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 | d1tqja_ | D-ribulose-5-phosphate 3-epimerase | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1p0ka_ | Isopentenyl-diphosphate delta-isomerase | FMN-linked oxidoreductases | TIM beta/alpha-barrel | α/β |
Query <-- 2.347 --> IntermediateDALI alignment (Z-score: 13.0 Raw score:1145.60) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCF---aTWSVFDLMRD-YMDGTT 56 ::::::::::: :::::::::: :::::: d1tqja_ 1 ---------------------------kNIVVAPSILSAdfsrLGEEIKAVDEaGADWIH 33 query 57 SSS------------LFEVRLGRERFGKETHAYSV--AYGDnEIDEVVS-HADKIIFNS- 100 ::: :::::::::::::::::::: :::: ::::::: ::::::::: d1tqja_ 34 VDVmdgrfvpnitigPLIVDAIRPLTKKTLDVHLMivEPEK-YVEDFAKaGADIISVHVe 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDRINGFMIHN-NCENkdf 154 :::::::::::: ::::::::::: :::::::::::::::::::: :::: d1tqja_ 93 hnaSPHLHRTLCQIRelGKKAGAVLNPS----TPLDFLEYVLPVCDLILIMSvNPQS--- 145 query 155 glFDRMLGEIEeRFGALIA---RVDWVSLGGGIHFtgddypvdaFSARLRAFSdrygvqI 211 ::::::::: ::::::: ::::::::::::: ::::::::: : d1tqja_ 146 -fIPEVLPKIR-ALRQMCDergLDPWIEVDGGLKP--------nNTWQVLEAG-----aN 190 query 212 YLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsy 271 ::::::::::: d1tqja_ 191 AIVAGSAVFNA------------------------------------------------- 201 query 272 micgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgs 331 d1tqja_ 202 ------------------------------------------------------------ 202 query 332 vrtvreftyadyeqsls 348 d1tqja_ 202 --pnyaeaiagvrnskr 216 FAST alignment (Normalized score: 7.32 Raw score:2007.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALK-CFA--TWSVFDLMRD-YMDGT 55 ::::::::: ::: :::::::::: ::::: d1tqja_ 1 ----------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWI 32 query 56 TS------------SSLFEVRLGRERFGKETHAYSVAY----GDNEIDEVVS-HADKIIF 98 :: ::::::::::::::::::::: :::::::::: ::::::: d1tqja_ 33 HVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHL---MIVEPEKYVEDFAKAGADIISV 89 query 99 N--SISQ---LERFADKA---AGIARGLRLNPQRLGE-WDVPKVERVMDRINGFMIHNNC 149 :::: ::::::: ::::::::::: :::::::::::::::::::: d1tqja_ 90 -HVEHNASPHLHRTLCQ-IRELGKKAGAVLNP-----STPLDFLEYVLPVCDLILIMS-- 140 query 150 ENKD------FGLFDRMLGEIEERFGALIARV----DWVSLGGGIHFTGDDYPVDA---F 196 ::::::::::::::::: ::::::::: : d1tqja_ 141 ----VNPQSFIPEVLPKIRALRQMCDE-----RGLDPWIEVDGGL-----------KPNN 180 query 197 SARLRAFSDRYGVQ---IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::: ::::::::: d1tqja_ 181 TWQVLE--------AGANAIVAGSAV---------------------------------- 198 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 d1tqja_ 199 ------------------------------------------------------------ 199 query 314 WFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------------------ 348 d1tqja_ 199 -----------------------------------FNAPNYAEAIAGVRNSKR 216 TMalign alignment (TM-score: 0.43 Raw score:149.23) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF-A--TWSVFDLMRD-YMDGTT 56 :::::::::::: : :::::::::: :::::: d1tqja_ 1 ---------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWIH 33 query 57 S-S-----------SLFEVRLGRERFGKETHAYSVA--YGDNEIDEVVS-HADKIIFNS- 100 : : :::::::::::::::::::::: ::: ::::::: ::::::::: d1tqja_ 34 VDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPEK-YVEDFAKAGADIISVHVE 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNN--CENKD 153 :::::::::::: ::::::::::: :::: ::::::::::::::::: ::: d1tqja_ 93 HNASPHLHRTLCQIRELGKKAGAVLNPS---TPLD-FLEYVLPVCDLILIMSVNPQSF-- 146 query 154 FGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQ 210 : ::::::::::::::: ::::::::::::: ::: :: :: ::: : d1tqja_ 147 ---I-PEVLPKIRALRQMCDERGLDPWIEVDGGLKP----NNT--WQ-VL-EAG-----A 189 query 211 IYLEPGEASITKST-------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYR 257 :::::::::::::: d1tqja_ 190 NAIVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 query 258 ETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNG 317 d1tqja_ 217 ------------------------------------------------------------ 217 query 318 VKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1tqja_ 217 ------------------------------- 217 HHsearch alignment (Probability: 0.21 E-value:0.01) query 75 HAYSVAYGDNEIDEVVSHADKIIFN--SISQLERFADKAAG--IARGLRLNPQRLGEWDV 130 ::::::::::::::::::::::::: :::::::::::::: :::::::::: ::: d1tqja_ 68 MIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPS----TPL 123 query 131 PKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDW-VSLG 181 ::::::::::::::::::::::::::::::::::::::::::::::: :::: d1tqja_ 124 DFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175
Intermediate <-- 2.185 --> HitDALI alignment (Z-score: 13.7 Raw score:1368.80) d1tqja_ 1 ---------------------------------kNIVVAPSIL----saDFSRL-GEEIK 22 ::::::::: ::::: ::::: d1p0ka_ 1 retgldditfvhvslpdlaleqvdistkigelssSSPIFINAMtggggkLTYEInKSLAR 60 d1tqja_ 23 AVDEaGADWIHVDVMdgrfvpnITIG-----PLIVDAIRPLT-KKTLDVHLmIVEPEK-Y 75 :::: :::::::::: :::: ::::::::::: :::::::: :::::: : d1p0ka_ 61 AASQ-AGIPLAVGSQ-------MSALkdpseRLSYEIVRKENpNGLIFANL-GSEATAaQ 111 d1tqja_ 76 VEDFAKA-GADIISVHVEH-----naSPHL-HRTLCQIrelGKKAGAVLNPSTPL-DFLE 127 ::::::: ::::::::::: :::: ::::::: :::::::::::::: :::: d1p0ka_ 112 AKEAVEMiGANALQIHLNViqeifsgALKRiEQICSRV---SVPVIVKEVGFGMSkASAG 168 d1tqja_ 128 YVLP-VCDLILIMS---vnpqsfipEVLPKIRALRQMCDerglDPWIEVDGGLKPNN-TW 182 :::: ::::::::: :::::::::::::: :::::::::::::: :: d1p0ka_ 169 KLYEaGAAAVDIGGrqisffnswgiSTAASLAEIRSEFP----ASTMIASGGLQDALdVA 224 d1tqja_ 183 QVLEAGANAIVAGSAVFNA------PNYAEAIAGVR-NSKR------------------- 216 ::::::::::::::::::: ::::::::::: :::: d1p0ka_ 225 KAIALGASCTGMAGHFLKAltdsgeEGLLEEIQLILeELKLimtvlgartiadlqkaplv 284 d1tqja_ 217 ---------------------- 217 d1p0ka_ 285 ikgethhwltergvntssysvr 306 FAST alignment (Normalized score: 10.44 Raw score:2683.00) d1tqja_ 1 KNI------------------------------------VVAPSIL--SADF-SRLGEEI 21 ::::: :::: ::::::: d1p0ka_ 1 ---RETGLDDITFVHVSLPDLALEQVDISTKIGELSSSSPIFIN--AMTGGGGKLTYEIN 55 d1tqja_ 22 KAVDEAGA------DWIHVDVMDGRFVPNITI-----------GPLIVDAIRPL-TKKTL 63 ::::: ::::: ::::::::::: ::::: d1p0ka_ 56 KSLAR---AASQAGIPLAV-------------GSQMSALKDPSERLSYEIVRKENPNGLI 99 d1tqja_ 64 DVHLMIVE----PEKYVEDFAK-AGADIISVHVEHN----ASPHLHRTLCQIR-ELGKKA 113 :::: :::::::::: ::::::::::: ::::::::::::: :::::: d1p0ka_ 100 FANL----GSEATAAQAKEAVEMIGANALQIHLN--VIQEIFSGALKRIEQICSRVSVPV 153 d1tqja_ 114 GAVLNP-STPLDFLEYVLP-VCDLILIMSVNPQSFIP------------EVLPKIRALRQ 159 :::::: :::::::::::: :::::::: ::::::::::: d1p0ka_ 154 IVKEVGFGMSKASAGKLYEAGAAAVDIG---------GRQISFFNSWGISTAASLAEIRS 204 d1tqja_ 160 MCDERG-LDPWIEVDGGL-KPNNTWQVLEAGANAIVAGSAVFNAP---------NYAEAI 208 : ::::::::::: ::::::::::::::::::::::: :::::: d1p0ka_ 205 E-----FPASTMIASGGLQDALDVAKAIALGASCTGMAGHFL---KALTDSGEEGLLEEI 256 d1tqja_ 209 AGVRNSKR---------------------------------------------- 216 :::: d1p0ka_ 257 QLIL----EELKLIMTVLGARTIADLQKAPLVIKGETHHWLTERGVNTSSYSVR 306 TMalign alignment (TM-score: 0.73 Raw score:158.08) d1tqja_ 1 -------------------------KN--------IVVAPSILSA----DF-SRLGEEIK 22 :: :::::::::: :: :::::::: d1p0ka_ 1 RETGLDDITFVHVSLPDLALEQVDISTKIGELSSSSPIFINAMTGGGGKLTYEINKSLAR 60 d1tqja_ 23 AVDEAGADWIHVDVMDGRFVPNITIGP-----L-IVDAIRPLT-KKTLDVHLMIVEPE-K 74 ::::::: :::::::: ::: : ::::::::: :::::::: ::::: : d1p0ka_ 61 AASQAGI-PLAVGSQM--------SALKDPSERLSYEIVRKENPNGLIFANL-GSEATAA 110 d1tqja_ 75 YVEDFAKA-GADIISVHVEH--N-ASPHLHRTLCQIRELGKKAGAVLNPSTPL-DFLEYV 129 :::::::: ::::::::::: : ::::::::::::::::::::::::::::: :::::: d1p0ka_ 111 QAKEAVEMIGANALQIHLNVIQEIFSGALKRIEQICSRVSVPVIVKEVGFGMSKASAGKL 170 d1tqja_ 130 LP-VCDLILIMS---------VNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGGL-KP 178 :: ::::::::: :::::::::::::::: ::: ::::::: :: d1p0ka_ 171 YEAGAAAVDIGGRQISFFNSW------GISTAASLAEIRSEFP---AST-MIASGGLQDA 220 d1tqja_ 179 NNTWQVLEAGANAIVAGSAVF-NA------P--NYAEAIAGVRNSK---R---------- 216 ::::::::::::::::::::: :: : ::::::::::::: : d1p0ka_ 221 LDVAKAIALGASCTGMAGHFLKALTDSGEEGLLEEIQLILEELKLIMTVLGARTIADLQK 280 d1tqja_ 217 -------------------------- 217 d1p0ka_ 281 APLVIKGETHHWLTERGVNTSSYSVR 306 HHsearch alignment (Probability: 0.94 E-value:0.00) d1tqja_ 63 LDVHLMIVEPEKYVEDF-AKAGADIISVHVEHNA--SPHLHRTLCQIRELGKKAGA---V 116 ::::::::::::::::: :::::::::::::::: :::::::::::::::::::: : d1p0ka_ 99 IFANLGSEATAAQAKEAVEMIGANALQIHLNVIQEIFSGALKRIEQICSRVSVPVIVKEV 158 d1tqja_ 117 LNPSTPLDFLEYVLPVCDLILIMSVNPQSFIP---EVLPKIRALRQMCDERGLDPWIEVD 173 :::::::::::::::::::::::::::::::: ::::::::::::: :::::::: d1p0ka_ 159 GFGMSKASAGKLYEAGAAAVDIGGRQISFFNSWGISTAASLAEIRSEF----PASTMIAS 214 d1tqja_ 174 GGL-KPNNTWQVLEAGANAIVAGSAVFN------APNYAEAIAGVR 212 ::: :::::::::::::::::::::::: :::::::::::: d1p0ka_ 215 GGLQDALDVAKAIALGASCTGMAGHFLKALTDSGEEGLLEEIQLIL 260