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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1hkva1 | Diaminopimelate decarboxylase LysA | Alanine racemase C-terminal domain-like | Domain of alpha and beta subunits of F1 ATP synthase-like | All β |
| Hit | d1vfsa1 | Alanine racemase | Alanine racemase C-terminal domain-like | Domain of alpha and beta subunits of F1 ATP synthase-like | All β |
Query <-- 1.456 --> IntermediateDALI 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 <-- 1.363 --> HitDALI alignment (Z-score: 4.3 Raw score:394.80) d1hkva1 1 nellhlapnvwprnttrdevgvvciagipltqlaqEYGTPLFVI-ITLYEVGTVKDVDVS 59 ::::::::: ::::::::::::::: d1vfsa1 1 -----------------------------------TPTRVYAEImTLRASLALVKTVPAG 25 d1hkva1 60 ----------aTAHRRYVSVDGGMSDNIRtALYGaQYDVRLvsrvsdappvparlvgkhc 109 :::::::::::::::::: :::: :::::: d1vfsa1 26 hgvsyghhyvtESETHLALVPAGYADGIP-RNASgRGPVLV------------agkirra 72 d1hkva1 110 eSGDI--ivrdtwvpDDIRPGDLVAVAA------------------tgAYCYSLSSrynm 149 :::: ::::::::::::: :::::::: d1vfsa1 73 aGRIAmdqfvvdlgeDLAEAGDEAVILGdaergeptaedwaqaahtiaYEIVTRIG---- 128 d1hkva1 150 vGRPAVVAVHAGNarlvlrretvddllslevr 181 :::::::::::: d1vfsa1 129 -GRVPRVYLGGLE--------------hhhhh 145 FAST alignment (Normalized score: 3.36 Raw score:543.90) d1hkva1 1 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQE-YGTPLFV-IITLYEVGTVKDVDV 58 ::::::: ::::::::::::: d1vfsa1 1 ------------------------------------TPTRVYAEIMTLRASLALVKTV-- 22 d1hkva1 59 SAT---------------AHRRYVSVDGGMSDNIRTALYG--------AQYDVRLVSRVS 95 ::::::::::::: ::::: d1vfsa1 23 ---PAGHGVSYGHHYVTESETHLALVPAGYA---------DGIPRNASGRGPV------- 63 d1hkva1 96 DAPPVPARLVGKHCESGDIIVRDTWVP------------------------DDIRPGDLV 131 ::::::::: d1vfsa1 64 ---------------------------LVAGKIRRAAGRIAMDQFVVDLGEDLAEAGDEA 96 d1hkva1 132 AVAAT---------------------GAYCYSLSSRYNMVG-RPAVVAVHAGNARLVLRR 169 :: ::::::::: :::::: d1vfsa1 97 VI---LGDAERGEPTAEDWAQAAHTIAYEIVTRIG------GRVPRVY------------ 135 d1hkva1 170 ETVDDLLSLEVR---------- 181 d1vfsa1 136 ------------LGGLEHHHHH 145 TMalign alignment (TM-score: 0.43 Raw score:77.65) d1hkva1 1 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFV-IITLYEVGTVKDVDVS 59 :::::::: :::::::::::::::: d1vfsa1 1 -----------------------------------TPTRVYAEIMTLRASLALVKTVPAG 25 d1hkva1 60 ----------ATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPP-VPARLVGKH 108 ::::::::::::::::::: ::::::::::: :: : ::::: d1vfsa1 26 HGVSYGHHYVTESETHLALVPAGYADGIP-RNASGRGPVLV---AG---KI-RRAAG--- 74 d1hkva1 109 CESGD--IIVRDTWVPDDIRPGDLVAVA--------AT----------G-AYCYSLSSRY 147 ::: :::: :::::::::::::::: :: : ::::::: d1vfsa1 75 --RIAMDQFVV-DLGEDLAEAGDEAVILGDAERGEPTAEDWAQAAHTIAYEIVTRIG--- 128 d1hkva1 148 NMVGRPAVVAVHAGN-ARLVLRRETVDDLLSLEVR 181 :::::::::::: :::: d1vfsa1 129 ---GRVPRVYLGGLEHHHHH--------------- 145 HHsearch alignment (Probability: 0.21 E-value:0.00) d1hkva1 100 VPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATG 137 :::::::::: ::::::::::: :::::::::::::: d1vfsa1 68 KIRRAAGRIA--MDQFVVDLGED-LAEAGDEAVILGDA 102