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 <-- 0.972 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1j23a_) 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 d1j23a_ Putative ATP-​dependent RNA helicase Hef,​ nuclease domainRestriction endonuclease-​likeRestriction endonuclease-​likeα/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 <-- 0.972 --> Hit
DALI alignment (Z-score: 5.0 Raw score:331.90) d1l1sa_ 1 --------------------------------------DYRVVFHIDEDD-ESRV--LLL 19 :::::::::::: :::: ::: d1j23a_ 1 vkvvvdsrelrsevvkrlkllgvklevktldvgdyiisEDVAIERKSANDlIQSIidGGL 60 d1l1sa_ 20 ISNVRNLMADLesVRIEVVAYSM-gvnvlrrDSEYSGDVSELTG-QGVRFCACSNtlras 77 ::::::::::: :::::::::: ::::::::::::: :::::::::: d1j23a_ 61 FDQVKRLKEAY--SRPIMIVEGSlygirnvhPNAIRGAIAAVTVdFGVPIIFSST----- 113 d1l1sa_ 78 gmdgddllegvdvvSSGVGHIVRRQTEGwayirp 111 :::::::::::::: d1j23a_ 114 -------------pEETAQYIFLIAKRE---qee 131 FAST alignment (Normalized score: 4.82 Raw score:581.50) d1l1sa_ 1 --------------------------------------DYRVVFHIDEDDESR------- 15 ::::::::: d1j23a_ 1 VKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKS------ANDLIQS 54 d1l1sa_ 16 --VLLLISNVRNLMADLESVRIEVVAYSMGVNVLRRD-----------SEYSGDVSELT- 61 ::::::::::::::: :::::::: ::::::::::: d1j23a_ 55 IIDGGLFDQVKRLKEAY--SRPIMIVE----------GSLYGIRNVHPNAIRGAIAAVTV 102 d1l1sa_ 62 GQGVRFCACSNTLRASGMDGDDLLEGVDVV--SSGVGHIVRRQTEGWAYIRP----- 111 :::::::::: :::::::::::: d1j23a_ 103 DFGVPIIFSS--------------------TPEETAQYIFLIAK--------REQEE 131 TMalign alignment (TM-score: 0.49 Raw score:53.92) d1l1sa_ 1 DYRVVF--H-------------------IDEDDESRVLLLISNVRNLMADLESVRIEVVA 39 :::::: : :::::: :: :::::::::: d1j23a_ 1 VKVVVDSRELRSEVVKRLKLLGVKLEVK-----------TLDVGD-YI--ISEDVAIERK 46 d1l1sa_ 40 YSMGV-NVLRRDSEYSGDVSELTG--QGVRFCACSNTLRASG---M--DGDDL-LEG--- 87 ::::: :: ::::::::::::::: :::::::: ::::::: : ::::: ::: d1j23a_ 47 SANDLIQS-IIDGGLFDQVKRLKEAYSRPIMIVE-GSLYGIRNVHPNAIRGAIAAVTVDF 104 d1l1sa_ 88 --VDVVSSGVGHIVRRQTEGW------AYIRP 111 ::::::::::::::::::: d1j23a_ 105 GVPIIFSSTPEETAQYIFLIAKREQEE----- 131 HHsearch alignment (Probability: 0.03 E-value:0.13) d1l1sa_ 18 LLISNVRNLMADLESVRIEVVAYSMGVNV-LRRDSEYSGDVSELT-GQGVRFCACSNTLR 75 :::::::::::::::: ::::::::::: ::::::::::::::: :::::::::::::: d1j23a_ 59 GLFDQVKRLKEAYSRP--IMIVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEE 116 d1l1sa_ 76 A 76 : d1j23a_ 117 T 117