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 | d1vfsa2 | Alanine racemase | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1nfga2 | D-hydantoinase | Metallo-dependent hydrolases | TIM beta/alpha-barrel | α/β |
Query <-- 2.281 --> IntermediateDALI alignment (Z-score: 14.8 Raw score:1354.10) query 1 mietpyyliDKAKLTRNMERIAHVREksGAKALLALKCFA----TWSVFDLMRD-YMDGT 55 ::::::::::::::::: :::::::::::: :::::::::: ::::: d1vfsa2 1 ---------DLDAVRANVRALRARAP--RSALMAVVKSNAyghgAVPCARAAQEaGAAWL 49 query 56 TSSSLFEVRLGRER-FGKETHAYSVAYGDnEIDEVVSHADKIIFNSISQLERFADKA--- 111 :::::::::::::: :::::::::::::: ::::::::::::::::::::::::::: d1vfsa2 50 GTATPEEALELRAAgIQGRIMCWLWTPGG-PWREAIETDIDVSVSGMWALDEVRAAAraa 108 query 112 -AGIARGLRLNPQ--RLGEW--DVPKVER-VMDR-------INGFMIHNNceNKDFGL-- 156 :::::::::::: ::::: ::::::: :::: ::::::::: :::::: d1vfsa2 109 gRTARIQLXADTGlgRNGCQpaDWAELVGaAVAAqaegtvqVTGVWSHFA-cADEPGHps 167 query 157 FDRMLGEIEERFGALIA---RVDWVSLGG-GIHFtgddypvdaFSARLrafsdrygvQIY 212 ::::::::::::::::: ::::::::: :::: ::::: ::: d1vfsa2 168 IRLQLDAFRDMLAYAEKegvDPEVRHIANsPATL---------TLPET--------hFDL 210 query 213 LEPGEASIT--------------KSTTlevtvldtlynknlaivdssieahmldlliyre 258 ::::::::: :::: d1vfsa2 211 VRTGLAVYGvspspelgtpaqlgLRPA--------------------------------- 237 query 259 takvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngv 318 d1vfsa2 238 ------------------------------------------------------------ 238 query 319 kmpaiaireldgsvrtvreftyadyeqsls 348 d1vfsa2 238 ------------------------------ 238 FAST alignment (Normalized score: 7.44 Raw score:2136.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFA---------TWSVFDLMRD- 50 :::::::::::::::: :::::::: :::::::::: d1vfsa2 1 ---------DLDAVRANVRALRARA--PRSALMAV-----VKSNAYGHGAVPCARAAQEA 44 query 51 YMDGTTSSSLFEVRLGRE-RFGKETHAYSVAYGDN-EIDEVVSHA--DKIIFNSISQLER 106 :::::::::::::::::: :::::::: :::::: ::::::: ::::::::::::: d1vfsa2 45 GAAWLGTATPEEALELRAAGIQGRIMC--WLWTPGGPWREAIE--TDIDVSVSGMWALDE 100 query 107 FADKAA----GIARGLRLNP--QRLGEW-------DVPKVERVMD-----RINGFMIHNN 148 :::::: :::::::::: ::::: ::::::::: ::::::: :: d1vfsa2 101 VRAAARAAGRTARIQLXADTGLGRNGC-QPADWAELVGAAVAAQ-AEGTVQVTGVWS-HF 157 query 149 CENKDF--GLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLRAF 203 :::::: ::::::::::::::::::: :::::: d1vfsa2 158 ACADEPGHPSIRLQLDAFRDMLAYAEKEGVDPEVRH------------------------ 193 query 204 SDRYGVQ---------------IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEA 248 ::::::::: d1vfsa2 194 -------IANSPATLTLPETHFDLVRTGLAV----------------------------- 217 query 249 HMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYT 308 d1vfsa2 218 ------------------------------------------------------------ 218 query 309 MVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-------------------- 348 d1vfsa2 218 ----------------------------------------YGVSPSPELGTPAQLGLRPA 237 TMalign alignment (TM-score: 0.49 Raw score:169.09) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-F--AT-WSVFDLMRD-YMDGT 55 :::::::::::::::: :: ::::::::: : :: ::::::::: ::::: d1vfsa2 1 ---------DLDAVRANVRALRARA-PR-SALMAVVKSNAYGHGAVPCARAAQEAGAAWL 49 query 56 TSSSLFEVRLGRER-FGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKA--- 111 :::::::::::::: :::::::::::::: ::::::::::::::::::::::::::: d1vfsa2 50 GTATPEEALELRAAGIQGRIMCWLWTPGG-PWREAIETDIDVSVSGMWALDEVRAAARAA 108 query 112 -AGIARGLRLNPQ--RLGEW--DVPKVERVMD-R------IN-GFMIHNNCENKDFGLFD 158 :::::::::::: ::::: :::::::::: : :: ::::::::::::::::: d1vfsa2 109 GRTARIQLXADTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVWSHFACADEPGHPSI 168 query 159 R-MLGEIEERFGALIA--RVD-WVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLE 214 : :::::::::::::: ::: :::::::::: :: :: ::: : :::: d1vfsa2 169 RLQLDAFRDMLAYAEKEGVDPEVRHIANSPAT----LT--LP--ETH--F------DLVR 212 query 215 PGEASITKS-------------TTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAK 261 ::::::::: d1vfsa2 213 TGLAVYGVSPSPELGTPAQLGL-------------------------------------- 234 query 262 VLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMP 321 :: : d1vfsa2 235 ----------------------------------------RP-A---------------- 237 query 322 AIAIRELDGSVRTVREFTYADYEQSLS 348 d1vfsa2 238 --------------------------- 238 HHsearch alignment (Probability: 0.97 E-value:0.00) query 10 DKAKLTRNMERIAHVREKSGAKALLALKCFA----TWSVFDLMRDYM-DGTTSSSLFEVR 64 :::::::::::::::: ::::::::::::: :::::::::::: :::::::::::: d1vfsa2 1 DLDAVRANVRALRARA--PRSALMAVVKSNAYGHGAVPCARAAQEAGAAWLGTATPEEAL 58 query 65 LGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIA----RGLRL 120 ::::::::::::::::::::::::::::::::::::::::::::::::::: ::::: d1vfsa2 59 ELRAAGIQGRIMCWLWTPGGPWREAIETDIDVSVSGMWALDEVRAAARAAGRTARIQLXA 118 query 121 NPQ--RLGEWDVPKVERVM----------DRINGFMIHNNCENKDFGLFDRM----LGEI 164 ::: :::::::::::::: ::::::::::::::::::::::: :::: d1vfsa2 119 DTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVWSHFACADEPGHPSIRLQLDAFRDM 178 query 165 EERFGALIARVDWVSLGG 182 :::::::::::::::::: d1vfsa2 179 LAYAEKEGVDPEVRHIAN 196
Intermediate <-- 1.016 --> HitDALI alignment (Z-score: 7.5 Raw score:919.80) d1vfsa2 1 --------------------------------------------dldAVRANVRALRARA 16 ::::::::::::: d1nfga2 1 ggidvhthvetvsfntqsadtfatatvaaacggtttivdfcqqdrghSLAEAVAKWDGMA 60 d1vfsa2 17 P-----RSALMAVVKSNayGHGAVPCARAAQEAGAAWLGTAT---------peEALELRA 62 : ::::::::::: ::::::::::::::::::::::: ::::::: d1nfga2 61 GgksaiDYGYHIIVLDP--TDSVIEELEVLPDLGITSFXVFMayrgmnmiddvTLLKTLD 118 d1vfsa2 63 A--GIQGRIMCWLW-------------------------------TPGG--PWREAIE-- 85 : ::::::::::: :::: ::::::: d1nfga2 119 KavKTGSLVMVHAEngdaadylrdkfvaegktapiyhalsrpprvEAEAtaRALALAEiv 178 d1vfsa2 86 -TDIDVS-VSGMWALDEVRAAARAAgRTARIQLXADtglgrngCQPA------------- 130 :::::: ::::::::::::::::: :::::::::: :::: d1nfga2 179 nAPIYIVhVTCEESLEEVMRAKSRG-VRALAETCTH-------YLYLtkedlerpdfega 230 d1vfsa2 131 ------------DWAELVGAAVAAQaegtvqVTGVWSHFAcADEPGH------------p 166 ::::::::::::: ::::::::: :::::: d1nfga2 231 kyvftpparakkDHDVLWNALRNGV------FETVSSDHC-SWLFKGhkdrgrndfraip 283 d1vfsa2 167 sirlQLDAFRDMLAY---------aEKEGV--DPEVrhianspatltlpethfdlvrtgl 215 ::::::::::: ::::: :::: d1nfga2 284 ngapGVEERLMMVYQgvnegrisltQFVELvaTRPA------------------------ 319 d1vfsa2 216 avygvspspelgtpaqlglrpa 237 d1nfga2 320 -----------kvfgmfpqkgt 330 FAST alignment (Normalized score: 4.41 Raw score:1233.00) d1vfsa2 1 DLDAVRA--------------------NVRALRARAP-------RSALMAVVKSN--AYG 31 :::::::: :::::: ::: d1nfga2 1 -------GGIDVHTHVETVSFNTQSADTFATATVA--AACGGTTTIVDFC-----QQDRG 46 d1vfsa2 32 HGAVPCARAAQEAGA-----------AWLGTA------TPEEALELRAAGIQGRIMCW-- 72 :::::::::::: ::::: ::::::::::::: ::::: d1nfga2 47 HSLAEAVAKWDG---MAGGKSAIDYGYHIIV-LDPTDSVIEELEVLPDLGI-TSFAV-FM 100 d1vfsa2 73 ------LWTPGGPWREAIE------TDIDVSVS--------------------------- 93 :::: :::::::: ::::::: d1nfga2 101 AYRGMNMIDD-VTLLKTLDKAVKTGSLVMVHA-ENGDAADYLRDKFVAEGKTAPIYHALS 158 d1vfsa2 94 -----GMWALDEVRAAARAAGRTARIQLAADTGLGRNGCQPAD----WAELVGAAVAAQA 144 ::::::::::::::::::::: ::::::::::::: d1nfga2 159 RPPRVEAEATARALALAEIVNAPIYI-----------------VHVTCEESLEEVMRAKS 201 d1vfsa2 145 EGTVQ---VTGVWSHFACADEPGHPS-----------------------------IRLQL 172 :: :::: ::::: d1nfga2 202 RG---VRALAET--------------CTHYLYLTKEDLERPDFEGAKYVFTPPARAKKDH 244 d1vfsa2 173 DAFRDMLAYAEKEGV--DPEVRHIANS---------------------------PATLTL 203 :::::::: ::::: :::: d1nfga2 245 DVLWNALR-------NGVFETV-----SSDHCSWLFKGHKDRGRNDFRAIPNGAPGVE-- 290 d1vfsa2 204 PETHFDLVRTGLAVYGVSPSPELGTPAQLGLRPA-------------------------- 237 d1nfga2 291 ----------------------------------ERLMMVYQGVNEGRISLTQFVELVAT 316 d1vfsa2 238 -------------- 238 d1nfga2 317 RPAKVFGMFPQKGT 330 TMalign alignment (TM-score: 0.56 Raw score:131.67) d1vfsa2 1 ---------DLDAV---------RANVRALRARAP--RS-ALMAVVKSNAYGH--GAVPC 37 : ::::::::::: :: ::::::::::::: ::::: d1nfga2 1 GGIDVHTHV----ETVSFNTQSA-DTFATATVAAACGGTTTIVDFCQQDRGHSLAEAVAK 55 d1vfsa2 38 ARAAQE--A--GAAWLGTATPE---EALELRAA-GIQGRIMCWLW--------TPG-G-P 79 :::::: : ::::::::::: :::::::: ::::::::::: ::: : : d1nfga2 56 WDGMAGGKSAIDYGYHIIVLDPTDSVIEELEVLPDLGITSFAVFMAYRGMNMIDDVTLLK 115 d1vfsa2 80 -WREAIET-DIDVS-V-----------------------------------SGMWALDEV 101 ::::::: ::::: : ::::::::: d1nfga2 116 TLDKAVKTGSLVMVHAENGDAADYLRDKFVAEGKTAPIYHALSRPPRVEAEATARALALA 175 d1vfsa2 102 RAAARAAGRTARIQLAADTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVW-SH--F- 157 :::: ::::::::: :::::::::::::: : :::::::: :: : d1nfga2 176 EIVN-----APIYIVHVT---------CEESLEEVMRAKSR--G-VRALAETCTHYLYLT 218 d1vfsa2 158 A--C---ADEPGHPSIR---LQLDA-FRDMLAYAEKEGVDPEVRHIANSP---------- 198 : : :::::::: ::::: :::::::::::::::::::::::: d1nfga2 219 KEDLERP--DFEGAKYVFTPPARAKKDHDVLWNALRNGVFETVSSDHCSWLFKGHKDRGR 276 d1vfsa2 199 ---------ATLTLPETH--F-----------------DL---------------VRTGL 215 :: :::::: : :: d1nfga2 277 NDFRAIPNGAP-GVEERLMMVYQGVNEGRISLTQFVELVATRPAKVFGMFPQKGT----- 330 d1vfsa2 216 AVYGVSPSPELGTPAQLGLRPA 237 d1nfga2 331 ---------------------- 331 HHsearch alignment (Probability: 0.08 E-value:0.13) d1vfsa2 30 YGHGAVPCARAAQEAGAAWLGT 51 ::::::::: :::::::::::: d1nfga2 78 TDSVIEELE-VLPDLGITSFXV 98