probable mediator of RNA polymerase II transcription subunit 26c-like [Cucumis sativus]

 Score =  357 bits (915), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 189/281 (67%), Positives = 215/281 (76%), Gaps = 26/281 (9%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYA-TCIASRCRNC 59
           +DLDDFR+IL TAGVDVWTFIDTA+ VASLDY  +LK RRD IVERLYA T   SRCRNC
Sbjct: 4   LDLDDFRTILDTAGVDVWTFIDTAMEVASLDYGNQLKNRRDGIVERLYALTSPPSRCRNC 63

Query: 60  DF-------GNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDPY 112
           D         NG      EI +G   EVK   +ASPSTP  V       +E D+D  DPY
Sbjct: 64  DTDRNHDGRSNGC-----EIKQGS-GEVK---EASPSTPQFVV------VEGDDDGADPY 108

Query: 113 GGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKH 172
            GLFDDEQK++LEIKE LE P Q EDAL++LLQ+LADMDITF+ALKETDIGRHVN+LRKH
Sbjct: 109 AGLFDDEQKKVLEIKEQLEIPQQPEDALVELLQNLADMDITFQALKETDIGRHVNRLRKH 168

Query: 173 SSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAY 232
            SNDVR+LVKHLVRKWK+IVDEWV+LNQPGE  ++ + DGDSPQQK PQNG HQVPDFAY
Sbjct: 169 PSNDVRRLVKHLVRKWKEIVDEWVRLNQPGEQTATLLADGDSPQQKAPQNGYHQVPDFAY 228

Query: 233 SPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSA 273
           SPNPHNG SGSD+NNSEPE K K   +PR++AL  +P Q A
Sbjct: 229 SPNPHNGGSGSDRNNSEPEPKGKS--VPRRDAL-PKPTQQA 266

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060453|ref|XP_002300207.1| predicted protein [Populus trichocarpa] gi|222847465|gb|EEE85012.1| predicted protein [Populus trichocarpa]

 Score =  352 bits (903), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 189/296 (63%), Positives = 228/296 (77%), Gaps = 21/296 (7%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYA-TCIASRCRNC 59
           MD+DDFRSIL+++GVDVW FIDTAI VASLD+ +ELK RRD IV RL+A +   SRCR+ 
Sbjct: 1   MDIDDFRSILESSGVDVWNFIDTAIDVASLDFGSELKRRRDDIVARLFAASSSCSRCRDR 60

Query: 60  DF----------GNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDII 109
            F          GNG+ D+ ++ S  + ++ +     SP TP SVNGD       D++ +
Sbjct: 61  SFDDIDINNTANGNGMKDLAEKESSHEEEKGRRVYADSPVTPRSVNGD------GDDEEL 114

Query: 110 DPYGGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQL 169
           DP+GGLFDDE K+IL+IK+ LED DQ ED+L+DLLQSLADMDITF+ALKETDIGRHVN+L
Sbjct: 115 DPFGGLFDDEPKKILDIKQQLEDLDQPEDSLVDLLQSLADMDITFQALKETDIGRHVNRL 174

Query: 170 RKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMD-GDSPQQKIPQNGNHQVP 228
           RKH SNDV++LVK LVRKWK+IVD+WV+LN  GE ASS +M  GDSPQQKIPQNG HQVP
Sbjct: 175 RKHPSNDVKRLVKQLVRKWKEIVDDWVRLNPHGERASSGLMAYGDSPQQKIPQNGRHQVP 234

Query: 229 DFAYSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQS--ASPAAPHSVQ 282
           DFAYSPNPHNGSSGSD+NNSEPERK K AP PR EAL+    +S  AS +APH+VQ
Sbjct: 235 DFAYSPNPHNGSSGSDRNNSEPERKPKLAP-PRNEALTKPIKKSVPASSSAPHNVQ 289

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224126771|ref|XP_002329469.1| predicted protein [Populus trichocarpa] gi|222870149|gb|EEF07280.1| predicted protein [Populus trichocarpa]

 Score =  348 bits (894), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 191/304 (62%), Positives = 226/304 (74%), Gaps = 29/304 (9%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIA------- 53
           MD+DDFR IL+++GVDVWTFIDTAI+VASLD+ +ELK RRD IVERL+A+  +       
Sbjct: 1   MDIDDFRLILESSGVDVWTFIDTAIVVASLDFGSELKRRRDDIVERLFASSSSCSRCRDR 60

Query: 54  -------SRCRNCDFGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDN 106
                  +   N D   G+V+        +   V A    SP TP SVNGD       D+
Sbjct: 61  SLNDINMNNTSNGDEIKGLVEKESSHEEEKGTRVAAD---SPVTPRSVNGD------GDD 111

Query: 107 DIIDPYGGLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHV 166
           D +DPYGGLFDDE K+IL IK+ LED DQ ED+L+DLLQSLADMDITF+ALKETDIGRHV
Sbjct: 112 DELDPYGGLFDDEPKKILVIKQQLEDIDQPEDSLVDLLQSLADMDITFQALKETDIGRHV 171

Query: 167 NQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMM-DGDSPQQKIPQNGNH 225
           N+LRKH SNDVR+LVK LVRKWK+IVD+WV+LN  GE ASS +M DGDSPQQKIPQNG+H
Sbjct: 172 NRLRKHPSNDVRRLVKQLVRKWKEIVDDWVRLNPQGEHASSGLMADGDSPQQKIPQNGHH 231

Query: 226 QVPDFAYSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPA---APHSVQ 282
           QVPDFAYSPNPHNGSSGSD+NNSEPERK K AP PR +A  ++P Q   PA   AP++VQ
Sbjct: 232 QVPDFAYSPNPHNGSSGSDRNNSEPERKPKPAP-PRNQA-PTKPTQKPVPASSPAPYNVQ 289

Query: 283 VSSS 286
           VS+S
Sbjct: 290 VSTS 293

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359476965|ref|XP_002279496.2| PREDICTED: uncharacterized protein LOC100260896 isoform 1 [Vitis vinifera]

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 166/273 (60%), Positives = 200/273 (73%), Gaps = 15/273 (5%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCD 60
           MD D+FR IL+ +GVDVW FI+TAI VA  DY  EL+ RRD IVER+Y   ++SRC +C+
Sbjct: 1   MDRDEFRLILRNSGVDVWEFINTAISVAYSDYGDELRHRRDGIVERMY---MSSRCGSCN 57

Query: 61  FGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDPYGGLFDDEQ 120
                  ++K     + DE    +  SP TP S+N     D          YGGL D+E+
Sbjct: 58  LRYQHSGLDKGCDEEKEDEKDDEKDKSPLTPQSINRSGSEDR---------YGGLLDEEE 108

Query: 121 KRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKL 180
            RIL+IKEHLE PDQ +D+++DLLQ+LADMDITFKALKETDIGRHVN+LRKH SNDVR+L
Sbjct: 109 ARILDIKEHLEAPDQPDDSIVDLLQTLADMDITFKALKETDIGRHVNRLRKHPSNDVRRL 168

Query: 181 VKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPNPHNGS 240
           VKHLVRKWKD+VDEWVK N  GE  SSA+M+GDSP QKIP+ G+HQVPDF YSPNP NGS
Sbjct: 169 VKHLVRKWKDLVDEWVKSNPAGEFTSSALMEGDSPPQKIPRTGHHQVPDFGYSPNPQNGS 228

Query: 241 SGSDKNNSEPERKSKQAPLPRKEALSSRPPQSA 273
           SGSDKNN+EPE K K   +PRKE + +RP QSA
Sbjct: 229 SGSDKNNAEPEPKVKA--IPRKE-VPTRPAQSA 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525574|ref|XP_003531399.1| PREDICTED: uncharacterized protein LOC100796457 [Glycine max]

 Score =  313 bits (802), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 166/279 (59%), Positives = 199/279 (71%), Gaps = 33/279 (11%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYA-TCIASRCRNC 59
           MD +DFRSIL++AGVDVW  +D AI VAS D+A ELK RRD IVERLYA +     CRNC
Sbjct: 1   MDSEDFRSILESAGVDVWALMDAAIAVASADHAHELKRRRDGIVERLYAASSPPPLCRNC 60

Query: 60  DFGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDPYGGLFDDE 119
           D G+G              E++   Q+SPS                 +  DPYGGLFDDE
Sbjct: 61  DAGDG-------------GEIRT--QSSPSA---------------EEEKDPYGGLFDDE 90

Query: 120 QKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRK 179
           Q++IL+IKE LEDP QSED+L++LLQ+LADMDITF+AL+ETDIGRHVN+LRKHSSNDV++
Sbjct: 91  QRKILDIKEQLEDPHQSEDSLVELLQNLADMDITFQALEETDIGRHVNRLRKHSSNDVKR 150

Query: 180 LVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPNPHNG 239
           LVK LVRKWK+IVDEWVKL  PGE  ++ M D DSPQQ+I QNG+ Q+PDFAYSPNPH G
Sbjct: 151 LVKLLVRKWKEIVDEWVKLKAPGEPGTAVMADEDSPQQRILQNGHRQIPDFAYSPNPHYG 210

Query: 240 SSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPAAP 278
           S GS++NN E ERK K   +PRKEA S   P   +PA P
Sbjct: 211 SFGSERNNIEAERKPKA--IPRKEAPSKPSPSVTTPAPP 247

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088637|emb|CBI37628.3| unnamed protein product [Vitis vinifera]

 Score =  313 bits (801), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 166/274 (60%), Positives = 200/274 (72%), Gaps = 16/274 (5%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCD 60
           MD D+FR IL+ +GVDVW FI+TAI VA  DY  EL+ RRD IVER+Y   ++SRC +C+
Sbjct: 1   MDRDEFRLILRNSGVDVWEFINTAISVAYSDYGDELRHRRDGIVERMY---MSSRCGSCN 57

Query: 61  FGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDIDIENDNDIIDPYGGLFDDEQ 120
                  ++K     + DE    +  SP TP S+N     D          YGGL D+E+
Sbjct: 58  LRYQHSGLDKGCDEEKEDEKDDEKDKSPLTPQSINRSGSEDR---------YGGLLDEEE 108

Query: 121 KRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKL 180
            RIL+IKEHLE PDQ +D+++DLLQ+LADMDITFKALKETDIGRHVN+LRKH SNDVR+L
Sbjct: 109 ARILDIKEHLEAPDQPDDSIVDLLQTLADMDITFKALKETDIGRHVNRLRKHPSNDVRRL 168

Query: 181 VKHLVRKWKDIVDEWVKLNQPGELASSAMM-DGDSPQQKIPQNGNHQVPDFAYSPNPHNG 239
           VKHLVRKWKD+VDEWVK N  GE  SSA+M +GDSP QKIP+ G+HQVPDF YSPNP NG
Sbjct: 169 VKHLVRKWKDLVDEWVKSNPAGEFTSSALMAEGDSPPQKIPRTGHHQVPDFGYSPNPQNG 228

Query: 240 SSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSA 273
           SSGSDKNN+EPE K K   +PRKE + +RP QSA
Sbjct: 229 SSGSDKNNAEPEPKVKA--IPRKE-VPTRPAQSA 259

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516327|ref|XP_003526847.1| PREDICTED: uncharacterized protein LOC100804034 [Glycine max]

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 174/289 (60%), Positives = 207/289 (71%), Gaps = 15/289 (5%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIAS-RCRNC 59
           MDLDDFRS+L TAGVDVW FID AI VAS D A ELK RRD IVERLYA   A+ +CR C
Sbjct: 1   MDLDDFRSVLDTAGVDVWMFIDAAIAVASADSAGELKRRRDGIVERLYAATAATPKCRIC 60

Query: 60  DFGNGVVDVNKEISRGQHD---EVKAAQQASPSTPHSVNGDDDIDIENDNDI---IDPYG 113
           D G    D+N    + Q     E +  Q+ + +   + +      +ENDND    +DPYG
Sbjct: 61  DDGGN--DLNGHQIKKQSSPSPERQPHQRRAAAIAAAASPATPQSLENDNDGEEDLDPYG 118

Query: 114 GLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHS 173
           GLFDDEQK+ILEIKE LE+PDQSED+L++LLQSLADMDITF+ALKETDIGRHVN+LRKH 
Sbjct: 119 GLFDDEQKKILEIKEQLEEPDQSEDSLVELLQSLADMDITFQALKETDIGRHVNRLRKHP 178

Query: 174 SNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQ-QKIPQNGNH----QVP 228
           SNDVR+LVK LVRKWK+IVDEWVKLN  G  +++ M DGDSP  QK  QNG+H    ++P
Sbjct: 179 SNDVRRLVKLLVRKWKEIVDEWVKLNPQGR-SNTLMADGDSPPVQKTTQNGHHHQQVEIP 237

Query: 229 DFAYSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPAA 277
           DFAYSPNPHNGSSGSD+NNSE E K K  P        +  P  ++PA+
Sbjct: 238 DFAYSPNPHNGSSGSDRNNSEAEHKPKVVPRSEPRPKPAPSPSVSTPAS 286

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416107|ref|NP_568218.1| Transcription elongation factor (TFIIS) family protein [Arabidopsis thaliana] gi|395406779|sp|F4KFC7.1|MD26C_ARATH RecName: Full=Probable mediator of RNA polymerase II transcription subunit 26c gi|332004072|gb|AED91455.1| Transcription elongation factor (TFIIS) family protein [Arabidopsis thaliana]

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 163/286 (56%), Positives = 205/286 (71%), Gaps = 11/286 (3%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCD 60
           MDLDDFRS++  AGVDVWTFIDTAILVASLDY  ELK RRD IVERLYAT +A++CRNCD
Sbjct: 1   MDLDDFRSVMDNAGVDVWTFIDTAILVASLDYGQELKRRRDNIVERLYATSMANKCRNCD 60

Query: 61  FGNGVVDVNKEISRGQHDEVKAAQQASPSTPHSVNGDDDI-----DIENDNDIIDPYGGL 115
           FG G       I R  +  V    +       +   ++++     ++E+D+D  DP+ GL
Sbjct: 61  FGGGGNVTEAAIGRVNNGRVHEETEEEDEEGVTAAAEEEVREKSVNVEDDDDF-DPFAGL 119

Query: 116 FDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN 175
           FDDEQK I+EIKE LEDPD SE++L++LLQ+L DMDITF+AL+ETDIGRHVN++RKH SN
Sbjct: 120 FDDEQKSIVEIKEKLEDPDLSEESLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSN 179

Query: 176 DVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMM-DGDSPQQKIPQNGN-HQVPDFAYS 233
           +VR+L K LV+KWK+ VDEWVK NQPG+L   +++ D DSP QK   NG+  QVPDF YS
Sbjct: 180 NVRRLAKQLVKKWKETVDEWVKFNQPGDLEPPSLIADEDSPVQKALHNGSRQQVPDFGYS 239

Query: 234 PNPHNGSSGSDKNN--SEPERKSKQ-APLPRKEALSSRPPQSASPA 276
           P P NG S S KN+  +EPERK +  AP PR+E+ S   P   SP+
Sbjct: 240 PVPQNGYSSSSKNSNITEPERKPRPVAPQPRRESPSPAKPSRPSPS 285

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509008|ref|XP_003523244.1| PREDICTED: uncharacterized protein LOC100790582 [Glycine max]

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 175/285 (61%), Positives = 213/285 (74%), Gaps = 18/285 (6%)

Query: 1   MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYA-TCIASRCRNC 59
           MDLDDFRSIL TAGVDVW FID AI VAS D A +LK RRD IVERLYA T     CRNC
Sbjct: 1   MDLDDFRSILDTAGVDVWMFIDAAIAVASSDSAGDLKRRRDGIVERLYAATAAPPWCRNC 60

Query: 60  DFGNGVVDVNKEISRGQHDEV------KAAQQASPSTPHSVNGDDDIDIENDNDIIDPYG 113
           D G   ++ ++   + +H         ++   ASP+TP S++   + + E++++ +DPYG
Sbjct: 61  DEGGHRLNGHRIKKQSRHSPSPERQPHRSTATASPATPQSLD---NGEDEDNDEDLDPYG 117

Query: 114 GLFDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHS 173
           GL DDEQK+ILEIKE LE+PDQSED+L++LLQSLADMDITF+ LKETDIGRHVN+LRKH 
Sbjct: 118 GLLDDEQKKILEIKEQLEEPDQSEDSLVELLQSLADMDITFQGLKETDIGRHVNRLRKHP 177

Query: 174 SNDVRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGD-SPQQKIPQNGNH-QVPDFA 231
           SND+R+LVK LVRKWK+IVDEWVKLN P   +++ M DGD SP QK  QNG+H Q+PDFA
Sbjct: 178 SNDLRRLVKLLVRKWKEIVDEWVKLN-PRGGSNTLMADGDSSPVQKTTQNGHHQQIPDFA 236

Query: 232 YSPNPHNGSSGSDKNNSEPERKSKQAPLPRKEALSSRPPQSASPA 276
           YSPNPHNGSSGSD+NNSE ERK K   +PR E    RP  + SP+
Sbjct: 237 YSPNPHNGSSGSDRNNSEAERKPKV--VPRSEP---RPKHAPSPS 276

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	286
TAIR|locus:2178173	353	AT5G09850 [Arabidopsis thalian	0.919	0.745	0.573	5e-76
TAIR|locus:2156814	436	AT5G05140 [Arabidopsis thalian	0.790	0.518	0.306	5.4e-20
ZFIN|ZDB-GENE-040426-1860	409	tcea3 "transcription elongatio	0.437	0.305	0.320	2e-08
ZFIN|ZDB-GENE-040426-985	301	tcea2 "transcription elongatio	0.363	0.345	0.348	2.5e-06
UNIPROTKB|E5RIS7	111	TCEA1 "Transcription elongatio	0.265	0.684	0.333	2.9e-06
UNIPROTKB|A5PKE4	208	TCEANC2 "Transcription elongat	0.279	0.384	0.349	3.8e-06
UNIPROTKB|F1MBR2	208	TCEANC2 "Transcription elongat	0.279	0.384	0.349	3.8e-06
ZFIN|ZDB-GENE-030131-8049	309	tcea1 "transcription elongatio	0.265	0.245	0.341	4.7e-06
UNIPROTKB|Q5JRI8	82	TCEA2 "Transcription elongatio	0.185	0.646	0.444	6.3e-06
UNIPROTKB|Q96MN5	208	TCEANC2 "Transcription elongat	0.237	0.326	0.367	6.9e-06

TAIR|locus:2178173 AT5G09850 [Arabidopsis thaliana (taxid:3702)]

 Score = 766 (274.7 bits), Expect = 5.0e-76, P = 5.0e-76
 Identities = 156/272 (57%), Positives = 193/272 (70%)

Query:     1 MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCD 60
             MDLDDFRS++  AGVDVWTFIDTAILVASLDY  ELK RRD IVERLYAT +A++CRNCD
Sbjct:     1 MDLDDFRSVMDNAGVDVWTFIDTAILVASLDYGQELKRRRDNIVERLYATSMANKCRNCD 60

Query:    61 FGNG--VVDVN-KEISRGQ-HDEVKAAQQASPSTPHSVNGXXXXXXXXXXXXXXPYGGLF 116
             FG G  V +     ++ G+ H+E +   +   +                     P+ GLF
Sbjct:    61 FGGGGNVTEAAIGRVNNGRVHEETEEEDEEGVTAAAEEEVREKSVNVEDDDDFDPFAGLF 120

Query:   117 DDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSND 176
             DDEQK I+EIKE LEDPD SE++L++LLQ+L DMDITF+AL+ETDIGRHVN++RKH SN+
Sbjct:   121 DDEQKSIVEIKEKLEDPDLSEESLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNN 180

Query:   177 VRKLVKHLVRKWKDIVDEWVKLNQPGELASSAMM-DGDSPQQKIPQNGNHQ-VPDFAYSP 234
             VR+L K LV+KWK+ VDEWVK NQPG+L   +++ D DSP QK   NG+ Q VPDF YSP
Sbjct:   181 VRRLAKQLVKKWKETVDEWVKFNQPGDLEPPSLIADEDSPVQKALHNGSRQQVPDFGYSP 240

Query:   235 NPHNGSSGSDKNNS--EPERKSKQ-APLPRKE 263
              P NG S S KN++  EPERK +  AP PR+E
Sbjct:   241 VPQNGYSSSSKNSNITEPERKPRPVAPQPRRE 272

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

GO:0016021 "integral to membrane" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2156814 AT5G05140 [Arabidopsis thaliana (taxid:3702)]

 Score = 242 (90.2 bits), Expect = 5.4e-20, P = 5.4e-20
 Identities = 79/258 (30%), Positives = 121/258 (46%)

Query:     3 LDDFRSILKTAG-VDVWTFIDTAILVASLDYATELKERRDKIVERLYATCIASRCRNCDF 61
             LD +R   +  G  D++  ID AI+VA+ D   + K RRDKI E L++ C  +RC  CD 
Sbjct:     7 LDSWREYFRRRGDSDIFGIIDHAIMVAATDCPNKFKSRRDKIAELLFS-CRVNRCVGCDH 65

Query:    62 GNGVVDVNKEISRGQ----------HDEVKAAQQASPSTPHSVNGXXXXXXXXXXXXXXP 111
                 V  + E +RG            ++ + A  +  S  +S  G               
Sbjct:    66 LELSVPGDDEANRGTTGNGGGGTAVDEDYEVAGGSKESKANSSRGDNNQIVSNYTFDEAE 125

Query:   112 YGGLFDD-EQ-----KRILEIKEHL-EDPDQSEDALIDLLQSLADMDITFKALKETDIGR 164
                L D+ E+     K +  IKE L    D+    L+D L+ L  M +    LK T+IG+
Sbjct:   126 --ALSDEIEEFSVVSKEVARIKEILLNKEDEPNSVLLDSLRHLKLMSLNVDILKSTEIGK 183

Query:   165 HVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKLNQP--G-----ELASSAMMDGDSPQQ 217
              VN LRKHSS+ +R+L K L+ +WK++VD+WV   +   G     E A+ +++D +    
Sbjct:   184 AVNGLRKHSSDKIRQLAKTLIAEWKELVDQWVNTTKEITGAEGTPESANPSVLDEEEAFP 243

Query:   218 KIPQNGNHQVPDFAYSPN 235
              +P    + V  F   PN
Sbjct:   244 SLP----YDVDIFTPEPN 257

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

GO:0016021 "integral to membrane" evidence=IEA

GO:0009611 "response to wounding" evidence=RCA

GO:0009620 "response to fungus" evidence=RCA

GO:0009695 "jasmonic acid biosynthetic process" evidence=RCA

GO:0009753 "response to jasmonic acid stimulus" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

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

 Score = 151 (58.2 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 43/134 (32%), Positives = 67/134 (50%)

Query:   138 DALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN-DVRKLVKHLVRKWKDIVD--E 194
             D  +DLL+ L D ++T K L++T IG  VN +RKH ++ DV  L K L++ WK +++  +
Sbjct:    24 DGALDLLRELKDFNMTLKLLQDTRIGMSVNGIRKHCTDEDVVNLAKILIKNWKRLLESAQ 83

Query:   195 WVKLNQPGEL--ASSAMMDGDSPQQKIPQNGNHQ-VP-DFAYSP--NPHNGSSGSDKNNS 248
               K  +P E+   S       SP +  P+  + +  P DF   P  N H     S  +  
Sbjct:    84 NPKSERPNEVKNGSHPSKPSGSPSRTSPEKDSRKDAPVDFFPPPSINSHPPLRRSSVDVK 143

Query:   249 EPERKSKQAPLPRK 262
               +    + PLPRK
Sbjct:   144 RKDSTDSKKPLPRK 157

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

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

 Score = 131 (51.2 bits), Expect = 2.5e-06, P = 2.5e-06
 Identities = 39/112 (34%), Positives = 61/112 (54%)

Query:   117 DDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSND 176
             D E +RI +  + +    ++ D  IDLLQ L +M ++ + L+ T IG  VN +RK SS++
Sbjct:     4 DQEVERIAKKLDKMVHK-KNTDGAIDLLQELKNMKMSLETLQSTRIGMSVNAVRKQSSDE 62

Query:   177 -VRKLVKHLVRKWKDIVD--EWVKLNQPGE--LASSAMMD--GDSPQQKIPQ 221
              V+ L K L++ WK ++D  E     + GE  L SS+  D  G S     P+
Sbjct:    63 EVQTLAKSLIKAWKKLLDGSEGKPEEKKGESPLQSSSSKDCPGSSDTSNKPE 114

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|E5RIS7 TCEA1 "Transcription elongation factor A protein 1" [Homo sapiens (taxid:9606)]

 Score = 112 (44.5 bits), Expect = 2.9e-06, P = 2.9e-06
 Identities = 26/78 (33%), Positives = 45/78 (57%)

Query:   117 DDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSND 176
             +DE  R  +  + +     +  AL DLL+ L ++ +T + L+ T IG  VN +RK S+++
Sbjct:     2 EDEVVRFAKKMDKMVQKKNAAGAL-DLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDE 60

Query:   177 -VRKLVKHLVRKWKDIVD 193
              V  L K L++ WK ++D
Sbjct:    61 EVTSLAKSLIKSWKKLLD 78

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|A5PKE4 TCEANC2 "Transcription elongation factor A N-terminal and central domain-containing protein 2" [Bos taurus (taxid:9913)]

 Score = 125 (49.1 bits), Expect = 3.8e-06, P = 3.8e-06
 Identities = 29/83 (34%), Positives = 50/83 (60%)

Query:   127 KEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVR 186
             K  LE PDQS++ L++ L+ L     + + LK T IG  VN++R+HS ++V  L + +  
Sbjct:    46 KTMLELPDQSKENLVEALRELKKKIPSREVLKSTKIGHTVNKMRQHSDSEVACLAREVYT 105

Query:   187 KWKDIVDEWVKLNQPG-ELASSA 208
             +W+  +++ V  N+P  E+ S A
Sbjct:   106 EWRTFIEKHV--NRPSIEVRSDA 126

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1MBR2 TCEANC2 "Transcription elongation factor A N-terminal and central domain-containing protein 2" [Bos taurus (taxid:9913)]

 Score = 125 (49.1 bits), Expect = 3.8e-06, P = 3.8e-06
 Identities = 29/83 (34%), Positives = 50/83 (60%)

Query:   127 KEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVR 186
             K  LE PDQS++ L++ L+ L     + + LK T IG  VN++R+HS ++V  L + +  
Sbjct:    46 KTMLELPDQSKENLVEALRELKKKIPSREVLKSTKIGHTVNKMRQHSDSEVACLAREVYT 105

Query:   187 KWKDIVDEWVKLNQPG-ELASSA 208
             +W+  +++ V  N+P  E+ S A
Sbjct:   106 EWRTFIEKHV--NRPSIEVRSDA 126

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 129 (50.5 bits), Expect = 4.7e-06, P = 4.7e-06
 Identities = 27/79 (34%), Positives = 50/79 (63%)

Query:   119 EQKRILEIKEHLEDPDQSEDAL--IDLLQSLADMDITFKALKETDIGRHVNQLRKHSSND 176
             E++ I+ I + ++   Q ++ +  +DLL+ L ++ +T + L+ T IG  VN +RK S++D
Sbjct:     5 EEEEIIRIAKKMDKMAQKKNGVGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDD 64

Query:   177 -VRKLVKHLVRKWKDIVDE 194
              V  L K L++ WK ++DE
Sbjct:    65 EVTSLAKSLIKSWKKLLDE 83

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|Q5JRI8 TCEA2 "Transcription elongation factor A protein 2" [Homo sapiens (taxid:9606)]

 Score = 109 (43.4 bits), Expect = 6.3e-06, P = 6.3e-06
 Identities = 24/54 (44%), Positives = 34/54 (62%)

Query:   141 IDLLQSLADMDITFKALKETDIGRHVNQLRKHSSND-VRKLVKHLVRKWKDIVD 193
             +DLL+ L  M IT   L+ T +G  VN LRK SS++ V  L K L++ WK ++D
Sbjct:     1 MDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLLD 54

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|Q96MN5 TCEANC2 "Transcription elongation factor A N-terminal and central domain-containing protein 2" [Homo sapiens (taxid:9606)]

 Score = 123 (48.4 bits), Expect = 6.9e-06, P = 6.9e-06
 Identities = 25/68 (36%), Positives = 41/68 (60%)

Query:   127 KEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVR 186
             K  LE PDQ+++ L++ LQ L     + + LK T IG  VN++RKHS ++V  L + +  
Sbjct:    46 KTMLELPDQTKENLVEALQELKKKIPSREVLKSTRIGHTVNKMRKHSDSEVASLAREVYT 105

Query:   187 KWKDIVDE 194
             +WK   ++
Sbjct:   106 EWKTFTEK 113

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
F4KFC7	MD26C_ARATH	No assigned EC number	0.5699	0.9615	0.7790	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

Fail to connect to STRING server

---

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	286
cd00183	76	cd00183, TFIIS_I, N-terminal domain (domain I) of	5e-20
pfam08711	51	pfam08711, Med26, TFIIS helical bundle-like domain	2e-15
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	8e-12
smart00509	75	smart00509, TFS2N, Domain in the N-terminus of tra	9e-12

>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 = 81.6 bits (202), Expect = 5e-20
 Identities = 34/76 (44%), Positives = 49/76 (64%), Gaps = 2/76 (2%)

Query: 120 QKRILEIKEHLEDPDQSE--DALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDV 177
            + +L  K+ LE  D +E    L+DLL+ L  + +T + LKET IG+ VN LRKHS+  +
Sbjct: 1   SEEVLRAKKKLEKKDSNEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKI 60

Query: 178 RKLVKHLVRKWKDIVD 193
           RKL K L++ WK +VD
Sbjct: 61  RKLAKALIKSWKKLVD 76

Length = 76

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

 Score = 68.3 bits (168), Expect = 2e-15
 Identities = 25/51 (49%), Positives = 38/51 (74%)

Query: 142 DLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIV 192
           +LL+ L  + IT + L+ET IG+ VN+LRKH + +V+KL K L++KWK +V
Sbjct: 1   ELLKELKKLPITEELLRETGIGKAVNKLRKHENEEVKKLAKKLIKKWKRLV 51

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

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

 Score = 64.1 bits (156), Expect = 8e-12
 Identities = 31/112 (27%), Positives = 52/112 (46%), Gaps = 11/112 (9%)

Query: 121 KRILEIKEHLEDPDQSED--ALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVR 178
             +    + L+    S++    +D+L  L +   T + L+ET +G  VN+LRKH + D+ 
Sbjct: 2   AEVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDIS 61

Query: 179 KLVKHLVRKWKDIVDEW---------VKLNQPGELASSAMMDGDSPQQKIPQ 221
           KL K +++ WK +VD+                GE  +S   +  S   KI Q
Sbjct: 62  KLAKKIIKSWKKVVDKNKSDHPGGNPEDKTTVGESVNSVKQEAKSQSDKIEQ 113

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

 Score = 59.2 bits (144), Expect = 9e-12
 Identities = 24/57 (42%), Positives = 36/57 (63%)

Query: 138 DALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDE 194
              +D+L+ L  + IT   L+ET IG+ VN LRKH + ++RKL K L++ WK +V  
Sbjct: 19  SRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVYS 75

Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	286
cd00183	76	TFIIS_I N-terminal domain (domain I) of transcript	99.75
smart00509	75	TFS2N Domain in the N-terminus of transcription el	99.68
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.64
PF08711	53	Med26: TFIIS helical bundle-like domain; InterPro:	99.52
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	99.35
KOG2821	433	consensus RNA polymerase II transcription elongati	97.43
PF11467	106	LEDGF: Lens epithelium-derived growth factor (LEDG	96.23
KOG1793	417	consensus Uncharacterized conserved protein [Funct	95.11
COG5139	397	Uncharacterized conserved protein [Function unknow	92.12
cd08815	77	Death_TNFRSF25_DR3 Death domain of Tumor Necrosis	91.46
PLN02976	1713	amine oxidase	90.06

>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=99.75  E-value=1.6e-18  Score=133.04  Aligned_cols=73  Identities=45%  Similarity=0.766  Sum_probs=68.9

Q ss_pred             HHHHHHHHHhCCCCC--CHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcCCCHHHHHHHHHHHHHHHHHHH
Q 023203          121 KRILEIKEHLEDPDQ--SEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVD  193 (286)
Q Consensus       121 ~EV~rIKk~Ld~~~~--sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH~s~~I~~LAk~LV~kWK~~V~  193 (286)
                      +++.++++.|+...+  +.+.++++|+.|+.+|||.++|++|+||+.||+||||.+++|+.+|+.||++||++|+
T Consensus         2 ~ev~r~~~~l~~~~~~~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~   76 (76)
T cd00183           2 EEVLRAKKKLEKKDSNEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD   76 (76)
T ss_pred             hHHHHHHHHhhccccCCCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence            479999999999765  8889999999999999999999999999999999999999999999999999999873

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

Probab=99.68  E-value=3.5e-17  Score=125.88  Aligned_cols=58  Identities=41%  Similarity=0.738  Sum_probs=55.9

Q ss_pred             CHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcCCCHHHHHHHHHHHHHHHHHHH
Q 023203          136 SEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVD  193 (286)
Q Consensus       136 sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH~s~~I~~LAk~LV~kWK~~V~  193 (286)
                      +.+.++++|+.|+.++||+++|+.|+||++||+||||++++|+.+|+.||++||++|+
T Consensus        17 ~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~   74 (75)
T smart00509       17 EVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY   74 (75)
T ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence            4788999999999999999999999999999999999999999999999999999985

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.64  E-value=6.3e-16  Score=145.99  Aligned_cols=75  Identities=31%  Similarity=0.580  Sum_probs=70.4

Q ss_pred             HHHHHHHHHhCCCC--CCHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcCCCHHHHHHHHHHHHHHHHHHHHh
Q 023203          121 KRILEIKEHLEDPD--QSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEW  195 (286)
Q Consensus       121 ~EV~rIKk~Ld~~~--~sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH~s~~I~~LAk~LV~kWK~~V~e~  195 (286)
                      +||.++++.|+++.  .+++.+|++|++|+.++||+++|++|+||++||+||||++++|+.||+.||++||++|..+
T Consensus         2 ~ei~~~~k~L~k~~~~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~   78 (299)
T TIGR01385         2 AEVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKN   78 (299)
T ss_pred             hHHHHHHHHhhhhccCCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhh
Confidence            37999999998854  3778899999999999999999999999999999999999999999999999999999997

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.

>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=99.52  E-value=1.1e-14  Score=104.11  Aligned_cols=52  Identities=50%  Similarity=0.872  Sum_probs=47.5

Q ss_pred             HHHHHhhcCCCcHHHhhccCccccchhhhcC-CCHHHHHHHHHHHHHHHHHHH
Q 023203          142 DLLQSLADMDITFKALKETDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDIVD  193 (286)
Q Consensus       142 elLr~L~~l~iT~dlLksT~IGkaVN~LRKH-~s~~I~~LAk~LV~kWK~~V~  193 (286)
                      ++|+.|+.+|||.++|++|+||++||.|||| .+++|+++|+.||++||.+|+
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 889999999999999999985

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.

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

Probab=99.35  E-value=2.1e-12  Score=122.13  Aligned_cols=75  Identities=37%  Similarity=0.628  Sum_probs=68.5

Q ss_pred             HHHHHHHHHhCCCCC--CHHHHHHHHHHhhcCCCcHHHhhccCccccch-hhhcCCCHHHHHHHHHHHHHHHHHHHHh
Q 023203          121 KRILEIKEHLEDPDQ--SEDALIDLLQSLADMDITFKALKETDIGRHVN-QLRKHSSNDVRKLVKHLVRKWKDIVDEW  195 (286)
Q Consensus       121 ~EV~rIKk~Ld~~~~--sed~llelLr~L~~l~iT~dlLksT~IGkaVN-~LRKH~s~~I~~LAk~LV~kWK~~V~e~  195 (286)
                      ++++++.+.|++..+  +.+.++++|.+|+.+|||+++|++|+||+.|| .|++|++++|+.+|+.||+.||++|...
T Consensus         4 e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~   81 (296)
T KOG1105|consen    4 EEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS   81 (296)
T ss_pred             HHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence            479999999998654  56789999999999999999999999999999 5678899999999999999999999975

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

Probab=97.43  E-value=8.4e-05  Score=74.08  Aligned_cols=73  Identities=34%  Similarity=0.458  Sum_probs=64.9

Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcCCCHHHHHHHHHHHHHHHHHHHHhh
Q 023203          121 KRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWV  196 (286)
Q Consensus       121 ~EV~rIKk~Ld~~~~sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH~s~~I~~LAk~LV~kWK~~V~e~~  196 (286)
                      .-|.+|...|++. .....++..|..|..+|++++.|.+|.||++|+.||||.  .+..++..|+..||++|....
T Consensus         9 ~~Vr~lQ~~l~~~-~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~d~   81 (433)
T KOG2821|consen    9 GAVRKLQARLENR-IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLVDF   81 (433)
T ss_pred             HHHHHHHHHHHhC-ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhccccc
Confidence            4577788888864 567889999999999999999999999999999999996  799999999999999997443

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

Probab=96.23  E-value=0.0079  Score=49.80  Aligned_cols=69  Identities=22%  Similarity=0.340  Sum_probs=51.4

Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHhhcCCCcHHHhhc-cCccccchhhhcC-CCHHHHHHHHHHHHHHHHHHH
Q 023203          125 EIKEHLEDPDQSEDALIDLLQSLADMDITFKALKE-TDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDIVD  193 (286)
Q Consensus       125 rIKk~Ld~~~~sed~llelLr~L~~l~iT~dlLks-T~IGkaVN~LRKH-~s~~I~~LAk~LV~kWK~~V~  193 (286)
                      .|+..|--...+...++++|..|..|+||..+|+. +.+--++.+||+. .|..|++.|..|+.+.|.++-
T Consensus        10 ~Ik~~L~~~~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~   80 (106)
T PF11467_consen   10 EIKSSLKVDNPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL   80 (106)
T ss_dssp             HHHHTCETTEE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence            34444432234788999999999999999998875 4588899999998 468999999999999999995

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.

>KOG1793 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.11  E-value=0.023  Score=56.65  Aligned_cols=52  Identities=29%  Similarity=0.519  Sum_probs=45.9

Q ss_pred             HHHHHHhhcCCCcH-HHhhccCccccchhhhcCCC--HHHHHHHHHHHHHHHHHH
Q 023203          141 IDLLQSLADMDITF-KALKETDIGRHVNQLRKHSS--NDVRKLVKHLVRKWKDIV  192 (286)
Q Consensus       141 lelLr~L~~l~iT~-dlLksT~IGkaVN~LRKH~s--~~I~~LAk~LV~kWK~~V  192 (286)
                      ..+|.-|..+||-. +.|+..+||++|==|-||+.  ..++.+|..||.+|-.-|
T Consensus       236 ~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI  290 (417)
T KOG1793|consen  236 KSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPI  290 (417)
T ss_pred             HHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccc
Confidence            45677788888888 99999999999999999975  799999999999997755

>COG5139 Uncharacterized conserved protein [Function unknown]

Probab=92.12  E-value=0.17  Score=49.35  Aligned_cols=51  Identities=31%  Similarity=0.513  Sum_probs=42.7

Q ss_pred             HHHHHhhcCCCcHHHhhccCccccchhh--hcCCCHHHHHHHHHHHHHHHHHH
Q 023203          142 DLLQSLADMDITFKALKETDIGRHVNQL--RKHSSNDVRKLVKHLVRKWKDIV  192 (286)
Q Consensus       142 elLr~L~~l~iT~dlLksT~IGkaVN~L--RKH~s~~I~~LAk~LV~kWK~~V  192 (286)
                      .+|..|..|||-.+.|+..+||+.|==.  -|...++|+.+|+.||.+|-.-|
T Consensus       234 sL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpI  286 (397)
T COG5139         234 SLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPI  286 (397)
T ss_pred             HHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhccc
Confidence            3566777899999999999999998755  45566899999999999997654

>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25

Probab=91.46  E-value=0.19  Score=39.78  Aligned_cols=40  Identities=20%  Similarity=0.265  Sum_probs=34.6

Q ss_pred             ChhHHHHHHHhcCCchHHHHHHHHHHhccCChHHHHHHHHHHHHHHHhh
Q 023203            2 DLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYAT   50 (286)
Q Consensus         2 ~ld~wR~ff~~~g~dI~~~ID~AI~VAA~D~p~elR~RRD~IvErL~~a   50 (286)
                      +.++|+.|||..|     +=|+.|..|-.++    |..||.+-+||-.=
T Consensus        10 P~~~wk~F~R~LG-----Lsdn~Ie~~E~~~----~~~rda~y~ML~~W   49 (77)
T cd08815          10 PARRWKEFVRTLG-----LREAEIEAVELEI----GRFRDQQYEMLKRW   49 (77)
T ss_pred             ChHHHHHHHHHcC-----CcHhHHHHHHhcc----cchHHHHHHHHHHH
Confidence            3689999999999     8899999998777    66789999999874

Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.

>PLN02976 amine oxidase

Probab=90.06  E-value=0.55  Score=54.01  Aligned_cols=61  Identities=21%  Similarity=0.365  Sum_probs=51.8

Q ss_pred             HHHHHHHHHhhcCCCcHHHhhccCccccch-hhhcCCCHHHHHHHHHHHHHHHHHHHHhhhc
Q 023203          138 DALIDLLQSLADMDITFKALKETDIGRHVN-QLRKHSSNDVRKLVKHLVRKWKDIVDEWVKL  198 (286)
Q Consensus       138 d~llelLr~L~~l~iT~dlLksT~IGkaVN-~LRKH~s~~I~~LAk~LV~kWK~~V~e~~~~  198 (286)
                      +-+...|+-|-.++..+..|+..+|||+|. ++.-|.+.+|+.+|++|+..|.+.+......
T Consensus      1301 ~l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~~ 1362 (1713)
T PLN02976       1301 QLLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKAS 1362 (1713)
T ss_pred             HHHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            345667777777888888999999999996 4789999999999999999999999877543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	286
1wjt_A	103	Solution Structure Of The N-Terminal Domain I Of Mo		3e-05
1pqv_S	309	Rna Polymerase Ii-Tfiis Complex Length = 309		2e-04

>pdb|1WJT|A Chain A, Solution Structure Of The N-Terminal Domain I Of Mouse Transcription Elongation Factor S-Ii Protein 3 Length = 103

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 116 FDDEQKRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN 175
            ++E  RI +  E +    ++E AL DLL+ L    ++ + L+ T IG  VN +RKH S+
Sbjct: 10  LEEELLRIAKKLEKMVSRKKTEGAL-DLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSD 68
Query: 176 -DVRKLVKHLVRKWKDIVD 193
            +V  L K L++ WK ++D
Sbjct: 69  KEVVSLAKVLIKNWKRLLD 87

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 46/75 (61%), Gaps = 1/75 (1%)
Query: 121 KRILEIKEHLEDPDQSEDALIDLLQSL-ADMDITFKALKETDIGRHVNQLRKHSSNDVRK 179
           K +L   ++LE    ++ A++++L  L  +   T K L+ET +G  VN+ +K ++ ++ K
Sbjct: 4   KEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISK 63
Query: 180 LVKHLVRKWKDIVDE 194
           LVK ++  WKD +++
Sbjct: 64  LVKKMISSWKDAINK 78

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	286
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	2e-24
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	3e-19
2xpp_A	145	IWS1, ECU08_0440; transcription, elongation, histo	9e-07
3nfq_A	170	Transcription factor IWS1; SPN1, RNA polymerase II	4e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>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 Length = 103

 Score = 93.9 bits (233), Expect = 2e-24
 Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 3/94 (3%)

Query: 118 DEQKRILEIKEHLED--PDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN 175
             ++ +L I + LE     +  +  +DLL+ L    ++ + L+ T IG  VN +RKH S+
Sbjct: 9   GLEEELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSD 68

Query: 176 D-VRKLVKHLVRKWKDIVDEWVKLNQPGELASSA 208
             V  L K L++ WK ++D         E   S+
Sbjct: 69  KEVVSLAKVLIKNWKRLLDSPRTTKGERESGPSS 102

>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 = 84.8 bits (208), Expect = 3e-19
 Identities = 25/134 (18%), Positives = 58/134 (43%), Gaps = 1/134 (0%)

Query: 119 EQKRILEIKEHLEDPDQSEDALIDLLQSL-ADMDITFKALKETDIGRHVNQLRKHSSNDV 177
           + K +L   ++LE    ++ A++++L  L  +   T K L+ET +G  VN+ +K ++ ++
Sbjct: 2   DSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEI 61

Query: 178 RKLVKHLVRKWKDIVDEWVKLNQPGELASSAMMDGDSPQQKIPQNGNHQVPDFAYSPNPH 237
            KLVK ++  WKD +++  +  Q  +            +  + ++ N      +   +  
Sbjct: 62  SKLVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAM 121

Query: 238 NGSSGSDKNNSEPE 251
                        +
Sbjct: 122 KQDKYVSTKPRNSK 135

>2xpp_A IWS1, ECU08_0440; transcription, elongation, histone chaperone, RNA polymerase mRNA export; 1.74A {Encephalitozoon cuniculi} PDB: 2xpo_A 2xpn_A 2xpl_A Length = 145

 Score = 46.5 bits (110), Expect = 9e-07
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 142 DLLQSLADMDITFKALKETDIGRHVNQLRKHS--SNDVRKLVKHLVRKWK 189
            LL  L  M I  + L  + +G+ V     +   S +VR   K LV+KW 
Sbjct: 86  RLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWT 135

>3nfq_A Transcription factor IWS1; SPN1, RNA polymerase II; 1.85A {Saccharomyces cerevisiae} PDB: 3o8z_A 3oak_A Length = 170

 Score = 42.4 bits (99), Expect = 4e-05
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 142 DLLQSLADMDITFKALKETDIGRHVNQLRKHS--SNDVRKLVKHLVRKWK 189
            L  +L D+ +  + LKE+ +GR V    K       + +L + L+ +W 
Sbjct: 101 SLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWT 150

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

 Score = 42.5 bits (99), Expect = 1e-04
 Identities = 38/258 (14%), Positives = 72/258 (27%), Gaps = 78/258 (30%)

Query: 16  DVW------TF-IDTAILVASLDYATELKERRDK-IVERLYATCIASRCRNCDFGNGVVD 67
           +V        F +   IL+ +          R K + + L A               +  
Sbjct: 252 NVQNAKAWNAFNLSCKILLTT----------RFKQVTDFLSAATTTHIS--------LDH 293

Query: 68  VNKEISRGQHDEV--KAAQQASPSTPHSVNGDDDID----------IENDNDIIDPYGGL 115
            +  ++  +   +  K         P  V      +          I +     D +  +
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKHV 350

Query: 116 FDDEQKRILEIK-EHLEDPDQSEDALIDLLQSLA----DMDITFKAL-------KETDIG 163
             D+   I+E     LE  +  +     +   L+       I    L        ++D+ 
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRK-----MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405

Query: 164 RHVNQLRKHSSNDVRKLVKHLVRKWK--------DI-VDEWVKLNQPGELASSAMMDGDS 214
             VN+L K+S          LV K           I ++  VKL     L  S ++D  +
Sbjct: 406 VVVNKLHKYS----------LVEKQPKESTISIPSIYLELKVKLENEYALHRS-IVDHYN 454

Query: 215 PQQKIPQNGNHQVPDFAY 232
             +    +         Y
Sbjct: 455 IPKTFDSDDLIPPYLDQY 472

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	286
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	99.77
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.65
2xpp_A	145	IWS1, ECU08_0440; transcription, elongation, histo	97.98
3nfq_A	170	Transcription factor IWS1; SPN1, RNA polymerase II	97.78
2b4j_C	98	PC4 and SFRS1 interacting protein; HIV, integratio	95.52
1z9e_A	127	PC4 and SFRS1 interacting protein 2; heat repeat-l	94.61

>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=99.77  E-value=6.2e-20  Score=148.22  Aligned_cols=78  Identities=32%  Similarity=0.565  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHhCCC--CCCHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcC-CCHHHHHHHHHHHHHHHHHHHHhh
Q 023203          120 QKRILEIKEHLEDP--DQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDIVDEWV  196 (286)
Q Consensus       120 ~~EV~rIKk~Ld~~--~~sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH-~s~~I~~LAk~LV~kWK~~V~e~~  196 (286)
                      ++||++|++.|++.  ..+.+.++++|++|+.++||+++|++|+||++||+|||| ++++|+.+|+.||++||++|..+.
T Consensus        11 e~ev~~i~k~L~k~~~~~~~~~~l~~L~~L~~~~iT~e~L~~T~IGk~Vn~LrKh~~~~~V~~lAk~Lv~~WK~~v~~~~   90 (103)
T 1wjt_A           11 EEELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLLDSPR   90 (103)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSSHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHHHHHHHHTCCSC
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhCCCCCHHHHHHcchhHHHHHHHccCCcHHHHHHHHHHHHHHHHHHHHhc
Confidence            46899999998874  345678999999999999999999999999999999999 789999999999999999999865


Q ss_pred             h
Q 023203          197 K  197 (286)
Q Consensus       197 ~  197 (286)
                      +
T Consensus        91 ~   91 (103)
T 1wjt_A           91 T   91 (103)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.65  E-value=1.8e-16  Score=148.17  Aligned_cols=79  Identities=29%  Similarity=0.529  Sum_probs=74.2

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHh-hcCCCcHHHhhccCccccchhhhcCCCHHHHHHHHHHHHHHHHHHHHhhhc
Q 023203          120 QKRILEIKEHLEDPDQSEDALIDLLQSL-ADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKL  198 (286)
Q Consensus       120 ~~EV~rIKk~Ld~~~~sed~llelLr~L-~~l~iT~dlLksT~IGkaVN~LRKH~s~~I~~LAk~LV~kWK~~V~e~~~~  198 (286)
                      ++||++|++.|++...+.+.++++|++| +.++||+++|++|+||++||+||||.+++|+.+|+.||++||++|..+...
T Consensus         3 ~~el~~~~~~L~k~~~~~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~~WK~~v~~~~~~   82 (309)
T 1pqv_S            3 SKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAINKNKRS   82 (309)
T ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHhcCCCCHHHHHhCChhHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhccC
Confidence            4689999999999667889999999999 999999999999999999999999999999999999999999999998654

>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=97.98  E-value=5.1e-06  Score=70.64  Aligned_cols=69  Identities=32%  Similarity=0.380  Sum_probs=55.9

Q ss_pred             HHHHHHhCCC-C---CCHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcCCC--HHHHHHHHHHHHHHHHHH
Q 023203          124 LEIKEHLEDP-D---QSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSS--NDVRKLVKHLVRKWKDIV  192 (286)
Q Consensus       124 ~rIKk~Ld~~-~---~sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH~s--~~I~~LAk~LV~kWK~~V  192 (286)
                      ..|+.-|+-. +   .+..---.+|+.|..|||+.+.|+.++|||+|.-|.||+.  ++++++|+.||.+|...+
T Consensus        64 ~~l~~WL~PLpDgsLP~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvv~~l~k~~~et~~nk~la~~Li~~WsRpi  138 (145)
T 2xpp_A           64 DEIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEV  138 (145)
T ss_dssp             HHHHHHHSCCTTSCCCCHHHHHHHHHHHHTSCCCHHHHHHHCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCCCCCCCCHHHHHHHHHHHHHCCCCHHHhhcCCCCcchhhhhcCCccCHHHHHHHHHHHHHHHHHH
Confidence            3444455531 2   2455557788889999999999999999999999999976  799999999999998765

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

Probab=97.78  E-value=1.4e-05  Score=69.63  Aligned_cols=56  Identities=25%  Similarity=0.421  Sum_probs=48.5

Q ss_pred             CHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcCCC--HHHHHHHHHHHHHHHHH
Q 023203          136 SEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSS--NDVRKLVKHLVRKWKDI  191 (286)
Q Consensus       136 sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH~s--~~I~~LAk~LV~kWK~~  191 (286)
                      +..---.+|+.|..|||+.+.|+.++|||+|.-|.||+.  ++++.+|..||.+|..-
T Consensus        95 ~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvV~~l~k~~~et~~nkrla~~Li~~WsRp  152 (170)
T 3nfq_A           95 SFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWTRP  152 (170)
T ss_dssp             CHHHHHHHHHHHHTSCCCHHHHHHHSHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTCC
T ss_pred             cHHHHHHHHHHHHHCCCCHHHHhhCCCCceeeehhcCCcccHHHHHHHHHHHHHHHHH
Confidence            344456778888899999999999999999999999976  78999999999999543

>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=95.52  E-value=0.032  Score=44.64  Aligned_cols=69  Identities=22%  Similarity=0.340  Sum_probs=55.0

Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHhhcCCCcHHHhh-ccCccccchhhhcC-CCHHHHHHHHHHHHHHHHHHH
Q 023203          125 EIKEHLEDPDQSEDALIDLLQSLADMDITFKALK-ETDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDIVD  193 (286)
Q Consensus       125 rIKk~Ld~~~~sed~llelLr~L~~l~iT~dlLk-sT~IGkaVN~LRKH-~s~~I~~LAk~LV~kWK~~V~  193 (286)
                      .|+..|--...+...++++|..|..|++|.-+|+ .+.+=-++.+||+. .+..|++.|..|+.+.|.++.
T Consensus        14 ~ik~~L~~~~~Dv~kcl~~L~~l~~l~~T~~mL~rnpe~V~t~kklRry~g~q~Ir~kA~~iY~kfK~~f~   84 (98)
T 2b4j_C           14 EIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL   84 (98)
T ss_dssp             HHHHHTCTTSCCHHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHccCCCCHHHHHHHHHHHhcccccHHHHhhChHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHh
Confidence            3444444334578999999999999999999665 55688899999886 569999999999999999885

>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=94.61  E-value=0.044  Score=45.74  Aligned_cols=68  Identities=21%  Similarity=0.327  Sum_probs=55.6

Q ss_pred             HHHHhCCCCCCHHHHHHHHHHhhcCCCcHHHhh-ccCccccchhhhcC-CCHHHHHHHHHHHHHHHHHHH
Q 023203          126 IKEHLEDPDQSEDALIDLLQSLADMDITFKALK-ETDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDIVD  193 (286)
Q Consensus       126 IKk~Ld~~~~sed~llelLr~L~~l~iT~dlLk-sT~IGkaVN~LRKH-~s~~I~~LAk~LV~kWK~~V~  193 (286)
                      |+..|--...+...++++|..|..|++|.-+|+ .+.|=-++.+||+. .|..|++.|..|+.+.|.++.
T Consensus        15 Ik~~L~v~~~Dv~kCl~~Leel~~l~vT~~mL~Rnpe~V~TlkklRrY~gnq~Ir~kA~~iY~kFK~lf~   84 (127)
T 1z9e_A           15 IKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL   84 (127)
T ss_dssp             HHHHTCGGGCCHHHHHHHHHHHHHSCCCHHHHGGGHHHHHHHHHHTTCTTCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCCCCHHHHHHHHHHHccccccHHHHhhChHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence            333343223578899999999999999999666 55688899999886 568999999999999999996

---

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	286
d1eo0a_	77	a.48.3.1 (A:) Transcription elongation factor TFII	2e-24
d1wjta_	103	a.48.3.1 (A:) Transcription elongation factor S-II	1e-20

>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 = 91.4 bits (227), Expect = 2e-24
 Identities = 23/76 (30%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 119 EQKRILEIKEHLEDPDQSEDALIDLLQSL-ADMDITFKALKETDIGRHVNQLRKHSSNDV 177
           + K +L   ++LE    ++ A++++L  L  +   T K L+ET +G  VN+ +K ++ ++
Sbjct: 2   DSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEI 61

Query: 178 RKLVKHLVRKWKDIVD 193
            KLVK ++  WKD ++
Sbjct: 62  SKLVKKMISSWKDAIN 77

>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 = 82.3 bits (203), Expect = 1e-20
 Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 3/91 (3%)

Query: 120 QKRILEIKEHLED--PDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSN-D 176
           ++ +L I + LE     +  +  +DLL+ L    ++ + L+ T IG  VN +RKH S+ +
Sbjct: 11  EEELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKE 70

Query: 177 VRKLVKHLVRKWKDIVDEWVKLNQPGELASS 207
           V  L K L++ WK ++D         E   S
Sbjct: 71  VVSLAKVLIKNWKRLLDSPRTTKGERESGPS 101

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	286
d1eo0a_	77	Transcription elongation factor TFIIS N-domain {Ba	99.79
d1wjta_	103	Transcription elongation factor S-II protein 3 {Mo	99.75
d2b4jc1	81	PC4 and SFRS1-interacting protein, PSIP1 {Human (H	97.48

>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=99.79  E-value=8.9e-21  Score=144.57  Aligned_cols=74  Identities=31%  Similarity=0.571  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhhc-CCCcHHHhhccCccccchhhhcCCCHHHHHHHHHHHHHHHHHHH
Q 023203          120 QKRILEIKEHLEDPDQSEDALIDLLQSLAD-MDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVD  193 (286)
Q Consensus       120 ~~EV~rIKk~Ld~~~~sed~llelLr~L~~-l~iT~dlLksT~IGkaVN~LRKH~s~~I~~LAk~LV~kWK~~V~  193 (286)
                      .+||+++++.|++...+++.++++|+.|+. ++||.++|++|+||++||+||||++++|+.+|+.||++||++|+
T Consensus         3 ~~ev~~~~k~Lek~~~~~~~~l~~L~~L~~~~~it~d~L~~T~iG~~Vn~LRkh~~~~v~~lAk~Lv~~WK~~Vd   77 (77)
T d1eo0a_           3 SKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAIN   77 (77)
T ss_dssp             HHHHHHHHHHHHHHCSSSHHHHHHHHHHTTTCSCSTTHHHHHHHHHHHHHCCSSSCTTHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcccCCHHHHHHHHHHHHhcCCCcHHHHHHCCccHHHHHHhcCCcHHHHHHHHHHHHHHHHhcC
Confidence            468999999999987888999999999996 99999999999999999999999999999999999999999984

>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=99.75  E-value=9.2e-20  Score=145.10  Aligned_cols=78  Identities=31%  Similarity=0.543  Sum_probs=70.2

Q ss_pred             HHHHHHHHHhCCC--CCCHHHHHHHHHHhhcCCCcHHHhhccCccccchhhhcCC-CHHHHHHHHHHHHHHHHHHHHhhh
Q 023203          121 KRILEIKEHLEDP--DQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHS-SNDVRKLVKHLVRKWKDIVDEWVK  197 (286)
Q Consensus       121 ~EV~rIKk~Ld~~--~~sed~llelLr~L~~l~iT~dlLksT~IGkaVN~LRKH~-s~~I~~LAk~LV~kWK~~V~e~~~  197 (286)
                      +||++|++.|++.  ..+.+.++++|+.|+.++||+++|++|+||++||+||||. +++|+.+|+.||++||++|..+..
T Consensus        12 eei~~i~k~L~~~~~~~~~~~vl~~L~~L~~~~it~e~L~~T~IGk~Vn~LrK~~~~~~v~~lAk~Lv~~WK~~v~~~~~   91 (103)
T d1wjta_          12 EELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLLDSPRT   91 (103)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSSHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHHHHHHHHTCCSCC
T ss_pred             HHHHHHHHHHHHHHccCCHHHHHHHHHHHHcCCCCHHHHHhCCccHhHHHHHccCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            5899999999863  4566789999999999999999999999999999999996 589999999999999999987754


Q ss_pred             c
Q 023203          198 L  198 (286)
Q Consensus       198 ~  198 (286)
                      .
T Consensus        92 ~   92 (103)
T d1wjta_          92 T   92 (103)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=97.48  E-value=0.00011  Score=55.16  Aligned_cols=67  Identities=22%  Similarity=0.373  Sum_probs=56.7

Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHhhcCCCcHHHhhc-cCccccchhhhcC-CCHHHHHHHHHHHHHHHHH
Q 023203          125 EIKEHLEDPDQSEDALIDLLQSLADMDITFKALKE-TDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDI  191 (286)
Q Consensus       125 rIKk~Ld~~~~sed~llelLr~L~~l~iT~dlLks-T~IGkaVN~LRKH-~s~~I~~LAk~LV~kWK~~  191 (286)
                      .|+..|--...+...++++|..|..+++|.-+|+. +.|=.++.+||++ .|.+|+..|..|+.+||.+
T Consensus        13 ~ik~sL~~~~~dv~kcL~~L~~l~~l~vt~~mL~kn~e~V~tikklRry~gn~~Ir~kA~~ly~kfKsl   81 (81)
T d2b4jc1          13 EIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNM   81 (81)
T ss_dssp             HHHHHTCTTSCCHHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhccCCCCHHHHHHHHHHHHcCCCCHHHHHHChHHHHHHHHHHHHhccHHHHHHHHHHHHHhccC
Confidence            44445554456889999999999999999998875 5599999999999 6799999999999999974