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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.456 --> Intermediate <-- 0.918 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d2piaa1) through the intermediate protein (d1hkva1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1hkva1 Diaminopimelate decarboxylase LysAAlanine racemase C-​terminal domain-​likeDomain of alpha and beta subunits of F1 ATP synthase-​likeAll β
Hit d2piaa1 Phthalate dioxygenase reductaseRiboflavin synthase domain-​likeReductase/​isomerase/​elongation factor common domainAll β

Supporting Alignments

Query <-- 1.456 --> Intermediate
DALI alignment (Z-score: 15.4 Raw score:1032.10) query 1 -----------------------------------MIETPYYLIdkakltrnmeriahvr 25 ::::::::: d1hkva1 1 nellhlapnvwprnttrdevgvvciagipltqlaqEYGTPLFVI---------------- 44 query 26 eksgakallalkcfatwsvfdlmrdymdgttssslfevrlgrerfgkethaysvaygdne 85 d1hkva1 45 ------------------------------------------------------------ 45 query 86 idevvshadkiifnsisqlerfadkaagiarglrlnpqrlgewdvpkvervmdringfmi 145 d1hkva1 45 ------------------------------------------------------------ 45 query 146 hnncenkdfglfdrmlgeieerfgaliarvdwvslgggihftgddypvdafsarlrafsd 205 d1hkva1 45 ------------------------------------------------------------ 45 query 206 rygvqiylepgeasitkstTLEVTVLDTLYN-------KNLAIVDSSIeAHMLDLLIYRE 258 :::::::::::: :::::::::: ::::::::::: d1hkva1 45 -------------------ITLYEVGTVKDVdvsatahRRYVSVDGGM-SDNIRTALYGA 84 query 259 TAKVL-----pneGSHSYMICGKSCLAGDVFG-EFRFAEELKVGDRISFQDAAGYTMVKK 312 ::::: ::::::::::::::::::: ::::::::::::::::::::::::::: d1hkva1 85 QYDVRlvsrvsdaPPVPARLVGKHCESGDIIVrDTWVPDDIRPGDLVAVAATGAYCYSLS 144 query 313 NWFNGVKMPAIAIRELDgSVRTVRE-FTYADYEQSLS- 348 ::::::::::::::::: ::::::: ::::::::::: d1hkva1 145 SRYNMVGRPAVVAVHAG-NARLVLRrETVDDLLSLEVr 181 FAST alignment (Normalized score: 8.24 Raw score:2069.00) query 1 -----------------------------------MIETPYYLIDKAKLTRNMERIAHVR 25 ::::::: d1hkva1 1 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLF------------------ 42 query 26 EKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNE 85 d1hkva1 43 ------------------------------------------------------------ 43 query 86 IDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMI 145 d1hkva1 43 ------------------------------------------------------------ 43 query 146 HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSD 205 d1hkva1 43 ------------------------------------------------------------ 43 query 206 RYGVQIYLEPGEASITKS-TTLEVTVLDTLYN---------KNLAIVDSSIEAHMLDLLI 255 ::::::::::: :::::::: :::::::::: d1hkva1 43 ------------------VIITLYEVGTVK--DVDVSATAHRRYVSVDG-GMSDNIRTAL 81 query 256 YRETAKVLPNEG----------SHSYMICGKSCLAGDV-FGEFRFAEELKVGDRISFQDA 304 ::::::: :::::::::::::::: ::::::::::::::::::::: d1hkva1 82 YGAQYDV-----RLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAAT 136 query 305 AGYTMVKKNWFNGVKMPAIAIRELDGSVRTV-REFTYADYEQSLS--- 348 ::::::::::::::::::::::: ::::::: ::::::::::: d1hkva1 137 GAYCYSLSSRYNMVGRPAVVAVH-AGNARLVLRRETVDDLLSL--EVR 181 TMalign alignment (TM-score: 0.35 Raw score:122.20) query 1 -----------------------------------MIETPYYLIDKAKLTRNMERIAHVR 25 ::::::::: d1hkva1 1 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVI---------------- 44 query 26 EKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNE 85 d1hkva1 45 ------------------------------------------------------------ 45 query 86 IDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMI 145 d1hkva1 45 ------------------------------------------------------------ 45 query 146 HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSD 205 d1hkva1 45 ------------------------------------------------------------ 45 query 206 RYGVQIYLEPGEASITKSTTLEVTVLDTLYN-------KNLAIVDSSIEAHMLDLLIYRE 258 :::::::::::: :::::::::: ::::::::::: d1hkva1 45 -------------------ITLYEVGTVKDVDVSATAHRRYVSVDGGM-SDNIRTALYGA 84 query 259 TAKVLP------NEGSHSYMICGKSCLAGDVFG-EFRFAEELKVGDRISFQDAAGYTMVK 311 :::::: :::::::::::::::::::: :::::::::::::::::::::::::: d1hkva1 85 QYDVRLVSRVSD-APPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSL 143 query 312 KNWFNGVKMPAIAIRELDGSVRTVRE-FTYADYEQSLS- 348 :::::::::::::::::: ::::::: ::::::::::: d1hkva1 144 SSRYNMVGRPAVVAVHAG-NARLVLRRETVDDLLSLEVR 181 HHsearch alignment (Probability: 1.00 E-value:0.00) query 189 DDYPVDAFSARLRAFSDRYG---VQIYLEPGEASITKSTTL---EVTVLDTLYN--KNLA 240 :::::::::::::::::::: :::::::::::::::::: :::::::::: :::: d1hkva1 8 PNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIITLYEVGTVKDVDVSATAHRRYV 67 query 241 IVDSSIEAHMLDLLIYRETAKVL-----PNEGSHSYMICGKSCLAGDVFGEFRFAEE-LK 294 ::::::: ::::::::::::::: ::::::::::::::::::::::::::::: :: d1hkva1 68 SVDGGMS-DNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIR 126 query 295 VGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 :::::::::::::::::::::::::::::::::::::::::::::::::::: d1hkva1 127 PGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSL 178
Intermediate <-- 0.918 --> Hit
DALI alignment (Z-score: 2.0 Raw score:236.10) d1hkva1 1 nellhlapnvwprnttrdevgvvciagipltqlaqeygtplfVIITLYEVGTVKDVDVsa 60 :::::::::::::::: d2piaa1 1 -------------------------------------ttpqeDGFLRLKIASKEKIAR-- 21 d1hkva1 61 taHRRYVSVDG--gmSDNIRtaLYGAQYDVRLvsrvsdappvparlvgkhcESGD----- 113 ::::::::: ::::: :::::::::: :::: d2piaa1 22 --DIWSFELTDpqgaPLPPF--EAGANLTVAV---------pngsrrtyslCNDSqernr 68 d1hkva1 114 ----------iivrdtwVPDDIRPGDLVAVAAtgaycyslssrynmvgrpavvavhagna 163 ::::::::::::::: d2piaa1 69 yviavkrdsngrggsisFIDDTSEGDAVEVSL---------------------------- 100 d1hkva1 164 rlvlrretvddllslevr 181 d2piaa1 101 ---------------prn 103 FAST alignment (Normalized score: 2.10 Raw score:286.40) d1hkva1 1 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFV------IITLYEVGTVK 54 ::::::::::: d2piaa1 1 -------------------------------------------TTPQEDGFLRLKIASKE 17 d1hkva1 55 DVDVSATA--HRRYVSVDGGMSDNIRT----------ALYGAQYDVRLVSRVSDAPPVPA 102 :: ::::::: :::::::::: d2piaa1 18 KI------ARDIWSFEL----------TDPQGAPLPPFEAGANLTVA------------- 48 d1hkva1 103 RLVGKHCESGDIIVRDTW-------------------------------------VPDDI 125 ::::: d2piaa1 49 ------------------VPNGSRRTYSLCNDSQERNRYVIAVKRDSNGRGGSISFIDDT 90 d1hkva1 126 RPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVR---- 181 ::::::::: d2piaa1 91 SEGDAVEVS-----------------------------------------------LPRN 103 TMalign alignment (TM-score: 0.33 Raw score:59.88) d1hkva1 1 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIITLYEVGTVKDVDVSA 60 :: : :: ::::::::::::::: d2piaa1 1 -------------TT-------P-QE----------------DGFLRLKIASKEKIA--- 20 d1hkva1 61 TAHRRYVSVDG--G-MSDNIRTALYGAQYDVRLVSRVS----DAPPVPARLVGKHCESG- 112 :::::::::: : ::::: :::::::::: ::: :::: :: d2piaa1 21 -RDIWSFELTDPQGA-PLPPF--EAGANLTVAV--PNGSRRT------YSLC-----NDS 63 d1hkva1 113 -D--IIVRDT---------W--VPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAV 158 : :::::: : :::::::::::::: :::: d2piaa1 64 QERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVS-LPRN------------------- 103 d1hkva1 159 HAGNARLVLRRETVDDLLSLEVR 181 d2piaa1 104 ----------------------- 104 HHsearch alignment (Probability: 0.12 E-value:0.03) d1hkva1 48 YEVGTVKDVDVSATAHRRYVSVDGGMSD-NIRTALYGAQYDVRLVSRVSDAPPVPARLVG 106 :::::::::::::::::::::::::::: ::::: :::::: ::::::::::::: d2piaa1 9 LRLKIASKEKIARDIWSFELTDPQGAPLPPFEAG----ANLTVA---VPNGSRRTYSLCN 61 d1hkva1 107 KHCESGDI--IVR--------DTWVPDDIRPGDLVAVA 134 :::::::: ::: ::::::::::::::::: d2piaa1 62 DSQERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVS 99