HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 2.229 --> Intermediate <-- 0.740 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1ga8a_) through the intermediate protein (d1l1sa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1l1sa_ Hypothetical protein MTH1491YchN-​likeYchN-​likeα/β
Hit d1ga8a_ Galactosyltransferase LgtCNucleotide-​diphospho-​sugar transferasesNucleotide-​diphospho-​sugar transferasesα/β

Supporting Alignments

Query <-- 2.229 --> Intermediate
DALI alignment (Z-score: 12.7 Raw score:767.50) query 1 gmeNKKMNLLLFSGDYDKALASLIIANAAREME--IEVTIFCAFWGLLLLRDpekasqed 58 :::::::::::::::::::::::::::::: ::::::::::::::::: d1l1sa_ 1 ---DYRVVFHIDEDDESRVLLLISNVRNLMADLesVRIEVVAYSMGVNVLRR-------- 49 query 59 kslyeqafssltpREAEelplskmnlggigkkmllemmkeekapklSDLLSGARKKEVKF 118 :::: :::::::::::::: d1l1sa_ 50 -------------DSEY-----------------------------SGDVSELTGQGVRF 67 query 119 YAXQLSVEIMGFKKEELFPEVQIMD--VKEYLKNA-LESDlQLFI 160 ::::::::::::::::::::::::: :::::::: :::: :::: d1l1sa_ 68 CACSNTLRASGMDGDDLLEGVDVVSsgVGHIVRRQtEGWA-YIRP 111 FAST alignment (Normalized score: 12.67 Raw score:1688.00) query 1 GMENKKMNLLLFSGDYDKALASLIIANAARE--MEIEVTIFCAFWGLLLLRDPEKASQED 58 :::::::::::::::::::::::::::: :::::::::::::::::: d1l1sa_ 1 ---DYRVVFHIDEDDESRVLLLISNVRNLMADLESVRIEVVAYSMGVNVLR--------- 48 query 59 KSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP---KLSDLLSGARKKE 115 ::::::::::::: d1l1sa_ 49 --------------------------------------------RDSEYSGDVSELTGQG 64 query 116 VKFYAXQLSVEIMGFKKEELFPEVQIM--DVKEYLKNALES--DLQLFI-- 160 ::::::::::::::::::::::::::: :::::::::: :::: d1l1sa_ 65 VRFCACSNTLRASGMDGDDLLEGVDVVSSGVGHIVRRQT--EGWAYI--RP 111 TMalign alignment (TM-score: 0.60 Raw score:95.28) query 1 GMENKKMNLLLFSGDYDKALASLIIANAARE-M-EIEVTIFCAFWGLLLLRDPEKASQED 58 :::::::::::::::::::::::::::: : ::::::::::::::::::: d1l1sa_ 1 ---DYRVVFHIDEDDESRVLLLISNVRNLMADLESVRIEVVAYSMGVNVLRRD------- 50 query 59 KSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKF 118 : : ::::::::::::::: d1l1sa_ 51 --------------S-E----------------------------YSGDVSELTGQGVRF 67 query 119 YAXQLSVEIMGFKKEELFPEVQIM-D-VKEYLKNAL-ESDLQLFI 160 :::::::::::::::::::::::: : ::::::::: ::: :::: d1l1sa_ 68 CACSNTLRASGMDGDDLLEGVDVVSSGVGHIVRRQTEGWA-YIRP 111 HHsearch alignment (Probability: 0.96 E-value:0.00) query 6 KMNLLLFSGDYDKALASLIIAN--AAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYE 63 :::::::::::::::::::::: :::::::::::::::::::::::: d1l1sa_ 3 RVVFHIDEDDESRVLLLISNVRNLMADLESVRIEVVAYSMGVNVLRRD------------ 50 query 64 QAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYAXQL 123 :::::::::::::::::::::: d1l1sa_ 51 --------------------------------------SEYSGDVSELTGQGVRFCACSN 72 query 124 SVEIMGFKKEELFPEVQI--MDVKEYLKNALES 154 :::::::::::::::::: ::::::::::::: d1l1sa_ 73 TLRASGMDGDDLLEGVDVVSSGVGHIVRRQTEG 105
Intermediate <-- 0.740 --> Hit
DALI alignment (Z-score: 3.1 Raw score:330.20) d1l1sa_ 1 dYRVVFHIDEDdesRVLLLISNVRNLMADL--ESVRIEVVAysmgVNVLrrdseySGDVS 58 :::::::::: :::::::::::::::: ::::::::: :::: ::::: d1ga8a_ 1 -MDIVFAADDN---YAAYLCVAAKSVEAAHpdTEIRFHVLD----AGIS------EANRA 46 d1l1sa_ 59 ELTG------QGVRFCACSnTLRASgmdgddllegvdvvsSGVGHIVR--rqTEGWAYIR 110 :::: ::::::::: ::::: :::::::: :::::::: d1ga8a_ 47 AVAAnlrgggGNIRFIDVN-PEDFA--gfplnirhisittYARLKLGEyiadCDKVLYLD 103 d1l1sa_ 111 P----------------------------------------------------------- 111 : d1ga8a_ 104 Idvlvrdsltplwdtdlgdnwlgasidlfverqegykqkigmadgeyyfnagvllinlkk 163 d1l1sa_ 112 ------------------------------------------------------------ 112 d1ga8a_ 164 wrrhdifkmssewveqykdvmqyqdqdilnglfkggvcyansrfnfmptnyafmasrhtd 223 d1l1sa_ 112 ------------------------------------------------------- 112 d1ga8a_ 224 plyrdrtntvmpvavshycgpakpwhrdctawgaerftelagslttvpeewrgkl 278 FAST alignment (Normalized score: 3.32 Raw score:583.80) d1l1sa_ 1 DYRVVFHIDEDDESRVLLLISNVRNLMADL--ESVRIEVVAYSMGVNVLRRDSE--YSGD 56 :::::::: :::::::::::::::::: :::::::::: :::: d1ga8a_ 1 -MDIVFAAD---DNYAAYLCVAAKSVEAAHPDTEIRFHVLDA------------GISEAN 44 d1l1sa_ 57 VSELTG------QGVRFCACSNTLRASGMDGDDLLEGVDVVS------------------ 92 :::::: :::::::: d1ga8a_ 45 RAAVAANLRGGGGNIRFIDV----------------------NPEDFAGFPLNIRHISIT 82 d1l1sa_ 93 -SGVGHIVRRQT--EGWAYIRP-------------------------------------- 111 ::::::::::: :::::: d1ga8a_ 83 TYARLKLGEYIADCDKVLYL--DIDVLVRDSLTPLWDTDLGDNWLGASIDLFVERQEGYK 140 d1l1sa_ 112 ------------------------------------------------------------ 112 d1ga8a_ 141 QKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSSEWVEQYKDVMQYQDQDILNGLFKGGV 200 d1l1sa_ 112 ------------------------------------------------------------ 112 d1ga8a_ 201 CYANSRFNFMPTNYAFMASRHTDPLYRDRTNTVMPVAVSHYCGPAKPWHRDCTAWGAERF 260 d1l1sa_ 112 ------------------ 112 d1ga8a_ 261 TELAGSLTTVPEEWRGKL 278 TMalign alignment (TM-score: 0.52 Raw score:57.50) d1l1sa_ 1 DYRVVFHIDEDDESRVLLLISNVRNLMADL-ESVRIEVVAYSMGVNVLRRDSEYSGDVSE 59 :::::::::: :::::::::::::::: :::::::::::: :: : ::::::::: d1ga8a_ 1 --MDIVFAADDN--YAAYLCVAAKSVEAAHPDTEIRFHVLDAG--IS-E--ANRAAVAAN 51 d1l1sa_ 60 L-TGQGVRFCACSNT----------------------LRASGMDGDDLLEGVDVVSSGV- 95 : :::::::::: :: :: d1ga8a_ 52 LRGGGGNIRFID-VNPEDFAGFPLNIRHISITTYARL--------------------KLG 90 d1l1sa_ 96 GHIVRRQTEGWAYIRP-------------------------------------------- 111 :::::: :::::::: d1ga8a_ 91 EYIADC--DKVLYLDIDVLVRDSLTPLWDTDLGDNWLGASIDLFVERQEGYKQKIGMADG 148 d1l1sa_ 112 ------------------------------------------------------------ 112 d1ga8a_ 149 EYYFNAGVLLINLKKWRRHDIFKMSSEWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFN 208 d1l1sa_ 112 ------------------------------------------------------------ 112 d1ga8a_ 209 FMPTNYAFMASRHTDPLYRDRTNTVMPVAVSHYCGPAKPWHRDCTAWGAERFTELAGSLT 268 d1l1sa_ 112 ---------- 112 d1ga8a_ 269 TVPEEWRGKL 278 HHsearch alignment (Probability: 0.01 E-value:0.45) d1l1sa_ 4 VVFHIDEDDESRVLLLISNVRNLMADLESVRIEVVAYSMGV 44 ::::::: ::::::::::::::::::::::::::::::: d1ga8a_ 3 IVFAADD---NYAAYLCVAAKSVEAAHPDTEIRFHVLDAGI 40