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 | d1oyba_ | Old yellow enzyme (OYE) | FMN-linked oxidoreductases | TIM beta/alpha-barrel | α/β |
| Hit | d1m7ja3 | N-acyl-D-aminoacid amidohydrolase, catalytic domain | Metallo-dependent hydrolases | TIM beta/alpha-barrel | α/β |
Query <-- 1.043 --> IntermediateDALI alignment (Z-score: 7.1 Raw score:899.90) query 1 mietpyylidkakltrnmeriahvrEKSG-------------AKALLALKC--------- 38 :::: ::::::::: d1oyba_ 1 -------------sfvkdfkpqalgDTNLfkpikignnellhRAVIPPLTRmralhpgni 47 query 39 ---faTWSVFDLMRDY-mDGTT-SSSL--------------------fevRLGRERFG-- 71 ::::::::::: :::: :::: :::::::: d1oyba_ 48 pnrdwAVEYYTQRAQRpgTMIItEGAFispqaggydnapgvwseeqmvewTKIFNAIHek 107 query 72 -KETHAYSV--------------------------------------------------- 79 :::::::: d1oyba_ 108 kSFVWVQLWvlgwaafpdnlardglrydsasdnvfmdaeqeakakkannpqhsltkdeik 167 query 80 ----AYGDnEIDEVVS-HADKIIFN--------------------------------SIS 102 :::: ::::::: :::::::: ::: d1oyba_ 168 qyikEYVQ-AAKNSIAaGADGVEIHsangyllnqfldphsntrtdeyggsienrarfTLE 226 query 103 QLERFADKAAGIARGLRLNPQ--------------rlgEWDV-PKVERVM---DRINGFM 144 ::::::::::::::::::::: :::: ::::::: ::::::: d1oyba_ 227 VVDALVEAIGHEKVGLRLSPYgvfnsmsggaetgivaqYAYVaGELEKRAkagKRLAFVH 286 query 145 IHN-----NCENKDfgLFDRmlGEIEeRFGALiARVDwVSLGGgIHFTgddypVDAFSAR 199 ::: :::::: :::: :::: ::::: :::: ::::: :::: ::::::: d1oyba_ 287 LVEprvtnPFLTEG-eGEYE-gGSND-FVYSI-WKGP-VIRAG-NFAL-----HPEVVRE 335 query 200 LRAFSdrygVQIYLePGEASI---------------TKSTtlevtvldtlynknlaivds 244 ::::: ::::: :::::: :::: d1oyba_ 336 EVKDK----RTLIG-YGRFFIsnpdlvdrlekglplNKYD-------------------- 370 query 245 sieahmldlliyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDA 304 :: d1oyba_ 371 ----------------------------------------------------------RD 372 query 305 AGYTMvkknwfngvkmpaiaiRELDGSvrtvreftyadyeqsls 348 ::::: :::::: d1oyba_ 373 TFYQM-----sahgyidyptyEEALKL------------gwdkk 399 FAST alignment (Normalized score: 3.40 Raw score:1266.00) query 1 MIETPYYLIDKAK----------------------------------------------- 13 d1oyba_ 1 -------------SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNI 47 query 14 ------------------------------------------LTRNMERIAHVREK---S 28 :::::::::::::: : d1oyba_ 48 PNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEK 107 query 29 GAKALLALKCFA------------------------------------------------ 40 ::::::: d1oyba_ 108 KSFVWVQ-----LWVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLT 162 query 41 ----------TWSVFDLMRD-YMDGTTSS------------------------------- 58 :::::::::: ::::::: d1oyba_ 163 KDEIKQYIKEYVQAAKNSIAAGADGVEI-HSANGYLLNQFLDPHSNTRTDEYGGSIENRA 221 query 59 --SLFEVRLGRERFGK---ETHAYSVAY--------------------GDNEIDEVVS-- 91 :::::::::::: :::::: :::::::::: d1oyba_ 222 RFTLEVVDALVEAI--GHEKVGLRL---SPYGVFNSMSGGAETGIVAQYAYVAGELEKRA 276 query 92 ----HADKIIFNSISQ--------------------LERFADKAAGIARGLRLNPQRLG- 126 :::::::: ::::::: :::::::: d1oyba_ 277 KAGKRLAFVHLV----EPRVTNPFLTEGEGEYEGGSNDFVYSI-WKGPVIRA-------G 324 query 127 --EWDVPKVERVMDRI---NGFMIHNNCENKDFGLF-------DRMLGEIEERFGALIAR 174 :::::::::::: ::::: :::::::: d1oyba_ 325 NFALHPEVVREEVK--DKRTLIGY------------GRFFISNPDLVDRLE--------- 361 query 175 VDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTL 234 d1oyba_ 362 ------------------------------------------------------------ 362 query 235 YNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELK 294 d1oyba_ 362 ------------------------------------------------------------ 362 query 295 VGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------ 348 d1oyba_ 362 ------------------------------------------------------KGLPLN 367 query 349 -------------------------------- 349 d1oyba_ 368 KYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK 399 TMalign alignment (TM-score: 0.37 Raw score:128.19) query 1 -MIETPYYLIDKAKLTRNMERIAHVREKSGAKAL-LALKCFATWSVFDLMRDYMDGTTSS 58 :::::::::::::: :: :: : ::::: :::::::::: d1oyba_ 1 S--FVKDFKPQALGDTN-LF-KP--I---KIGNNE---------------LLHRAVIPPL 36 query 59 ----------------SLFEVRLGRERFGKETHAYSVA----------YGDNEIDEVVSH 92 :::::::::::::::::::::: d1oyba_ 37 TRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDN------------ 84 query 93 ADKIIFNSISQLERFADK-AA-GI--------ARGLRLNPQ--RL--------------- 125 :::::: :::::: :: :: ::::::::: :: d1oyba_ 85 ----APGVWS--EEQMVEWTKIFNAIHEKKSFVWVQLWVLGWAAFPDNLARDGLRYDSAS 138 query 126 ---------------------------GE-WDVPKVERVMDRIN-----GFMIHNNCE-- 150 : :::::::::::::: ::::::::: d1oyba_ 139 DNVFMDAEQEAKAKKANNPQHSLTKDE-IKQYIKEYVQAAKNSIAAGADGVEIHSANGYL 197 query 151 ----NKDFGLF------------DR-MLGEIEERFGALIARVD--WVSLGGGIH------ 185 ::: :: ::::::::::::::::: ::::::::: d1oyba_ 198 LNQF----LDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSM 253 query 186 --------FTGDDYP-VDAFSARLRAFSDRYGVQIYLEPGEASITK--STTLEVTVLDTL 234 :: :::::::::::::::::::::::::: :: d1oyba_ 254 SGGAETGI-----VAQYAYVAGELEKRAKAGKRLAFVHLVEP--RVTN------------ 294 query 235 YNKNLAIVDSSIEAHMLDLLIYRETAK--------------------VLPNEGSHSYMIC 274 ::::: ::::: d1oyba_ 295 ---------------PFLTE--GEGEYEGGSNDFVYSIWKGPVIRAG------------- 324 query 275 GKSCLAGDVFGEFRFAEELKVGDRISFQDAA----------------GYTMVKKN----W 314 ::::: :::::::: d1oyba_ 325 --------------------------NFALHPEVVREEVKDKRTLIGYGRFFISNPDLV- 357 query 315 FNGVKMPAIAIRELDGSVRTVR---------------------E--FTYADYE--QSLS 348 ::::: :::: : ::::::: d1oyba_ 358 --------DRLEK-----GLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK---- 399 HHsearch alignment (Probability: 0.04 E-value:0.05) query 101 ISQLERFADKAAGIARGLRLNPQRL 125 ::::::::::::::::::::::::: d1oyba_ 225 LEVVDALVEAIGHEKVGLRLSPYGV 249
Intermediate <-- 1.181 --> HitDALI alignment (Z-score: 9.3 Raw score:1189.30) d1oyba_ 1 sfvkdfkpqalgdtnlfkpikignnellhraVIPPLTrmralhpgnipnrdWAVEyyTQR 60 :::::: :::: ::: d1m7ja3 1 ----------------------------gfiDSHTHD---------dnyllKHRD--MTP 21 d1oyba_ 61 AQ-RPGTMIITE----GAFIspqaGGYDN---------------apGVWSeeQMVEWTKi 100 :: ::::::::: :::: ::::: :::: ::::::: d1m7ja3 22 KIsQGVTTVVTGncgiSLAP----LAHANppapldlldeggsfrfaRFSD--YLEALRA- 74 d1oyba_ 101 fNAIHekksFVWVQLW--VLGWaafpdnlardglrYDSASdnvfmdaeqeakakkannpq 158 :::: ::::::: :::: ::::: d1m7ja3 75 aPPAV----NAACMVGhsTLRA----------avmPDLRR-------------------- 100 d1oyba_ 159 hSLTKDEIKQYIKEYVQAAKNSiaagadGVEIHSA-NGYLlNQFLdphsntrtdeyggsi 217 ::::::::::::::::::::: ::::::: :::: :::: d1m7ja3 101 -EATADEIQAMQALADDALASG------AIGISTGaFYPP-AAHA--------------- 137 d1oyba_ 218 enRARFTLEVVDaLVEAIGheKVGLRLSPYgvfnsmsGGAEtgIVAQYAYVAGELEKRak 277 :::::::::: :::::: ::::::::: :::: ::::::::::::::: d1m7ja3 138 --STEEIIEVCR-PLITHG--GVYATHMRD-------EGEH--IVQALEETFRIGREL-- 181 d1oyba_ 278 agkRLAFVHLVEPRvtnpfltegegEYEGG------SNDFVYSIW--KGPVIRAGnFALH 329 ::::::::::: ::::: ::::::::: :::::::: :::: d1m7ja3 182 ---DVPVVISHHKV-----------MGKLNfgrskeTLALIEAAMasQDVSLDAY-PYVA 226 d1oyba_ 330 ------------------------------------------------------------ 330 d1m7ja3 227 gstmlkqdrvllagrtlitwckpypelsgrdleeiaaergkskydvvpelqpagaiyfmm 286 d1oyba_ 330 -PEVVREEVKDKRTLIGYGR--------FFISNpdLVDRLEKGlplnkydrdtfyqmsah 380 ::::::::::::::::::: ::::: :::::::: d1m7ja3 287 dEPDVQRILAFGPTMIGSDGlphderphPRLWG--TFPRVLGH-----ysrdlglfplet 339 d1oyba_ 381 gyidyptyeealklgwdkk 399 d1m7ja3 340 avwkmtgltaakfglaerg 358 FAST alignment (Normalized score: 3.51 Raw score:1328.00) d1oyba_ 1 SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQR 60 d1m7ja3 1 ------------------------------------------------------------ 1 d1oyba_ 61 AQ--------------------------RPGTMIITEGAFISPQAGGYDNAPGVWSEEQM 94 ::::: d1m7ja3 1 --GFIDSHTHDDNYLLKHRDMTPKISQGVTTVV--------------------------- 31 d1oyba_ 95 V--------------------------------EWTKIFNAIHE----KKSFVWVQLWVL 118 ::::::::::: :::::::: d1m7ja3 32 -TGNCGISLAPLAHANPPAPLDLLDEGGSFRFARFSDYLEALRAAPPAVNAACMVG---- 86 d1oyba_ 119 GWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNP------------QHSLTKDEI 166 :::: : d1m7ja3 87 ---------------------------------------HSTLRAAVMPDLRREA----T 103 d1oyba_ 167 KQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIEN-----RA 221 ::::::::::::::::::::::::::::: :: d1m7ja3 104 ADEIQAMQALADDALASGAIGISTGAFYP------------------------PAAHAST 139 d1oyba_ 222 RFTLEVVDALVEAIGHE----KVGLRLSPYGVFNSMSGGAETGI----VAQYAYVAGELE 273 ::::::::::: ::::: :::::::::::: d1m7ja3 140 EEIIEVCRPLI------THGGVYATH------------------MRDEGEHIVQALEETF 175 d1oyba_ 274 KRAK-AGKRLAFVHLVEPRVTNPFLTEGEGEYEGG---------------SNDFVYSIWK 317 :::: :::: :::::::: d1m7ja3 176 RIGRELDVP--------------------------VVISHHKVMGKLNFGRSKETLAL-- 207 d1oyba_ 318 ---------GPVIRAGNFA----------------------------------------- 327 ::::: d1m7ja3 208 IEAAMASQDVSLDA-----YPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIA 262 d1oyba_ 328 -----------------------LHPEVVREEVKDKRTLIGYGRFFISN----------- 353 ::::::::::::::::::: d1m7ja3 263 AERGKSKYDVVPELQPAGAIYFMMDEPDVQRILAFGPTMIGS-------DGLPHDERPHP 315 d1oyba_ 354 --PDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK------------ 399 :::::::: d1m7ja3 316 RLWGTFPRVL--------------------------------------GHYSRDLGLFPL 337 d1oyba_ 400 --------------------- 400 d1m7ja3 338 ETAVWKMTGLTAAKFGLAERG 358 TMalign alignment (TM-score: 0.39 Raw score:154.33) d1oyba_ 1 -------------SFVKDFKP--QAL-GDTNLFKPIKIGNNELLHRAVIPPL--TRMRAL 42 :::: ::: : ::: ::::::: :::::: d1m7ja3 1 GFIDSHTHDDNYLLKHR-DMTPK--IS--QGV-------------TTVVTGNCGISLAPL 42 d1oyba_ 43 ------------------HPGNIPNRDWAVEYYTQRAQ-R--PGTMIITEGAF--ISP-- 77 :::::::::::::: : :::::::::: : d1m7ja3 43 AHANPPAPLDLLDEGGSF------RFARFSDYLEALRAAPPA-VNAACMVGHSTL--RAA 93 d1oyba_ 78 -QAGG-YDN-APG-VW-SEE-QMVEWTKIFNAIHEKKSFVWVQLWVLGWAAFPDNLAR-- 129 : ::: :: : ::: ::::::::::::: :::::::: :::: :::: d1m7ja3 94 V---MPDLRR-EAT-ADEIQAMQALADDALASGA-----IGISTGAF--YPPA-AHASTE 140 d1oyba_ 130 --------------------DGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQY 169 :::: :: ::: : d1m7ja3 141 EIIEVCRPLITHGGVYATHM-----RDEG---------------------EH---IVQ-A 170 d1oyba_ 170 IKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVD 229 ::::::::::::: ::::::: : :: ::: : :: ::::::::::: d1m7ja3 171 LEETFRIGRELDV----PVVISHH-----K--VM--GKL-----N-FG-RSKETLALIEA 210 d1oyba_ 230 ALVEAIGHEKVGLRLSPYGVFN-------SM-SG-------------------------- 255 :::::: : :::::::::::: :: :: d1m7ja3 211 AMASQD-V--SLDAYPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIAAERGK 267 d1oyba_ 256 --------------GAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGE 301 ::::::::::::::: :: :: ::::: : ::::: :: d1m7ja3 268 SKYDVVPELQPAGAIYFMMDEPDVQRILA-FG-------PT-MIGSD---G-LPHDE-RP 313 d1oyba_ 302 GEY-EGG--SN-DFVY---SIW---K-GPVIRAGNFALHPEVVREEVKDKRTLI------ 344 ::: ::: :: :::: ::: : :::: ::::: d1m7ja3 314 HPRLWGTFPRVLGHYSRDLGLFPLETAVWKM------------------TGLTAAKFGLA 355 d1oyba_ 345 ---GYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK 399 d1m7ja3 356 ERG------------------------------------------------------- 358 HHsearch alignment (Probability: 0.00 E-value:1.10) d1oyba_ 58 TQRAQRPGTMIITEGAFISPQ 78 ::::::::::::::::::::: d1m7ja3 20 TPKISQGVTTVVTGNCGISLA 40