Citrus Sinensis ID: 021095

---

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-------
Protein Sequence
MSMKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGCDRVELAVPSGNEFDDDEEDCKRDGCEFEAGGSKESKVNSCRDDHVSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKVEENLQWRTKISQSGNSKLLMSRMCLPRITIVYR
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccHHHHccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHcccHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHcccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccHHHcccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHcHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccEEEEEEcccccEEEccccHHHHHHHHHcccEEEEcc
Coil and Loop (DISEMBL)
msmksgsldnWRNYFrsangdifdIIDHAVMVAALDCPKEFKLRRDRIAEKLFTckltrcsgcdrvelavpsgnefdddeedckrdgcefeaggskeskvnscrddhvsnqivsnfssgdIAEALTDEIEEESQVVGEVLRIKEILhnsrdesdSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIaegtpdsvnpsvvdeeeglpsppldelafftgpsagieLSQVFLMAWMILEILETvgnssrtvkVEENLQWRTKIsqsgnskllmsrmclpritivyr
Flexible Loop (DISEMBL)
MSMKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKlftckltrcsgcdrvelavpsgnefdddeedCKRDGCEFeaggskeskvnscRDDHVSnqivsnfssgDIAEALTDEIEEESQVVGEVLRIKeilhnsrdesdsVLFESLRRLQLMALTVDTLKATEIGKavnglrkhgskqIRHLARTLIEGWKDLVDEWVNATKaiaegtpdsvnpsvVDEEEGLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILEtvgnssrtvkveenlqwrtkisqsgnskllmsrmclpritivyr
Low Complexity Region (SEG)
MSMKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGCDRVELAVPSGNEFDDDEEDCKRDGCEFEAGGSKESKVNSCRDDHVSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKVEENLQWRTKISQSGNSKLLMSRMCLPRITIVYR
Disordered region (IsUnstruct)
*********NWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGCDRVELAV***************************************************************QVVGEVLRIKEILHN*****DSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIA************************ELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKVEENLQWRTKIS****SKLLMSRMCLPRITIVY*
Disordered Region (DISOPRED)
******S***WRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFT*********************************************************************************VGEVLRIKEILHN****SDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKD**************************************************LSQVFLMAWMILE************************************MCLPRITIV**
Disordered Region (DISEMBL)
********DNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGCDRVELAVPSGN**********RDGCEF*************RDDHVSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKVEENLQWRTKISQSGNSKLLMSRMCLPRITIVYR
Disordered Region (DISPRO)
*****GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGCDRV***************************************************************EEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNAT*********************LPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKVEENLQWRTKISQSGNSKLLMSRMCLPRITIVYR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSMKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGCDRVELAVPSGNEFDDDEEDCKRDGCEFEAGGSKESKVNSCRDDHVSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKVEENLQWRTKISQSGNSKLLMSRMCLPRITIVYR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	317	2.2.26 [Sep-21-2011]
Q9FHK9	436	Probable mediator of RNA	yes	no	0.801	0.582	0.597	8e-77
F4J4Y5	580	Probable mediator of RNA	no	no	0.757	0.413	0.469	3e-57
F4KFC7	353	Probable mediator of RNA	no	no	0.564	0.507	0.297	4e-18
P23881	347	Transcription elongation	yes	no	0.227	0.207	0.407	1e-05
O75764	348	Transcription elongation	yes	no	0.227	0.206	0.394	2e-05
Q2KI09	349	Transcription elongation	yes	no	0.227	0.206	0.394	5e-05
Q9QVN7	299	Transcription elongation	no	no	0.258	0.274	0.340	9e-05
Q63799	299	Transcription elongation	no	no	0.258	0.274	0.340	0.0001
A5PKE4	208	Transcription elongation	no	no	0.299	0.456	0.312	0.0002
Q15560	299	Transcription elongation	no	no	0.201	0.214	0.369	0.0002

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

 Score =  287 bits (734), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 159/266 (59%), Positives = 190/266 (71%), Gaps = 12/266 (4%)

Query: 5   SGSLDNWRNYFRS-ANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGC 63
           SGSLD+WR YFR   + DIF IIDHA+MVAA DCP +FK RRD+IAE LF+C++ RC GC
Sbjct: 4   SGSLDSWREYFRRRGDSDIFGIIDHAIMVAATDCPNKFKSRRDKIAELLFSCRVNRCVGC 63

Query: 64  DRVELAVPSGNEFDDDEEDCKRDGC----EFE-AGGSKESKVNSCRDDHVSNQIVSNFSS 118
           D +EL+VP  +E +         G     ++E AGGSKESK NS R D+  NQIVSN++ 
Sbjct: 64  DHLELSVPGDDEANRGTTGNGGGGTAVDEDYEVAGGSKESKANSSRGDN--NQIVSNYTF 121

Query: 119 GDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATE 178
            D AEAL+DEIEE S V  EV RIKEIL N  DE +SVL +SLR L+LM+L VD LK+TE
Sbjct: 122 -DEAEALSDEIEEFSVVSKEVARIKEILLNKEDEPNSVLLDSLRHLKLMSLNVDILKSTE 180

Query: 179 IGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAI--AEGTPDSVNPSVVDEEE 236
           IGKAVNGLRKH S +IR LA+TLI  WK+LVD+WVN TK I  AEGTP+S NPSV+DEEE
Sbjct: 181 IGKAVNGLRKHSSDKIRQLAKTLIAEWKELVDQWVNTTKEITGAEGTPESANPSVLDEEE 240

Query: 237 GLPSPPLDELAFFTGPSAGIELSQVF 262
             PS P D +  FT    G E+S  F
Sbjct: 241 AFPSLPYD-VDIFTPEPNGFEISHFF 265

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 =  222 bits (566), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 132/281 (46%), Positives = 166/281 (59%), Gaps = 41/281 (14%)

Query: 5   SGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSGCD 64
           S SLD WR YFR  + DIF IIDHA+MVAA D PKEFK R DRIAE LF+CK++RC GCD
Sbjct: 7   SVSLDTWREYFRRGDSDIFGIIDHAIMVAAADWPKEFKSRSDRIAELLFSCKVSRCIGCD 66

Query: 65  RVELAVPSGNEFDDDEEDCKRDGCEFEAGGSKESKVNSCRDDHVSNQIVSNFSSGDIAEA 124
            +EL++ +G+E                                V    V        +  
Sbjct: 67  HLELSI-AGDEA------------------------------AVEIVGVGGGGDRGDSGV 95

Query: 125 LTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVN 184
            T E EE S  V EV+RI++IL N  DE DSVL ESLR+L+ M+++VD LK TEIGKAVN
Sbjct: 96  ATGEGEEASVSVDEVMRIRDILSNKDDEKDSVLLESLRKLESMSMSVDILKDTEIGKAVN 155

Query: 185 GLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIA--EGTPDSVNPSVVDEEEGLPSPP 242
           GLR+H S +I  LA+TL   WK LVD+W+N  + +A  EGTP+S+N SV+DEEE  PSPP
Sbjct: 156 GLRRHSSDKISKLAKTLFAEWKRLVDQWMNTPEEMAGTEGTPESLNLSVIDEEEAFPSPP 215

Query: 243 LDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVK 283
            D L  +     G ELSQ       IL+ L+  GN   +V+
Sbjct: 216 HD-LDIYAPEPNGFELSQ-------ILDCLDCDGNPRHSVE 248

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

 Score = 92.4 bits (228), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 107/225 (47%), Gaps = 46/225 (20%)

Query: 8   LDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKL-TRCSGCDRV 66
           LD++R+   +A  D++  ID A++VA+LD  +E K RRD I E+L+   +  +C  CD  
Sbjct: 3   LDDFRSVMDNAGVDVWTFIDTAILVASLDYGQELKRRRDNIVERLYATSMANKCRNCD-- 60

Query: 67  ELAVPSGNEFDDDEEDCKRDGCEFEAGGS-KESKVNSCRDDHVSNQIVSNFSSGDIAEAL 125
                                  F  GG+  E+ +    +  V  +       G +  A 
Sbjct: 61  -----------------------FGGGGNVTEAAIGRVNNGRVHEETEEEDEEG-VTAAA 96

Query: 126 TDEIEEESQVVGE-----------------VLRIKEILHNSRDESDSVLFESLRRLQLMA 168
            +E+ E+S  V +                 ++ IKE L +  D S+  L E L+ L+ M 
Sbjct: 97  EEEVREKSVNVEDDDDFDPFAGLFDDEQKSIVEIKEKLEDP-DLSEESLVELLQNLEDMD 155

Query: 169 LTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWV 213
           +T   L+ T+IG+ VN +RKH S  +R LA+ L++ WK+ VDEWV
Sbjct: 156 ITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVDEWV 200

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

 Score = 51.2 bits (121), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 49/76 (64%), Gaps = 4/76 (5%)

Query: 138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
           E+LRI + L    SR +++  L + L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct: 6   ELLRIAKKLEKMVSRKKTEGAL-DLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEV 64

Query: 195 RHLARTLIEGWKDLVD 210
             LA+ LI+ WK L+D
Sbjct: 65  VSLAKVLIKNWKRLLD 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)

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

 Score = 50.1 bits (118), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 48/76 (63%), Gaps = 4/76 (5%)

Query: 138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
           E+LRI + L    +R  ++  L + L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct: 6   ELLRIAKKLEKMVARKNTEGAL-DLLKKLHSCQMSIQLLQTTRIGVAVNGVRKHCSDKEV 64

Query: 195 RHLARTLIEGWKDLVD 210
             LA+ LI+ WK L+D
Sbjct: 65  VSLAKVLIKNWKRLLD 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.

Homo sapiens (taxid: 9606)

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

 Score = 48.9 bits (115), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 48/76 (63%), Gaps = 4/76 (5%)

Query: 138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
           E+LRI + L    +R +++  L + L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct: 6   ELLRIAKKLEKMVARKKTEGAL-DLLKKLGSWQMSIQLLQTTRIGVAVNGVRKHCSNKEV 64

Query: 195 RHLARTLIEGWKDLVD 210
             LA+ LI  WK L+D
Sbjct: 65  VALAKVLIRNWKQLLD 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.

Bos taurus (taxid: 9913)

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

 Score = 48.1 bits (113), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 6/88 (6%)

Query: 161 LRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQIRHLARTLIEGWKDLVDEWVNATKAI 219
           LR L+ M +T+  L++T +G +VN LRK  S +++  LA++LI+ WK L+D     ++  
Sbjct: 30  LRELKNMPITLHLLQSTRVGMSVNALRKQSSDEELIALAKSLIKSWKKLLDVSDGKSRNQ 89

Query: 220 AEGTPDSVNPS-----VVDEEEGLPSPP 242
             GTP   + S       D     P PP
Sbjct: 90  GRGTPLPTSSSKDASRTTDLSCKKPDPP 117

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

Mus musculus (taxid: 10090)

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

 Score = 47.8 bits (112), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 6/88 (6%)

Query: 161 LRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQIRHLARTLIEGWKDLVDEWVNATKAI 219
           LR L+ M +T+  L++T +G +VN LRK  S +++  LA++LI+ WK L+D     ++  
Sbjct: 30  LRELKNMPITLHLLQSTRVGMSVNALRKQSSDEELIALAKSLIKSWKKLLDVSDGKSRDQ 89

Query: 220 AEGTPDSVNPS-----VVDEEEGLPSPP 242
             GTP   + S       D     P PP
Sbjct: 90  GRGTPLPTSSSKDASGTTDLSCKKPDPP 117

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|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 = 47.0 bits (110), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 52/96 (54%), Gaps = 1/96 (1%)

Query: 119 GDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATE 178
           G I +  T E  +   V+ ++ R K +L    D+S   L E+LR L+    + + LK+T+
Sbjct: 22  GKIYKQATIESLKRVVVIEDIKRWKTMLELP-DQSKENLVEALRELKKKIPSREVLKSTK 80

Query: 179 IGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVN 214
           IG  VN +R+H   ++  LAR +   W+  +++ VN
Sbjct: 81  IGHTVNKMRQHSDSEVACLAREVYTEWRTFIEKHVN 116

Bos taurus (taxid: 9913)

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

 Score = 46.6 bits (109), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 161 LRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQIRHLARTLIEGWKDLVDEWVNATKAI 219
           LR L+ M +T+  L++T +G +VN LRK  S +++  LA++LI+ WK L+D      +  
Sbjct: 31  LRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLLDASDAKARER 90

Query: 220 AEGTP 224
             G P
Sbjct: 91  GRGMP 95

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)

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	317
255552481	473	conserved hypothetical protein [Ricinus	0.817	0.547	0.702	1e-103
224139692	474	predicted protein [Populus trichocarpa]	0.817	0.546	0.662	8e-98
449437690	452	PREDICTED: probable mediator of RNA poly	0.823	0.577	0.695	8e-97
224139684	480	predicted protein [Populus trichocarpa]	0.817	0.539	0.645	2e-96
359481563	521	PREDICTED: uncharacterized protein LOC10	0.798	0.485	0.688	1e-94
224089941	483	predicted protein [Populus trichocarpa]	0.817	0.536	0.645	3e-94
255647376	336	unknown [Glycine max]	0.823	0.776	0.676	1e-92
356504664	452	PREDICTED: uncharacterized protein LOC10	0.801	0.561	0.670	3e-87
356571901	458	PREDICTED: uncharacterized protein LOC10	0.807	0.558	0.640	4e-86
388520529	451	unknown [Medicago truncatula]	0.788	0.554	0.653	1e-85

>gi|255552481|ref|XP_002517284.1| conserved hypothetical protein [Ricinus communis] gi|223543547|gb|EEF45077.1| conserved hypothetical protein [Ricinus communis]

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/289 (70%), Positives = 229/289 (79%), Gaps = 30/289 (10%)

Query: 3   MKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSG 62
           MKS SLD WRNYFR+AN DIF IIDHA+MVAA DCPKEF+LRRDRIAE+LF+C+LTRCSG
Sbjct: 1   MKSVSLDYWRNYFRTANSDIFAIIDHAIMVAASDCPKEFRLRRDRIAERLFSCRLTRCSG 60

Query: 63  CDRVELAVPSGNEFDDDEEDCKR----------------DGCEFEAGG-SKESKVNSC-- 103
           C+ V+LAVP+    +DD   CKR                D CEFEAGG SKESKVNS   
Sbjct: 61  CNHVDLAVPAHEGENDDGGACKRRDDHHVEDDDDDDVDIDVCEFEAGGTSKESKVNSSNN 120

Query: 104 RDDH--------VSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDS 155
           RDD+        V++Q++SNFS G+ AEALTDEIEEES VVGEVLRIK+IL +SRDES+S
Sbjct: 121 RDDNDIDIGEVNVNDQLLSNFSYGE-AEALTDEIEEESMVVGEVLRIKDILLHSRDESES 179

Query: 156 VLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNA 215
           VLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS+QIRHLAR LI+GWK LVDEW + 
Sbjct: 180 VLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSQQIRHLARVLIDGWKVLVDEWYST 239

Query: 216 TKAIA--EGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           TKAI   EGTP+SVNPSVVDEE+GLPSPPLDE  FF   + GIEL+Q F
Sbjct: 240 TKAIRGDEGTPESVNPSVVDEEDGLPSPPLDEAFFFAAQNTGIELAQFF 288

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224139692|ref|XP_002323230.1| predicted protein [Populus trichocarpa] gi|222867860|gb|EEF04991.1| predicted protein [Populus trichocarpa]

 Score =  363 bits (931), Expect = 8e-98,   Method: Compositional matrix adjust.
 Identities = 194/293 (66%), Positives = 221/293 (75%), Gaps = 34/293 (11%)

Query: 3   MKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSG 62
           MKS SLD WR+YFR+A+ DIF IIDHA++VAA DCPKEFKLRRDRIAE+LF+C+L +CSG
Sbjct: 1   MKSVSLDYWRDYFRTASSDIFGIIDHAILVAASDCPKEFKLRRDRIAERLFSCRLIKCSG 60

Query: 63  CDRVELAVPSGNEFDDDEEDC--KR---------------------DGCEFEAGGSKESK 99
           C++VELAVP  +E + D+  C  KR                      G E+E GGSKESK
Sbjct: 61  CNQVELAVPGHDEDERDDRGCCSKRRDGDNSGSDDDEEEVDIDIDDGGFEYEGGGSKESK 120

Query: 100 VNSCRDDH--------VSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRD 151
           VNS   D+        V++Q+VSNFS G+ AEALTDEIEE SQ V EVLRIK+IL+NS+D
Sbjct: 121 VNSSNRDNDFDNGEVNVNDQLVSNFSFGE-AEALTDEIEEVSQTVDEVLRIKDILYNSQD 179

Query: 152 ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDE 211
           ESDSVL ESLR+L+LMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIE WK LVDE
Sbjct: 180 ESDSVLLESLRKLRLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEDWKVLVDE 239

Query: 212 WVNATKAIA--EGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           W +A   I   EGTPDSVNPSVVDEEEGLPSPPLDE AFF      +ELSQ F
Sbjct: 240 WYSAANVIRGNEGTPDSVNPSVVDEEEGLPSPPLDEGAFFATQPTSMELSQFF 292

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437690|ref|XP_004136624.1| PREDICTED: probable mediator of RNA polymerase II transcription subunit 26b-like [Cucumis sativus]

 Score =  359 bits (922), Expect = 8e-97,   Method: Compositional matrix adjust.
 Identities = 192/276 (69%), Positives = 217/276 (78%), Gaps = 15/276 (5%)

Query: 1   MSMKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRC 60
           M+ KSGSLD+WRNYFR+AN DIF IID+A++VAA DCPKEF+LRRDRIAE+LF+C+LTRC
Sbjct: 1   MAAKSGSLDSWRNYFRNANSDIFGIIDYAILVAASDCPKEFRLRRDRIAEQLFSCRLTRC 60

Query: 61  SGCDRVELAVPSGNEFDDDE----EDCKRDGCEFEAGGSKESKVNSCRDD--HVSNQIVS 114
            GCDRVELAV    + DD E     D  RDGCEFEAGGSKESKV S RDD   ++   VS
Sbjct: 61  LGCDRVELAVAGDIDGDDGETGFKSDFVRDGCEFEAGGSKESKVYSSRDDIGEMNCNRVS 120

Query: 115 NFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTL 174
           NFS G+ AEALTDEIE+ESQ+VGEVLRIKEIL+N  DESD VLFESLRRL+LMAL+VDTL
Sbjct: 121 NFSFGE-AEALTDEIEQESQIVGEVLRIKEILNNFEDESDPVLFESLRRLELMALSVDTL 179

Query: 175 KATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAI--AEGTPDSVNPSVV 232
           +ATEIGKAVN LRKHGSK+IRHLAR LI  WK++VD WV AT A+  AE TPDS N S  
Sbjct: 180 QATEIGKAVNCLRKHGSKRIRHLARVLIMEWKEMVDLWVQATAAVQGAEVTPDSKNKSAA 239

Query: 233 ------DEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
                  EEEGLPSPPLDE AFFT     +ELSQ F
Sbjct: 240 VKEEDDYEEEGLPSPPLDEAAFFTTQPTSMELSQFF 275

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224139684|ref|XP_002323227.1| predicted protein [Populus trichocarpa] gi|222867857|gb|EEF04988.1| predicted protein [Populus trichocarpa]

 Score =  358 bits (920), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 193/299 (64%), Positives = 221/299 (73%), Gaps = 40/299 (13%)

Query: 3   MKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSG 62
           MKS SLD WR+YFR+A+ DIF IIDHA++VAA DCPKEFKLRRDRIAE+LF+C+L +CSG
Sbjct: 1   MKSVSLDYWRDYFRTASSDIFGIIDHAILVAASDCPKEFKLRRDRIAERLFSCRLIKCSG 60

Query: 63  CDRVELAVPSGNEFDDDEEDC--KR---------------------DGCEFEAGGSKESK 99
           C++VELAVP  +E + D+  C  KR                      G E+E GGSKESK
Sbjct: 61  CNQVELAVPGHDEDERDDRGCCSKRRDGDNSGSDDDEEEVDIDIDDGGFEYEGGGSKESK 120

Query: 100 VNSCRDDH--------VSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRD 151
           VNS   D+        V++Q+VSNFS G+ AEALTDEIEE SQ V EVLRIK+IL+NS+D
Sbjct: 121 VNSSNRDNDFDNGEVNVNDQLVSNFSFGE-AEALTDEIEEVSQTVDEVLRIKDILYNSQD 179

Query: 152 ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDE 211
           ESDSVL ESLR+L+LMALTVDTLKATEIGKAVNGLRKHGS+QIRHLARTLIE WK LVDE
Sbjct: 180 ESDSVLLESLRKLRLMALTVDTLKATEIGKAVNGLRKHGSEQIRHLARTLIEDWKVLVDE 239

Query: 212 WVNATKAIA--------EGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           W +A   I         EGTPDSVNPSVVDEEEGLPSPPLDE AFF      +ELSQ F
Sbjct: 240 WYSAANVIRGRNLLASNEGTPDSVNPSVVDEEEGLPSPPLDEGAFFATQPTSMELSQFF 298

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481563|ref|XP_002277659.2| PREDICTED: uncharacterized protein LOC100250012 [Vitis vinifera]

 Score =  352 bits (903), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 186/270 (68%), Positives = 216/270 (80%), Gaps = 17/270 (6%)

Query: 1   MSMKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRC 60
           M+  SG+LD WRNYFR+AN DIF II+HA++VAA DCPKEF+LRRDRIAE+LF+CKLTRC
Sbjct: 1   MATNSGALDQWRNYFRTANSDIFGIIEHAILVAASDCPKEFRLRRDRIAERLFSCKLTRC 60

Query: 61  SGCDRVELAVPSGNEFDDDEEDCKRDGCEFEA---GGSKESKVNSCRDDH--VSNQIVSN 115
            GCDRVELAVP     ++D   CK    EF+      SKESK NS R+DH  ++   VSN
Sbjct: 61  FGCDRVELAVP-----ENDGGGCK---IEFDMDVNSSSKESKANSIREDHGEMNMNQVSN 112

Query: 116 FSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLK 175
           +S G+ AEALTDEIEEE+Q+ GEVLRI+EIL +S+DESDSVLF+SLRRLQLM L+VD LK
Sbjct: 113 YSYGE-AEALTDEIEEETQIAGEVLRIREILEHSKDESDSVLFDSLRRLQLMVLSVDNLK 171

Query: 176 ATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPS---VV 232
           ATEIGKAVNGLRKHGSKQIR LARTLI+ WKD+VDEWVNAT AIAEGTPDSVNPS     
Sbjct: 172 ATEIGKAVNGLRKHGSKQIRQLARTLIDEWKDMVDEWVNATAAIAEGTPDSVNPSVVDDD 231

Query: 233 DEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           D+EEGLP PP+DEL+F T     +ELSQ F
Sbjct: 232 DDEEGLPFPPMDELSFLTTQPTSLELSQFF 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224089941|ref|XP_002308874.1| predicted protein [Populus trichocarpa] gi|222854850|gb|EEE92397.1| predicted protein [Populus trichocarpa]

 Score =  351 bits (900), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 193/299 (64%), Positives = 217/299 (72%), Gaps = 40/299 (13%)

Query: 3   MKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSG 62
           MKS SLD WRNYFR+A+ DIF IIDHA++VAA DCPKEFKLRRDRIAE+LF+C+L +CSG
Sbjct: 1   MKSVSLDYWRNYFRTASSDIFGIIDHAILVAASDCPKEFKLRRDRIAERLFSCRLIKCSG 60

Query: 63  CDRVELAVPSGNEFDDDEEDC--KR---------------------------DGCEFEAG 93
           C+RVELAVP  +E   D+  C  KR                            G E+E G
Sbjct: 61  CNRVELAVPGHDEGVSDDGGCCSKRRDGDNSGGVGGGGDDDDDDDVDIDIDDGGFEYEGG 120

Query: 94  GSKESKVNSCRDDH--------VSNQIVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEI 145
           GSK SKVNS   D+        V++Q+V NFS GD AEALTDEIEE SQ V EVLRIK+I
Sbjct: 121 GSKGSKVNSSNRDNDIDNGEVNVNDQLVYNFSYGD-AEALTDEIEEVSQTVDEVLRIKDI 179

Query: 146 LHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGW 205
           L+NS+DESDSVL ESLR+L+LMALTVDTLKATEIGKAVN LRKHGSKQIR+LARTLIE W
Sbjct: 180 LYNSQDESDSVLLESLRKLRLMALTVDTLKATEIGKAVNVLRKHGSKQIRYLARTLIEDW 239

Query: 206 KDLVDEWVNATKAIA--EGTPDSVNPSVVDEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           K LVDEW +   AI   EGTPDSVNPSVVDEEEGLPSPPLDE AFF      +ELSQ F
Sbjct: 240 KVLVDEWYSTANAIRGDEGTPDSVNPSVVDEEEGLPSPPLDEGAFFATQPTSMELSQFF 298

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255647376|gb|ACU24154.1| unknown [Glycine max]

 Score =  345 bits (886), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 184/272 (67%), Positives = 209/272 (76%), Gaps = 11/272 (4%)

Query: 1   MSMKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRC 60
           M M  GSLD WRNYF +AN DIF IIDHA+MVAA DCPKEF LRRD IAE+LF+C+L+RC
Sbjct: 1   MRMNKGSLDYWRNYFGAANSDIFGIIDHAIMVAASDCPKEFTLRRDGIAERLFSCRLSRC 60

Query: 61  SGCDRVELAVPSGNEFDDDEEDCKR----DGCEF--EAGGSKESKVNSCRD--DHVSNQI 112
            GC+RVELAVP  ++ D   E CK     DG EF  EAG SKESKVNS RD    ++   
Sbjct: 61  LGCERVELAVPVDDDDDGGGEGCKSGFDGDGDEFKFEAGASKESKVNSARDYPGEMNTNQ 120

Query: 113 VSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVD 172
           VSN+S G+ AEALTDEIE+ESQ V EV RIK+I  N  +ESD+VLF+SLRRLQLM LTVD
Sbjct: 121 VSNYSYGE-AEALTDEIEKESQYVEEVFRIKDIFLNYEEESDTVLFDSLRRLQLMELTVD 179

Query: 173 TLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIA--EGTPDSVNPS 230
            LKATEIGKAVN LRKHGS+ I  LARTLI+GWK +VDEWV  T AIA  EGTPDSVNPS
Sbjct: 180 LLKATEIGKAVNPLRKHGSRDICQLARTLIDGWKQMVDEWVKDTTAIAGSEGTPDSVNPS 239

Query: 231 VVDEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           VVD+EEGLPSPP+DE A F  P+  +ELSQ F
Sbjct: 240 VVDDEEGLPSPPMDEGALFAAPTGSMELSQFF 271

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504664|ref|XP_003521115.1| PREDICTED: uncharacterized protein LOC100817835 [Glycine max]

 Score =  327 bits (839), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 183/273 (67%), Positives = 213/273 (78%), Gaps = 19/273 (6%)

Query: 3   MKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSG 62
           MKS SLD WRNYF SAN DIF+II+HA++VAA DCPKEF++RRD IAE+LF+C+LTRC G
Sbjct: 1   MKSWSLDEWRNYFGSANSDIFEIIEHAIIVAASDCPKEFRVRRDWIAERLFSCRLTRCVG 60

Query: 63  CDRVELAVPS--------GNEFDDDEEDCKRDGCEFE-AGGSKESKVNSCRDDHVSNQIV 113
           CDRVELAV +        G++ D+D+   +RDG EFE AG SKESKVN       +N   
Sbjct: 61  CDRVELAVGADSKKEKHDGDDGDNDKSGFERDGVEFEGAGASKESKVNGD-----ANLGD 115

Query: 114 SNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDT 173
           SN+S G+ AEAL+DE+EEESQ V E+LRIK++L N  DES++V+FESLRRLQLM LTVD 
Sbjct: 116 SNYSFGE-AEALSDEMEEESQYVAEILRIKDVLLNPEDESEAVIFESLRRLQLMELTVDC 174

Query: 174 LKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNA--TKAIAEGTPDSVNPSV 231
           LKATEIGKAVN LRKHGSK IR LARTLI GWK++VDEWV A  T AI EGTPDSVNPSV
Sbjct: 175 LKATEIGKAVNPLRKHGSKDIRQLARTLINGWKEMVDEWVKATTTTAITEGTPDSVNPSV 234

Query: 232 V--DEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           V  DEEEGLPSPPLDE AFF   +  +ELSQ F
Sbjct: 235 VDDDEEEGLPSPPLDEGAFFVTQAGSMELSQFF 267

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571901|ref|XP_003554109.1| PREDICTED: uncharacterized protein LOC100799367 [Glycine max]

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 178/278 (64%), Positives = 214/278 (76%), Gaps = 22/278 (7%)

Query: 3   MKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSG 62
           MKS SLD WR YF SAN DIF+II+HA++VAA DCPKEF++RRD IAE+LF+C+LTRC G
Sbjct: 1   MKSWSLDEWRKYFGSANSDIFEIIEHAIIVAASDCPKEFRVRRDGIAERLFSCRLTRCVG 60

Query: 63  CDRVELAVPSGNE--------FDDDEEDCKRDGCEFE-AGGSKESKVNS--CRDDHVSNQ 111
           CDRVELAV + ++         D+D+   +RDG EFE AG SKESKVN    RD ++ + 
Sbjct: 61  CDRVELAVGADSKEKHDGDGDDDNDKSGYERDGVEFEGAGASKESKVNGDGGRDVNLGD- 119

Query: 112 IVSNFSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTV 171
             SN+S G+ AEAL+DE+EEES+ V E+LRI+++L N  DES++VLF+SLRRLQLM LTV
Sbjct: 120 --SNYSFGE-AEALSDEMEEESRYVAEILRIRDVLLNPEDESEAVLFDSLRRLQLMELTV 176

Query: 172 DTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIA-----EGTPDS 226
           D LKATEIGKAVN LRKHGSK IR L+RTLI+GWK++VDEWV AT   A     EGTPDS
Sbjct: 177 DCLKATEIGKAVNPLRKHGSKDIRQLSRTLIDGWKEMVDEWVKATTTTAITGSEEGTPDS 236

Query: 227 VNPSVV--DEEEGLPSPPLDELAFFTGPSAGIELSQVF 262
           VNPSVV  DEEEGLPSPPLDE AFF   +  +ELSQ F
Sbjct: 237 VNPSVVDDDEEEGLPSPPLDEGAFFVTQAGSMELSQFF 274

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388520529|gb|AFK48326.1| unknown [Medicago truncatula]

 Score =  322 bits (825), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 177/271 (65%), Positives = 204/271 (75%), Gaps = 21/271 (7%)

Query: 3   MKSGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRCSG 62
           MKSGSLD WR+YFRS+N DIFDIIDHA++VAA DCPKEFK RRD IAE+LF+  L RC G
Sbjct: 4   MKSGSLDQWRSYFRSSNSDIFDIIDHAIVVAASDCPKEFKSRRDGIAERLFSVMLNRCKG 63

Query: 63  CDRVELAVPSGNEFDDDEED--CKRDGCEFEAGGSKESKVNSCRDDH--VSNQIVSNFSS 118
           C++VEL+VP     DDD  D  CKR       G SKESKV+  R+++  +    +SN+S 
Sbjct: 64  CEKVELSVP-----DDDNGDELCKR--SSVREGASKESKVDCSREENGVMDANPISNYSF 116

Query: 119 GDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATE 178
           G+ AEALTDE+EE+SQ+V EV RIKEIL+N  DESDSVLFESLRRLQLM L VD LK+TE
Sbjct: 117 GE-AEALTDELEEQSQLVAEVTRIKEILNNHEDESDSVLFESLRRLQLMQLCVDLLKSTE 175

Query: 179 IGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNAT-----KAIAEGTPDSVNPSVVD 233
           IGKAVN LRKHGSK IR LARTLI+GWK+LV+ WV AT      A  EGTPDS NPSVV+
Sbjct: 176 IGKAVNHLRKHGSKDIRQLARTLIDGWKELVNAWVKATTTTPVAASEEGTPDSRNPSVVE 235

Query: 234 EEE----GLPSPPLDELAFFTGPSAGIELSQ 260
            EE    GLPSPPLDE AFF  P+  IELSQ
Sbjct: 236 NEEEEEGGLPSPPLDEGAFFVAPTGTIELSQ 266

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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	317
TAIR|locus:2156814	436	AT5G05140 [Arabidopsis thalian	0.807	0.587	0.598	3.2e-72
TAIR|locus:2178173	353	AT5G09850 [Arabidopsis thalian	0.678	0.609	0.313	5.5e-22
UNIPROTKB|Q5DR83	154	TCEA3 "Rhabdomyosarcoma antige	0.227	0.467	0.394	2.4e-07
UNIPROTKB|E2R638	154	TCEA3 "Uncharacterized protein	0.227	0.467	0.407	3.9e-07
UNIPROTKB|Q5JRI8	82	TCEA2 "Transcription elongatio	0.246	0.951	0.365	3.8e-06
ZFIN|ZDB-GENE-030131-8049	309	tcea1 "transcription elongatio	0.321	0.330	0.311	1.2e-05
MGI|MGI:1196908	347	Tcea3 "transcription elongatio	0.227	0.207	0.407	1.5e-05
UNIPROTKB|F1NBF9	312	TCEA2 "Uncharacterized protein	0.305	0.310	0.317	2.6e-05
UNIPROTKB|A5PKE4	208	TCEANC2 "Transcription elongat	0.299	0.456	0.312	2.9e-05
UNIPROTKB|F1MBR2	208	TCEANC2 "Transcription elongat	0.299	0.456	0.312	2.9e-05

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

 Score = 730 (262.0 bits), Expect = 3.2e-72, P = 3.2e-72
 Identities = 161/269 (59%), Positives = 192/269 (71%)

Query:     3 MK-SGSLDNWRNYFRS-ANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTCKLTRC 60
             MK SGSLD+WR YFR   + DIF IIDHA+MVAA DCP +FK RRD+IAE LF+C++ RC
Sbjct:     1 MKASGSLDSWREYFRRRGDSDIFGIIDHAIMVAATDCPNKFKSRRDKIAELLFSCRVNRC 60

Query:    61 SGCDRVELAVPSGNEFDDDEEDCKRDGC----EFE-AGGSKESKVNSCRDDHVSNQIVSN 115
              GCD +EL+VP  +E +         G     ++E AGGSKESK NS R D+  NQIVSN
Sbjct:    61 VGCDHLELSVPGDDEANRGTTGNGGGGTAVDEDYEVAGGSKESKANSSRGDN--NQIVSN 118

Query:   116 FSSGDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLK 175
             ++  D AEAL+DEIEE S V  EV RIKEIL N  DE +SVL +SLR L+LM+L VD LK
Sbjct:   119 YTF-DEAEALSDEIEEFSVVSKEVARIKEILLNKEDEPNSVLLDSLRHLKLMSLNVDILK 177

Query:   176 ATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNATKAI--AEGTPDSVNPSVVD 233
             +TEIGKAVNGLRKH S +IR LA+TLI  WK+LVD+WVN TK I  AEGTP+S NPSV+D
Sbjct:   178 STEIGKAVNGLRKHSSDKIRQLAKTLIAEWKELVDQWVNTTKEITGAEGTPESANPSVLD 237

Query:   234 EEEGLPSPPLDELAFFTGPSAGIELSQVF 262
             EEE  PS P D +  FT    G E+S  F
Sbjct:   238 EEEAFPSLPYD-VDIFTPEPNGFEISHFF 265

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

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

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 72/230 (31%), Positives = 115/230 (50%)

Query:     8 LDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLF-TCKLTRCSGCDRV 66
             LD++R+   +A  D++  ID A++VA+LD  +E K RRD I E+L+ T    +C  CD  
Sbjct:     3 LDDFRSVMDNAGVDVWTFIDTAILVASLDYGQELKRRRDNIVERLYATSMANKCRNCD-- 60

Query:    67 ELAVPSGNEFDDDEEDCKRDGCEFEAGGSKESKVNSCRDDHVSNQIVSNFSSGDIAEALT 126
                   GN  +             E     E  V +  ++ V  + V N    D  +   
Sbjct:    61 --FGGGGNVTEAAIGRVNNGRVHEETEEEDEEGVTAAAEEEVREKSV-NVEDDDDFDPFA 117

Query:   127 DEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGL 186
                ++E +    ++ IKE L +  D S+  L E L+ L+ M +T   L+ T+IG+ VN +
Sbjct:   118 GLFDDEQK---SIVEIKEKLEDP-DLSEESLVELLQNLEDMDITFQALQETDIGRHVNRV 173

Query:   187 RKHGSKQIRHLARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPSVVDEEE 236
             RKH S  +R LA+ L++ WK+ VDEWV   +    G  D   PS++ +E+
Sbjct:   174 RKHPSNNVRRLAKQLVKKWKETVDEWVKFNQP---G--DLEPPSLIADED 218

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

UNIPROTKB|Q5DR83 TCEA3 "Rhabdomyosarcoma antigen MU-RMS-40.22" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 2.4e-07, P = 2.4e-07
 Identities = 30/76 (39%), Positives = 48/76 (63%)

Query:   138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
             E+LRI + L    +R  ++  L + L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct:     6 ELLRIAKKLEKMVARKNTEGAL-DLLKKLHSCQMSIQLLQTTRIGVAVNGVRKHCSDKEV 64

Query:   195 RHLARTLIEGWKDLVD 210
               LA+ LI+ WK L+D
Sbjct:    65 VSLAKVLIKNWKRLLD 80

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|E2R638 TCEA3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 122 (48.0 bits), Expect = 3.9e-07, P = 3.9e-07
 Identities = 31/76 (40%), Positives = 46/76 (60%)

Query:   138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
             E+LRI   L    +R  S+  L   L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct:     6 ELLRIARKLEKMVARKNSEGAL-GLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEV 64

Query:   195 RHLARTLIEGWKDLVD 210
               LA+ LI+ WK L+D
Sbjct:    65 VSLAKVLIKNWKRLLD 80

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 113 (44.8 bits), Expect = 3.8e-06, P = 3.8e-06
 Identities = 30/82 (36%), Positives = 46/82 (56%)

Query:   161 LRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQIRHLARTLIEGWKDLVDEWVNATKAI 219
             LR L+ M +T+  L++T +G +VN LRK  S +++  LA++LI+ WK L+D   +  KA 
Sbjct:     4 LRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLLD--ASDAKAR 61

Query:   220 AEGTPDSVNPSVVDEEEGLPSP 241
               G    +  S  D  E  P P
Sbjct:    62 ERGRGMPLPTSSRDASEA-PDP 82

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

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

 Score = 128 (50.1 bits), Expect = 1.2e-05, P = 1.2e-05
 Identities = 33/106 (31%), Positives = 58/106 (54%)

Query:   138 EVLRIKEILHNSRDESDSV-LFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSK-QIR 195
             E++RI + +     + + V   + L+ L+ + +T++ L++T IG +VN +RK  +  ++ 
Sbjct:     8 EIIRIAKKMDKMAQKKNGVGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDDEVT 67

Query:   196 HLARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPSVVDEEEGLPSP 241
              LA++LI+ WK L+DE   A K   E   +   P VV   E  P P
Sbjct:    68 SLAKSLIKSWKKLLDEPA-ADKNSEEKKKERTTP-VVSPSETSPEP 111

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

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

 Score = 128 (50.1 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 31/76 (40%), Positives = 49/76 (64%)

Query:   138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
             E+LRI + L    SR +++  L + L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct:     6 ELLRIAKKLEKMVSRKKTEGAL-DLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEV 64

Query:   195 RHLARTLIEGWKDLVD 210
               LA+ LI+ WK L+D
Sbjct:    65 VSLAKVLIKNWKRLLD 80

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IDA

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

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

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

GO:0006414 "translational elongation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F1NBF9 TCEA2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 125 (49.1 bits), Expect = 2.6e-05, P = 2.6e-05
 Identities = 33/104 (31%), Positives = 65/104 (62%)

Query:   138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
             E++RI + L    ++  +D  + + L+ L+ M +T+D L++T IG +VN LRK  S +++
Sbjct:    32 EIVRIAKRLDKMVAKKSADGAM-DLLKELKSMPMTLDLLQSTRIGMSVNALRKQSSDEEV 90

Query:   195 RHLARTLIEGWKDLVDEWVNATKAIAEGTPDSVN-PSVVDEEEG 237
               LA++LI+ WK L+D  ++A++  +E    +++ P+   +E G
Sbjct:    91 IALAKSLIKSWKKLLD--LDASEEKSEEKKKNLSLPTSSSKETG 132

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005813 "centrosome" evidence=IEA

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

 Score = 120 (47.3 bits), Expect = 2.9e-05, P = 2.9e-05
 Identities = 30/96 (31%), Positives = 52/96 (54%)

Query:   119 GDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATE 178
             G I +  T E  +   V+ ++ R K +L    D+S   L E+LR L+    + + LK+T+
Sbjct:    22 GKIYKQATIESLKRVVVIEDIKRWKTMLELP-DQSKENLVEALRELKKKIPSREVLKSTK 80

Query:   179 IGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVN 214
             IG  VN +R+H   ++  LAR +   W+  +++ VN
Sbjct:    81 IGHTVNKMRQHSDSEVACLAREVYTEWRTFIEKHVN 116

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 = 120 (47.3 bits), Expect = 2.9e-05, P = 2.9e-05
 Identities = 30/96 (31%), Positives = 52/96 (54%)

Query:   119 GDIAEALTDEIEEESQVVGEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATE 178
             G I +  T E  +   V+ ++ R K +L    D+S   L E+LR L+    + + LK+T+
Sbjct:    22 GKIYKQATIESLKRVVVIEDIKRWKTMLELP-DQSKENLVEALRELKKKIPSREVLKSTK 80

Query:   179 IGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVN 214
             IG  VN +R+H   ++  LAR +   W+  +++ VN
Sbjct:    81 IGHTVNKMRQHSDSEVACLAREVYTEWRTFIEKHVN 116

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

GO:0005634 "nucleus" 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

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	317
cd00183	76	cd00183, TFIIS_I, N-terminal domain (domain I) of	3e-20
pfam08711	51	pfam08711, Med26, TFIIS helical bundle-like domain	5e-16
smart00509	75	smart00509, TFS2N, Domain in the N-terminus of tra	4e-15
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	3e-09

>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 = 82.7 bits (205), Expect = 3e-20
 Identities = 38/74 (51%), Positives = 49/74 (66%), Gaps = 1/74 (1%)

Query: 138 EVLRIKEILHNS-RDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRH 196
           EVLR K+ L     +E  S L + LR L+ + LTV+ LK T IGK VN LRKH +++IR 
Sbjct: 3   EVLRAKKKLEKKDSNEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRK 62

Query: 197 LARTLIEGWKDLVD 210
           LA+ LI+ WK LVD
Sbjct: 63  LAKALIKSWKKLVD 76

Length = 76

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

 Score = 70.6 bits (174), Expect = 5e-16
 Identities = 24/51 (47%), Positives = 37/51 (72%)

Query: 159 ESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLV 209
           E L+ L+ + +T + L+ T IGKAVN LRKH +++++ LA+ LI+ WK LV
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|197766 smart00509, TFS2N, Domain in the N-terminus of transcription elongation factor S-II (and elsewhere)

 Score = 68.9 bits (169), Expect = 4e-15
 Identities = 28/63 (44%), Positives = 42/63 (66%)

Query: 149 SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDL 208
           +  +  S   + L++L+ + +TVD L+ T IGK VNGLRKH +++IR LA+ LI+ WK L
Sbjct: 13  NNGKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKL 72

Query: 209 VDE 211
           V  
Sbjct: 73  VYS 75

Length = 75

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

 Score = 56.8 bits (137), Expect = 3e-09
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 138 EVLRIKEILH-NSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRH 196
           EV    + L  N   ++     + L +L+    T + L+ T++G  VN LRKH ++ I  
Sbjct: 3   EVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISK 62

Query: 197 LARTLIEGWKDLVDE 211
           LA+ +I+ WK +VD+
Sbjct: 63  LAKKIIKSWKKVVDK 77

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	317
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.89
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	99.79
cd00183	76	TFIIS_I N-terminal domain (domain I) of transcript	99.72
smart00509	75	TFS2N Domain in the N-terminus of transcription el	99.66
PF08711	53	Med26: TFIIS helical bundle-like domain; InterPro:	99.46
KOG2821	433	consensus RNA polymerase II transcription elongati	97.25
KOG1793	417	consensus Uncharacterized conserved protein [Funct	95.42
COG5139	397	Uncharacterized conserved protein [Function unknow	93.91
PF11467	106	LEDGF: Lens epithelium-derived growth factor (LEDG	93.56
cd08815	77	Death_TNFRSF25_DR3 Death domain of Tumor Necrosis	90.37
PLN02976	1713	amine oxidase	82.54

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.89  E-value=7.7e-23  Score=195.76  Aligned_cols=137  Identities=22%  Similarity=0.287  Sum_probs=101.1

Q ss_pred             HHHHHHHHHHhcCCC-CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHHHhhhh
Q 021095          137 GEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNA  215 (317)
Q Consensus       137 ~EV~rIkk~Lek~~~-~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~~~~~~  215 (317)
                      +||.++++.|+++.. .+++.++++|++|+.++||+++|++|+||++||+||||++++|++||+.||++||++|..++..
T Consensus         2 ~ei~~~~k~L~k~~~~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~k~~   81 (299)
T TIGR01385         2 AEVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKNKSD   81 (299)
T ss_pred             hHHHHHHHHhhhhccCCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhhccc
Confidence            589999999999753 5667899999999999999999999999999999999999999999999999999999887443


Q ss_pred             cccc----ccCCCCCCC---C--C---CCCcC-C---CCCCCCcccCcccCCCCCCcchhhHHHHHHHHHHHHHhcCC
Q 021095          216 TKAI----AEGTPDSVN---P--S---VVDEE-E---GLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGN  277 (317)
Q Consensus       216 ~~a~----se~sp~ss~---~--s---~~~ee-~---~~P~~p~d~~af~~~~~T~d~vR~~~kc~emLy~AL~~~~~  277 (317)
                      +.+.    ....+.+++   .  +   ...+. .   +.++++.  ..+++.+.|+|.||  ++|++|||+||+.+.+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~t~d~~R--dk~r~~L~~aL~~~~~  155 (299)
T TIGR01385        82 HPGGNPEDKTTVGESVNSVKQEAKSQSDKIEQPKYVSSSPRNAK--NDFVPTAVTNDKVR--DKCRELLYDALAKDSD  155 (299)
T ss_pred             CcccccccccccCCCCCCCCccccCCcccccCCCCCCCcccccC--CCCCCCccCCcHHH--HHHHHHHHHHHhhcCC
Confidence            2211    000000000   0  0   00000 1   1222222  33456678999999  9999999999998753

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

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

Probab=99.79  E-value=4.6e-19  Score=169.09  Aligned_cols=156  Identities=24%  Similarity=0.275  Sum_probs=112.5

Q ss_pred             HHHHHHHHHHHhcCCC-CChHHHHHHHHHHhcCcCcHHhhccCCcceecc-ccccCCCHHHHHHHHHHHHHHHHHHHHhh
Q 021095          136 VGEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVN-GLRKHGSKQIRHLARTLIEGWKDLVDEWV  213 (317)
Q Consensus       136 ~~EV~rIkk~Lek~~~-~s~e~llelL~~L~~v~iT~dlL~~T~IGk~Vn-kLRKh~s~eV~~LAk~LIkkWK~~V~~~~  213 (317)
                      .+|+.++.++|+++.+ .+.+.++++|.+|+++|||+++|++|+||+.|| .|+||++++|+++||.||+.||++|....
T Consensus         3 ~e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~~   82 (296)
T KOG1105|consen    3 EEEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKSP   82 (296)
T ss_pred             cHHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhccc
Confidence            3789999999999865 467899999999999999999999999999999 55678888999999999999999998641


Q ss_pred             hhcccc--ccCCCCCC--C-CCCCC--cC--CCCCCCCcccCcccCCCCCCcchhhHHHHHHHHHHHHHhcCCCCccchh
Q 021095          214 NATKAI--AEGTPDSV--N-PSVVD--EE--EGLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKV  284 (317)
Q Consensus       214 ~~~~a~--se~sp~ss--~-~s~~~--ee--~~~P~~p~d~~af~~~~~T~d~vR~~~kc~emLy~AL~~~~~~~~t~~~  284 (317)
                      ...+..  ..+.|...  + ++..+  +.  ...++.+. .++-++.+++++.+|  ++|++|||+||.++..++.+.++
T Consensus        83 ~~~k~~~~~~~~p~~~~~~~~s~~~~~~ks~~~~~~~~~-~~~~~~~~~~~d~~r--~k~~e~l~~al~~~~~~~~~~~~  159 (296)
T KOG1105|consen   83 GREKSGDNKSHDPGEASSKSPSGAKQPEKSRGDSKRDKH-SGSKDPVPITNDPVR--DKCRELLYAALTTEDDSRVTGAD  159 (296)
T ss_pred             ccccCccccCCCCCcCCcCCccCCCCccccccccccccc-cCcCCCCCCCCchHH--HHHHHHHHHHhcccccccccCCC
Confidence            111111  11112111  1 11111  00  01111110 112144677899999  99999999999999999999999


Q ss_pred             hhhhHHHHHh
Q 021095          285 EENLQWRTKI  294 (317)
Q Consensus       285 e~~~~~~~~~  294 (317)
                      .+.++.-++-
T Consensus       160 ~~~~a~~iE~  169 (296)
T KOG1105|consen  160 PLELAVQIEE  169 (296)
T ss_pred             HHHHHHHHHH
Confidence            7777766553

>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=99.72  E-value=9.7e-18  Score=130.65  Aligned_cols=74  Identities=51%  Similarity=0.749  Sum_probs=68.9

Q ss_pred             HHHHHHHHHHhcCCC-CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHH
Q 021095          137 GEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       137 ~EV~rIkk~Lek~~~-~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~  210 (317)
                      +||.+++++|+++.+ .+.+.++++|+.|+.+|||.++|++|+||+.||+||||.+++|+++|+.||++||++|+
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            689999999998753 57778999999999999999999999999999999999999999999999999999873

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

Probab=99.66  E-value=7e-17  Score=125.89  Aligned_cols=70  Identities=43%  Similarity=0.681  Sum_probs=61.7

Q ss_pred             HHHHHHhcCCC--CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHH
Q 021095          141 RIKEILHNSRD--ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       141 rIkk~Lek~~~--~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~  210 (317)
                      ++.++++++..  .+.+.++++|+.|+.++||.++|++|+||+.||+||||++++|+.+|+.||++||++|+
T Consensus         3 ~~~k~~~k~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~   74 (75)
T smart00509        3 RAAKKLDKVANNGKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY   74 (75)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence            44556666432  44678999999999999999999999999999999999999999999999999999985

>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=99.46  E-value=3.2e-14  Score=103.24  Aligned_cols=52  Identities=54%  Similarity=0.827  Sum_probs=47.3

Q ss_pred             HHHHHHhcCcCcHHhhccCCcceeccccccC-CCHHHHHHHHHHHHHHHHHHH
Q 021095          159 ESLRRLQLMALTVDTLKATEIGKAVNGLRKH-GSKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       159 elL~~L~~v~iT~dlL~~T~IGk~VnkLRKh-~s~eV~~LAk~LIkkWK~~V~  210 (317)
                      ++|+.|+.+|||.++|++|+||++||.|||| .+++|+++|+.||++||.+|+
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 888999999999999999874

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.

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

Probab=97.25  E-value=0.00015  Score=73.24  Aligned_cols=70  Identities=31%  Similarity=0.450  Sum_probs=63.3

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHH
Q 021095          137 GEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       137 ~EV~rIkk~Lek~~~~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~  210 (317)
                      .-|.++...|++.  .+...++..|..|..+|++++.|.+|.+|+.|+.||||.  .|..++..|+..||+.|-
T Consensus         9 ~~Vr~lQ~~l~~~--~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~   78 (433)
T KOG2821|consen    9 GAVRKLQARLENR--IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVL   78 (433)
T ss_pred             HHHHHHHHHHHhC--ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcc
Confidence            5677888888875  356789999999999999999999999999999999997  799999999999999984

>KOG1793 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.42  E-value=0.017  Score=58.06  Aligned_cols=52  Identities=27%  Similarity=0.376  Sum_probs=45.8

Q ss_pred             HHHHHHHhcCcCcH-HhhccCCcceeccccccCCCH--HHHHHHHHHHHHHHHHH
Q 021095          158 FESLRRLQLMALTV-DTLKATEIGKAVNGLRKHGSK--QIRHLARTLIEGWKDLV  209 (317)
Q Consensus       158 lelL~~L~~v~iT~-dlL~~T~IGk~VnkLRKh~s~--eV~~LAk~LIkkWK~~V  209 (317)
                      ..+|.-|..+||-. +.|+..+||++|-=|-||+.+  +++.+|..||.+|-.-+
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            45677788888877 999999999999999999765  99999999999998754

>COG5139 Uncharacterized conserved protein [Function unknown]

Probab=93.91  E-value=0.069  Score=52.30  Aligned_cols=51  Identities=22%  Similarity=0.433  Sum_probs=43.2

Q ss_pred             HHHHHHhcCcCcHHhhccCCcceeccccc--cCCCHHHHHHHHHHHHHHHHHH
Q 021095          159 ESLRRLQLMALTVDTLKATEIGKAVNGLR--KHGSKQIRHLARTLIEGWKDLV  209 (317)
Q Consensus       159 elL~~L~~v~iT~dlL~~T~IGk~VnkLR--Kh~s~eV~~LAk~LIkkWK~~V  209 (317)
                      .+|..|..|||-.++|++.+||+.|-=.-  |...++|+.+|+.||..|-.-|
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            46677888999999999999999997664  4456699999999999998754

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

Probab=93.56  E-value=0.2  Score=42.04  Aligned_cols=59  Identities=24%  Similarity=0.272  Sum_probs=47.1

Q ss_pred             CChHHHHHHHHHHhcCcCcHHhhcc-CCcceeccccccCC-CHHHHHHHHHHHHHHHHHHH
Q 021095          152 ESDSVLFESLRRLQLMALTVDTLKA-TEIGKAVNGLRKHG-SKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       152 ~s~e~llelL~~L~~v~iT~dlL~~-T~IGk~VnkLRKh~-s~eV~~LAk~LIkkWK~~V~  210 (317)
                      .+...++++|..|..+++|..+|+. +.+--++.+||+.. |..|++.|..|+.+-|.++.
T Consensus        20 ~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~   80 (106)
T PF11467_consen   20 PDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL   80 (106)
T ss_dssp             E-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence            5677999999999999999998874 55888899999875 56999999999999999985

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.

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

Probab=90.37  E-value=0.35  Score=38.54  Aligned_cols=42  Identities=17%  Similarity=0.252  Sum_probs=33.7

Q ss_pred             CCChhhHHHHhhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhhHHHHhhh
Q 021095            5 SGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTC   55 (317)
Q Consensus         5 ~~~ld~Wr~~f~~ag~di~~~Id~AI~VAA~D~p~elr~RRD~I~ErL~~~   55 (317)
                      -.++++|+.|||..|-.     |+.|..|-.++    +..||.+-++|-.=
T Consensus         8 ~VP~~~wk~F~R~LGLs-----dn~Ie~~E~~~----~~~rda~y~ML~~W   49 (77)
T cd08815           8 AVPARRWKEFVRTLGLR-----EAEIEAVELEI----GRFRDQQYEMLKRW   49 (77)
T ss_pred             cCChHHHHHHHHHcCCc-----HhHHHHHHhcc----cchHHHHHHHHHHH
Confidence            46889999999997753     77899888777    56679999988753

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=82.54  E-value=2.1  Score=50.15  Aligned_cols=59  Identities=25%  Similarity=0.400  Sum_probs=47.8

Q ss_pred             HHHHHHHHhcCcCcHHhhccCCcceecc-ccccCCCHHHHHHHHHHHHHHHHHHHHhhhh
Q 021095          157 LFESLRRLQLMALTVDTLKATEIGKAVN-GLRKHGSKQIRHLARTLIEGWKDLVDEWVNA  215 (317)
Q Consensus       157 llelL~~L~~v~iT~dlL~~T~IGk~Vn-kLRKh~s~eV~~LAk~LIkkWK~~V~~~~~~  215 (317)
                      +..+|+-|-.++..+-.|+..+||++|. ++--|.+.+|+.+|+.|+..|-+++..++.+
T Consensus      1303 ~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~~ 1362 (1713)
T PLN02976       1303 LRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKAS 1362 (1713)
T ss_pred             HHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            3445555555777788889999999984 6688999999999999999999999766543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	317
1wjt_A	103	Solution Structure Of The N-Terminal Domain I Of Mo		1e-06

>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 = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 54/92 (58%), Gaps = 5/92 (5%)
Query: 138 EVLRIKEILHN--SRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQI 194
           E+LRI + L    SR +++  L + L++L    +++  L+ T IG AVNG+RKH S K++
Sbjct: 13  ELLRIAKKLEKMVSRKKTEGAL-DLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEV 71
Query: 195 RHLARTLIEGWKDLVDEWVNATKAIAEGTPDS 226
             LA+ LI+ WK L+D     TK   E  P S
Sbjct: 72  VSLAKVLIKNWKRLLDS-PRTTKGERESGPSS 102

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	317
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	7e-21
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	7e-13
2xpp_A	145	IWS1, ECU08_0440; transcription, elongation, histo	1e-04
3nfq_A	170	Transcription factor IWS1; SPN1, RNA polymerase II	4e-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 = 84.7 bits (209), Expect = 7e-21
 Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 138 EVLRIKEILHNSRDESDS-VLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQIR 195
           E+LRI + L        +    + L++L    +++  L+ T IG AVNG+RKH S K++ 
Sbjct: 13  ELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVV 72

Query: 196 HLARTLIEGWKDLVDEWVNATKAIAEGTP 224
            LA+ LI+ WK L+D           G  
Sbjct: 73  SLAKVLIKNWKRLLDSPRTTKGERESGPS 101

>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 = 67.1 bits (162), Expect = 7e-13
 Identities = 24/106 (22%), Positives = 43/106 (40%), Gaps = 2/106 (1%)

Query: 138 EVLRIKEILHNSRDESDSVLFESLRRLQ-LMALTVDTLKATEIGKAVNGLRKHGSKQIRH 196
           EVL   + L  ++    +VL E L  L      T   L+ T++G  VN  +K  + +I  
Sbjct: 5   EVLVHVKNLEKNKSNDAAVL-EILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISK 63

Query: 197 LARTLIEGWKDLVDEWVNATKAIAEGTPDSVNPSVVDEEEGLPSPP 242
           L + +I  WKD +++   + +A       +   +      G     
Sbjct: 64  LVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAEDKTTVGESVNG 109

>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 = 40.8 bits (95), Expect = 1e-04
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 146 LHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHG--SKQIRHLARTLIE 203
           L +    +  +    L  L+ M +  + L  + +GK V     +   SK++R  A+ L++
Sbjct: 73  LPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQ 132

Query: 204 GWK 206
            W 
Sbjct: 133 KWT 135

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

 Score = 39.7 bits (92), Expect = 4e-04
 Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 2/63 (3%)

Query: 146 LHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHG--SKQIRHLARTLIE 203
           L +    S  +       L  + +  + LK + +G+ V    K      Q+  LA  LI 
Sbjct: 88  LPDGSLPSFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIA 147

Query: 204 GWK 206
            W 
Sbjct: 148 EWT 150

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	317
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.86
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	99.77
2xpp_A	145	IWS1, ECU08_0440; transcription, elongation, histo	97.77
3nfq_A	170	Transcription factor IWS1; SPN1, RNA polymerase II	97.52
2lw4_A	113	Transcription elongation factor A protein 2; struc	97.2
3ndq_A	108	Transcription elongation factor A protein 1; helix	97.0
3po3_S	178	Transcription elongation factor S-II; RNA polymera	96.04
2b4j_C	98	PC4 and SFRS1 interacting protein; HIV, integratio	93.55
1z9e_A	127	PC4 and SFRS1 interacting protein 2; heat repeat-l	91.31

>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=99.86  E-value=2.4e-21  Score=184.40  Aligned_cols=137  Identities=20%  Similarity=0.256  Sum_probs=101.8

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHH-hcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 021095          136 VGEVLRIKEILHNSRDESDSVLFESLRRL-QLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVN  214 (317)
Q Consensus       136 ~~EV~rIkk~Lek~~~~s~e~llelL~~L-~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~~~~~  214 (317)
                      ++||.+|++.|++. ..+.+.++++|++| +.++||+++|++|+||++||+||||.+++|+.+|+.||++||++|..+..
T Consensus         3 ~~el~~~~~~L~k~-~~~~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~~WK~~v~~~~~   81 (309)
T 1pqv_S            3 SKEVLVHVKNLEKN-KSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAINKNKR   81 (309)
T ss_pred             HHHHHHHHHHHhcc-CCCHHHHHHHHHHHHhcCCCCHHHHHhCChhHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            47999999999993 46778999999999 88999999999999999999999999999999999999999999988755


Q ss_pred             hccc----------c--ccCCCCCC-----CC--CC----C--CcCCCCCCCCcccCcccCCCCCCcchhhHHHHHHHHH
Q 021095          215 ATKA----------I--AEGTPDSV-----NP--SV----V--DEEEGLPSPPLDELAFFTGPSAGIELSQVFLMAWMIL  269 (317)
Q Consensus       215 ~~~a----------~--se~sp~ss-----~~--s~----~--~ee~~~P~~p~d~~af~~~~~T~d~vR~~~kc~emLy  269 (317)
                      .+..          .  ..++|.+.     ++  +.    .  ......+++|..++  ++.+.|++.+|  ++|++|||
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~d~~R--~k~r~~L~  157 (309)
T 1pqv_S           82 SRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAMKQDKYVSTKPRNSKNDG--VDTAIYHHKLR--DQVLKALY  157 (309)
T ss_pred             CCcccccccccccccccCCCCCCCCcCCCCCCcccccccccCCCCCCCCCCCCCCCC--CCcCcCChHHH--HHHHHHHH
Confidence            4221          0  00000000     00  00    0  00112234444333  34667889999  99999999


Q ss_pred             HHHHhcCC
Q 021095          270 EILETVGN  277 (317)
Q Consensus       270 ~AL~~~~~  277 (317)
                      +||+.+..
T Consensus       158 ~aL~~~~~  165 (309)
T 1pqv_S          158 DVLAKESE  165 (309)
T ss_pred             HHHhcCCC
Confidence            99998754

>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=4.5e-20  Score=151.00  Aligned_cols=79  Identities=34%  Similarity=0.548  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHhcCC-CCChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccC-CCHHHHHHHHHHHHHHHHHHHHhh
Q 021095          136 VGEVLRIKEILHNSR-DESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKH-GSKQIRHLARTLIEGWKDLVDEWV  213 (317)
Q Consensus       136 ~~EV~rIkk~Lek~~-~~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh-~s~eV~~LAk~LIkkWK~~V~~~~  213 (317)
                      ++||.+|+++|+++. ..+.+.++++|++|+.++||+++|++|+||++||+|||| ++++|+++|+.||++||++|..+.
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            378999999999853 345678999999999999999999999999999999999 778999999999999999998644


Q ss_pred             h
Q 021095          214 N  214 (317)
Q Consensus       214 ~  214 (317)
                      +
T Consensus        91 ~   91 (103)
T 1wjt_A           91 T   91 (103)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=97.77  E-value=2.6e-05  Score=67.08  Aligned_cols=70  Identities=23%  Similarity=0.285  Sum_probs=56.3

Q ss_pred             HHHHHHhcCCC---CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCH--HHHHHHHHHHHHHHHHHH
Q 021095          141 RIKEILHNSRD---ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSK--QIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       141 rIkk~Lek~~~---~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~--eV~~LAk~LIkkWK~~V~  210 (317)
                      .|+.-|+-.++   .+..---.+|+.|..+||+.+.|++++||++|..|.||+.+  +++++|+.||.+|...+-
T Consensus        65 ~l~~WL~PLpDgsLP~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvv~~l~k~~~et~~nk~la~~Li~~WsRpi~  139 (145)
T 2xpp_A           65 EIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVF  139 (145)
T ss_dssp             HHHHHHSCCTTSCCCCHHHHHHHHHHHHTSCCCHHHHHHHCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhCcCCCCCCCCHHHHHHHHHHHHHCCCCHHHhhcCCCCcchhhhhcCCccCHHHHHHHHHHHHHHHHHHh
Confidence            34445554433   34444567888889999999999999999999999999764  999999999999998663

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

Probab=97.52  E-value=7.5e-05  Score=65.86  Aligned_cols=68  Identities=22%  Similarity=0.296  Sum_probs=53.8

Q ss_pred             HHHHHhcCCC---CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCC--HHHHHHHHHHHHHHHHHH
Q 021095          142 IKEILHNSRD---ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS--KQIRHLARTLIEGWKDLV  209 (317)
Q Consensus       142 Ikk~Lek~~~---~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s--~eV~~LAk~LIkkWK~~V  209 (317)
                      ++.-|+-.++   .+..---.+|+.|..+||+.+.|+.++||++|+-|.||+.  ++++++|..||.+|..-+
T Consensus        81 l~~WLePLpDgSLP~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvV~~l~k~~~et~~nkrla~~Li~~WsRpI  153 (170)
T 3nfq_A           81 VRIWLEPLPDGSLPSFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWTRPI  153 (170)
T ss_dssp             HHHHHSCCTTSCCCCHHHHHHHHHHHHTSCCCHHHHHHHSHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHhCcCCCCCCCcHHHHHHHHHHHHHCCCCHHHHhhCCCCceeeehhcCCcccHHHHHHHHHHHHHHHHHH
Confidence            3444554443   3334446788888899999999999999999999999975  499999999999996644

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

Probab=97.20  E-value=0.00014  Score=59.97  Aligned_cols=28  Identities=14%  Similarity=0.019  Sum_probs=25.3

Q ss_pred             ccCCCCCCcchhhHHHHHHHHHHHHHhcCC
Q 021095          248 FFTGPSAGIELSQVFLMAWMILEILETVGN  277 (317)
Q Consensus       248 f~~~~~T~d~vR~~~kc~emLy~AL~~~~~  277 (317)
                      |++.+.|+|.||  ++|++|||+||+++.+
T Consensus         2 ~~p~p~t~D~vR--dk~~e~L~~aL~~~~~   29 (113)
T 2lw4_A            2 HMPVPVTCDAVR--NKCREMLTAALQTDHD   29 (113)
T ss_dssp             CCCSCCCCSTTH--HHHHHHHHHHHHSSTH
T ss_pred             CCCCCCCCcHHH--HHHHHHHHHHHHcCCC
Confidence            577899999999  9999999999998765

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

Probab=97.00  E-value=0.00023  Score=58.24  Aligned_cols=31  Identities=16%  Similarity=0.070  Sum_probs=24.3

Q ss_pred             cCcccCCCCCCcchhhHHHHHHHHHHHHHhcCC
Q 021095          245 ELAFFTGPSAGIELSQVFLMAWMILEILETVGN  277 (317)
Q Consensus       245 ~~af~~~~~T~d~vR~~~kc~emLy~AL~~~~~  277 (317)
                      +..||+.+.|+++||  ++|++|||+||+++.+
T Consensus         3 ~~~~~~~~~t~d~vR--~k~~~lL~~aL~~~~d   33 (108)
T 3ndq_A            3 DPFTPRAPSTSDSVR--LKCREMLAAALRTGDD   33 (108)
T ss_dssp             -----CCCCCCCHHH--HHHHHHHHHHTTGGGH
T ss_pred             CCCCCCCCCCCChHH--HHHHHHHHHHHHcCCC
Confidence            457889999999999  9999999999999753

>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=96.04  E-value=0.0019  Score=56.98  Aligned_cols=34  Identities=6%  Similarity=-0.031  Sum_probs=18.8

Q ss_pred             CCCcccCcccCCCCCCcchhhHHHHHHHHHHHHHhcCC
Q 021095          240 SPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGN  277 (317)
Q Consensus       240 ~~p~d~~af~~~~~T~d~vR~~~kc~emLy~AL~~~~~  277 (317)
                      |+++.||+  .+++|+|+||  ++|++|||+||+.+..
T Consensus         1 r~~~~d~v--~~~~~~d~vR--dk~~~lL~~aL~~~~~   34 (178)
T 3po3_S            1 RNSKNDGV--DTAIYHHKLR--DQVLKALYDVLAKESE   34 (178)
T ss_dssp             ----------------CHHH--HHHHHHHHHHTTSSSS
T ss_pred             CCccCCCc--CcCcCCChHH--HHHHHHHHHHHhcCCC
Confidence            34667784  8899999999  9999999999999765

>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=93.55  E-value=0.15  Score=41.12  Aligned_cols=59  Identities=19%  Similarity=0.227  Sum_probs=50.0

Q ss_pred             CChHHHHHHHHHHhcCcCcHHhhc-cCCcceeccccccC-CCHHHHHHHHHHHHHHHHHHH
Q 021095          152 ESDSVLFESLRRLQLMALTVDTLK-ATEIGKAVNGLRKH-GSKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       152 ~s~e~llelL~~L~~v~iT~dlL~-~T~IGk~VnkLRKh-~s~eV~~LAk~LIkkWK~~V~  210 (317)
                      .+...++++|..|..+++|.-+|+ .+.+--++.+||+. .+..|++.|..|+.+.|.++.
T Consensus        24 ~Dv~kcl~~L~~l~~l~~T~~mL~rnpe~V~t~kklRry~g~q~Ir~kA~~iY~kfK~~f~   84 (98)
T 2b4j_C           24 LDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL   84 (98)
T ss_dssp             CCHHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC--
T ss_pred             CCHHHHHHHHHHHhcccccHHHHhhChHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHh
Confidence            567899999999999999999665 56688889999876 467999999999999999885

>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=91.31  E-value=0.25  Score=41.55  Aligned_cols=59  Identities=19%  Similarity=0.227  Sum_probs=51.5

Q ss_pred             CChHHHHHHHHHHhcCcCcHHhhc-cCCcceeccccccC-CCHHHHHHHHHHHHHHHHHHH
Q 021095          152 ESDSVLFESLRRLQLMALTVDTLK-ATEIGKAVNGLRKH-GSKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       152 ~s~e~llelL~~L~~v~iT~dlL~-~T~IGk~VnkLRKh-~s~eV~~LAk~LIkkWK~~V~  210 (317)
                      .+...++++|..|..+++|.-+|+ -+.+--++.+||+. .|..|++.|..|+.+.|.++.
T Consensus        24 ~Dv~kCl~~Leel~~l~vT~~mL~Rnpe~V~TlkklRrY~gnq~Ir~kA~~iY~kFK~lf~   84 (127)
T 1z9e_A           24 LDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL   84 (127)
T ss_dssp             CCHHHHHHHHHHHHHSCCCHHHHGGGHHHHHHHHHHTTCTTCSSHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHccccccHHHHhhChHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence            567899999999999999999665 56688899999876 466999999999999999985

---

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	317
d1wjta_	103	a.48.3.1 (A:) Transcription elongation factor S-II	1e-19
d1eo0a_	77	a.48.3.1 (A:) Transcription elongation factor TFII	3e-19

>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 = 80.3 bits (198), Expect = 1e-19
 Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 138 EVLRIKEILHNSRDESDS-VLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGS-KQIR 195
           E+LRI + L        +    + L++L    +++  L+ T IG AVNG+RKH S K++ 
Sbjct: 13  ELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVV 72

Query: 196 HLARTLIEGWKDLVDEWVNATKAIAEGTP 224
            LA+ LI+ WK L+D           G  
Sbjct: 73  SLAKVLIKNWKRLLDSPRTTKGERESGPS 101

>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 = 78.3 bits (193), Expect = 3e-19
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 138 EVLRIKEILHNSRDESDSVLFESLRRLQ-LMALTVDTLKATEIGKAVNGLRKHGSKQIRH 196
           EVL   + L  ++    +VL E L  L      T   L+ T++G  VN  +K  + +I  
Sbjct: 5   EVLVHVKNLEKNKSNDAAVL-EILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISK 63

Query: 197 LARTLIEGWKDLVD 210
           L + +I  WKD ++
Sbjct: 64  LVKKMISSWKDAIN 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	317
d1eo0a_	77	Transcription elongation factor TFIIS N-domain {Ba	99.77
d1wjta_	103	Transcription elongation factor S-II protein 3 {Mo	99.75
d2b4jc1	81	PC4 and SFRS1-interacting protein, PSIP1 {Human (H	97.23
d1enwa_	114	Elongation factor TFIIS domain 2 {Baker's yeast (S	96.31

>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=99.77  E-value=3.9e-20  Score=142.47  Aligned_cols=73  Identities=29%  Similarity=0.482  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHhc-CcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHH
Q 021095          137 GEVLRIKEILHNSRDESDSVLFESLRRLQL-MALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD  210 (317)
Q Consensus       137 ~EV~rIkk~Lek~~~~s~e~llelL~~L~~-v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~  210 (317)
                      +||.++++.|++.. .+++.++++|+.|++ ++||.++|++|+||++||+||||++++|+++|+.||++||+.|+
T Consensus         4 ~ev~~~~k~Lek~~-~~~~~~l~~L~~L~~~~~it~d~L~~T~iG~~Vn~LRkh~~~~v~~lAk~Lv~~WK~~Vd   77 (77)
T d1eo0a_           4 KEVLVHVKNLEKNK-SNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAIN   77 (77)
T ss_dssp             HHHHHHHHHHHHHC-SSSHHHHHHHHHHTTTCSCSTTHHHHHHHHHHHHHCCSSSCTTHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhccc-CCHHHHHHHHHHHHhcCCCcHHHHHHCCccHHHHHHhcCCcHHHHHHHHHHHHHHHHhcC
Confidence            78999999999863 567899999999997 99999999999999999999999999999999999999999884

>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=1.1e-19  Score=146.69  Aligned_cols=79  Identities=34%  Similarity=0.537  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHHhcCC-CCChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCC-CHHHHHHHHHHHHHHHHHHHHhh
Q 021095          136 VGEVLRIKEILHNSR-DESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHG-SKQIRHLARTLIEGWKDLVDEWV  213 (317)
Q Consensus       136 ~~EV~rIkk~Lek~~-~~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~-s~eV~~LAk~LIkkWK~~V~~~~  213 (317)
                      .+||.+|++.|+++. +.+.+.++++|+.|+.++||+++|++|+||++||+||||+ +++|+++|+.||++||++|..+.
T Consensus        11 eeei~~i~k~L~~~~~~~~~~~vl~~L~~L~~~~it~e~L~~T~IGk~Vn~LrK~~~~~~v~~lAk~Lv~~WK~~v~~~~   90 (103)
T d1wjta_          11 EEELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLLDSPR   90 (103)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSSHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHHHHHHHHTCCSC
T ss_pred             HHHHHHHHHHHHHHHccCCHHHHHHHHHHHHcCCCCHHHHHhCCccHhHHHHHccCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            379999999999863 3556789999999999999999999999999999999996 56999999999999999997554


Q ss_pred             h
Q 021095          214 N  214 (317)
Q Consensus       214 ~  214 (317)
                      +
T Consensus        91 ~   91 (103)
T d1wjta_          91 T   91 (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=97.23  E-value=0.00028  Score=53.41  Aligned_cols=74  Identities=20%  Similarity=0.280  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHhcC---CCCChHHHHHHHHHHhcCcCcHHhhcc-CCcceeccccccC-CCHHHHHHHHHHHHHHHHH
Q 021095          135 VVGEVLRIKEILHNS---RDESDSVLFESLRRLQLMALTVDTLKA-TEIGKAVNGLRKH-GSKQIRHLARTLIEGWKDL  208 (317)
Q Consensus       135 v~~EV~rIkk~Lek~---~~~s~e~llelL~~L~~v~iT~dlL~~-T~IGk~VnkLRKh-~s~eV~~LAk~LIkkWK~~  208 (317)
                      +++.+..+...|...   ...+...++++|.+|..+++|.-+|+. +.+--++.++|++ .|.+|++.|..|+.+||.+
T Consensus         3 ~E~~l~~L~~~ik~sL~~~~~dv~kcL~~L~~l~~l~vt~~mL~kn~e~V~tikklRry~gn~~Ir~kA~~ly~kfKsl   81 (81)
T d2b4jc1           3 MDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNM   81 (81)
T ss_dssp             HHHHHHHHHHHHHHHTCTTSCCHHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCCCHHHHHHChHHHHHHHHHHHHhccHHHHHHHHHHHHHhccC
Confidence            334555555544433   136778999999999999999998865 5588999999998 5779999999999999974

>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=96.31  E-value=0.002  Score=51.05  Aligned_cols=37  Identities=8%  Similarity=0.053  Sum_probs=32.6

Q ss_pred             CCCCCCcccCcccCCCCCCcchhhHHHHHHHHHHHHHhcCC
Q 021095          237 GLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGN  277 (317)
Q Consensus       237 ~~P~~p~d~~af~~~~~T~d~vR~~~kc~emLy~AL~~~~~  277 (317)
                      ..|+.|+.++  +.++.|++.+|  ++|+++||+||+.+..
T Consensus         3 ~~pr~~k~d~--v~~~~~~d~~R--~~~~~~L~~aL~~~~~   39 (114)
T d1enwa_           3 HMPRNSKNDG--VDTAIYHHKLR--DQVLKALYDVLAKESE   39 (114)
T ss_dssp             CCSCSTTTTC--CCCCSSTTTTH--HHHHHHHHHHHHHHCS
T ss_pred             CCCCCccCCC--CCCccCCcHHH--HHHHHHHHHHHhCcCc
Confidence            4688898888  48899999999  9999999999998755