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 <-- 1.887 --> Intermediate <-- 1.184 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1byra_) through the intermediate protein (d1jx7a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jx7a_ Hypothetical protein YchNYchN-​likeYchN-​likeα/β
Hit d1byra_ Nuclease NucPhospholipase D/​nucleasePhospholipase D/​nucleaseα+β

Supporting Alignments

Query <-- 1.887 --> Intermediate
DALI alignment (Z-score: 13.0 Raw score:806.90) query 1 gmeNKKMNLLLFSGDY--DKALASLIIANAAREME--IEVTIFCAFWGLLLLRDPekasq 56 ::::::::::::: ::::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYgsESLFNSLRLAIALREQEsnLDLRLFLMSDAVTAGLRG----- 52 query 57 edkslyeqafssltpreaeelplskmnlggigkkmlLEMMkeekaPKLSDLLSGARKKEV 116 :::: ::::::::::::::: d1jx7a_ 53 ----------------------------------qkPGEG-----YNIQQMLEILTAQNV 73 query 117 KFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 74 PVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 FAST alignment (Normalized score: 12.96 Raw score:1774.00) query 1 GMENKKMNLLLFSGD---YDKALASLIIANAARE--MEIEVTIFCAFWGLLLLRDPEKAS 55 ::::::::::: :::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGA-PYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGL------ 50 query 56 QEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEE------KAPKLSDLLS 109 :::::::::: d1jx7a_ 51 --------------------------------------------RGQKPGEGYNIQQMLE 66 query 110 GARKKEVKFYAXQLSVEIMGFKKE-ELFPEVQIMDVKEYLKNALESDLQLFI-- 160 :::::::::::::::::::: ::: ::::::::::::::::::::::::: d1jx7a_ 67 ILTAQNVPVKLCKTCTDGRG-ISTLPLIDGVEIGTLVELAQWTLSADKVL--TF 117 TMalign alignment (TM-score: 0.61 Raw score:97.67) query 1 GMENKKMNLLLFSGDY--DKALASLIIANAARE-M-EIEVTIFCAFWGLLLLRDPEKASQ 56 ::::::::::::: ::::::::::::::: : ::::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRG----- 52 query 57 EDKSLYEQAFSSLTPREAEE-LPLSKMNLGGIGKKMLLEMMKEEKAPKLS-DLLSGARKK 114 : :: : : ::: ::::::::: d1jx7a_ 53 ----------------Q-KPG-------------E--G---------YNIQQMLEILTAQ 71 query 115 EVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 72 NVPVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 HHsearch alignment (Probability: 0.99 E-value:0.00) query 5 KKMNLLLFSG--DYDKALASLIIANAAREMEI--EVTIFCAFWGLLLLRDPEKASQEDKS 60 :::::::::: :::::::::::::::::::: ::::::::::::::::::::: d1jx7a_ 2 QKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRGQKPG----- 56 query 61 LYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYA 120 ::::::::::::::::::::: d1jx7a_ 57 ---------------------------------------EGYNIQQMLEILTAQNVPVKL 77 query 121 XQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQL 158 :::::::::::::::::::::::::::::::::::::: d1jx7a_ 78 CKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVL 115
Intermediate <-- 1.184 --> Hit
DALI alignment (Z-score: 2.8 Raw score:264.70) d1jx7a_ 1 -------------------------MQKIVIVANGapygsesLFNSLRLAIALREQEsnL 35 :::::::::: ::::::::::::::: : d1byra_ 1 epsvqvgyspegsarvlvlsaidsaKTSIRMMAYS-----ftAPDIMKALVAAKKRG--V 53 d1jx7a_ 36 DLRLFLMsdavTAGLrgqkpgegyNIQQMLEILTAQNVPVKLCKTCT------------- 82 ::::::: :::: ::::::::::::::::::::::: d1byra_ 54 DVKIVID--erGNTG--------rASIAAMNYIANSGIPLRTDSNFPiqhdkviivdnvt 103 d1jx7a_ 83 ------------dgrgistlplidgveigtlvelAQWTL--sadkvltf 117 ::::: d1byra_ 104 vetgsfnftkaaetknsenavviwnmpklaesflEHWQDrwnqgrdyrs 152 FAST alignment (Normalized score: 4.09 Raw score:545.40) d1jx7a_ 1 -------------------------MQKIVIVANGAPYGSES----LFNSLRLAIALREQ 31 :::::::: ::::::::::::: d1byra_ 1 EPSVQVGYSPEGSARVLVLSAIDSAKTSIRMMA---------YSFTAPDIMKALVAAKK- 50 d1jx7a_ 32 ESNLDLRLFLMSDAVTAGLRGQKPGEGY-NIQQMLEILTAQNVPVKLCKTCTDGRGISTL 90 ::::::::: ::::::: ::::::::::::::::::::: d1byra_ 51 -RGVDVKIVI---DERGNTG--------RASIAAMNYIANSGIPLRTDSN---------- 88 d1jx7a_ 91 PLIDGVEIGTLVELAQWTLS------------ADKVLTF--------------------- 117 ::::: d1byra_ 89 --------------------FPIQHDKVIIVDNVTVE--TGSFNFTKAAETKNSENAVVI 126 d1jx7a_ 118 -------------------------- 118 d1byra_ 127 WNMPKLAESFLEHWQDRWNQGRDYRS 152 TMalign alignment (TM-score: 0.46 Raw score:53.58) d1jx7a_ 1 -------------------------MQKIVIVANGAPYGSESLFNSLRLAIALREQES-N 34 :::::::::: ::: :::::::::::: : d1byra_ 1 EPSVQVGYSPEGSARVLVLSAIDSAKTSIRMMAYS-------FTA-PDIMKALVAAKKRG 52 d1jx7a_ 35 LDLRLFLMSDAVT-AGLRGQKPGEGYNIQQMLEILTAQNVPVKLCKTCTDGR------GI 87 ::::::: ::: : : :: :::::::::::::::::::::: :: d1byra_ 53 VDVKIVI---DERGN-T--GR-----ASIAAMNYIANSGIPLRTDSNF--PIQHDKVI-- 97 d1jx7a_ 88 STLPLIDGVEIGTLVELAQWT-LSADKVLT---F-------------------------- 117 : ::::::: : d1byra_ 98 --------------------IV-DNVTVETGSFNFTKAAETKNSENAVVIWNMPKLAESF 136 d1jx7a_ 118 ---------------- 118 d1byra_ 137 LEHWQDRWNQGRDYRS 152 HHsearch alignment (Probability: 0.02 E-value:0.32) d1jx7a_ 13 YGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRGQKPGEGYNIQQMLEILTAQN 72 ::::::::::: ::::: :::::::::::::: ::::::::::::::: d1byra_ 36 FTAPDIMKALV---AAKKR--GVDVKIVIDERGNT----------GRASIAAMNYIANSG 80 d1jx7a_ 73 VPVKLCKT 80 :::::::: d1byra_ 81 IPLRTDSN 88