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 | d7odca2 | Eukaryotic ornithine decarboxylase | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1muwa_ | D-xylose isomerase | Xylose isomerase-like | TIM beta/alpha-barrel | α/β |
Query <-- 1.000 --> IntermediateDALI alignment (Z-score: 19.4 Raw score:1731.40) query 1 mietpyyliDKAKLTRNMERIAHVREksGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::::::: :::::::::::::::::::::::::::::::: d7odca2 1 ---------DLGDILKKHLRWLKALP--RVTPFYAVKCNDSRAIVSTLAAIGTGFDCASK 49 query 61 FEVRLGRE-RFGK-ETHAYSVAYGDNEIDEVV-SHADKIIFNSISQLERFADKAAGIARG 117 :::::::: :::: :::::::::::::::::: ::::::::::::::::::::::::::: d7odca2 50 TEIQLVQGlGVPAeRVIYANPCKQVSQIKYAAsNGVQMMTFDSEIELMKVARAHPKAKLV 109 query 118 LRLNPqRLGEW--DVPKVERVMD----RINGFMIHNNCENkdfGLFDrMLGEIEERFGAL 171 ::::: ::::: :::::::::: ::::::::::::: :::: :::::::::::: d7odca2 110 LRIAT-KFGATlkTSRLLLERAKelniDVIGVSFHVGSGC---TDPD-TFVQAVSDARCV 164 query 172 IA-------RVDWVSLGGGIHfTGDDY--PVDAFSARLRAFSDRYG-----VQIYLEPGE 217 :: :::::::::::: ::::: ::::::::::::::::: ::::::::: d7odca2 165 FDmatevgfSMHLLDIGGGFP-GSEDTklKFEEITSVINPALDKYFpsdsgVRIIAEPGR 223 query 218 ASITKSttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgks 277 :::::: d7odca2 224 YYVASA------------------------------------------------------ 229 query 278 clagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvre 337 d7odca2 230 ------------------------------------------------------------ 230 query 338 ftyadyeqsls 348 d7odca2 230 ----------- 230 FAST alignment (Normalized score: 11.24 Raw score:3173.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREK--SGAKALLALKCFATWSVFDLMRDYM--DGTT 56 :::::::::::::: ::::::::::::::::::::::: :::: d7odca2 1 ---------DLGDILKKHLRWLK----ALPRVTPFYAVKCNDSRAIVSTLAA--IGTGFD 45 query 57 SSSLFEVRLGRERFGK------ETHAYSVAYGDNEIDEVVS-HADKIIFNSISQLERFAD 109 :::::::::::: ::::::::::::::::::: :::::::::::::::::: d7odca2 46 CASKTEIQLVQG----LGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVAR 101 query 110 KAAGIARGLRLNPQRLGEWDVPKVERVMD-------RINGFMIHNN--CENKDFGLFDRM 160 :::::::::::: :::: ::::::::::: :::::::: :::::::::::: d7odca2 102 AHPKAKLVLRIA-TKFG-ATLKTSRLLLERAKELNIDVIGVSFH--VGSGCTDPDTFVQA 157 query 161 LGEIEERFGALIA----------RVDWVSLGGGIHFTG------DDYPVDAFSARLRAFS 204 :::::: :::::::::: :::::::::::::::: d7odca2 158 VSDARC-------VFDMATEVGFSMHLLDIGGG-----FPGSEDTKLKFEEITSVINPAL 205 query 205 DR-----YGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRET 259 :: :::::::::::::::: d7odca2 206 DKYFPSDSGVRIIAEPGRYYVAS------------------------------------- 228 query 260 AKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVK 319 d7odca2 229 ------------------------------------------------------------ 229 query 320 MPAIAIRELDGSVRTVREFTYADYEQSLS- 348 d7odca2 229 -----------------------------A 229 TMalign alignment (TM-score: 0.53 Raw score:182.79) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 :::::::::::::::: :: ::::::::::::::::::::::::::::::: d7odca2 1 ---------DLGDILKKHLRWLKAL-PR-VTPFYAVKCNDSRAIVSTLAAIGTGFDCASK 49 query 61 FEVRLGRERFGK--ETHAYSVAYGDNEIDEVVSH-ADKIIFNSISQLERFADKAAGIARG 117 :::::::::::: :::::::::::::::::::: ::::::::::::::::::::::::: d7odca2 50 TEIQLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVARAHPKAKLV 109 query 118 LRLNPQRLGEW--DVPKVERVMD---R-INGFMIHNNCENKDFGLFDRMLGEIEERFGAL 171 ::::: ::::: :::::::::: : ::::::::::::::::::::::::::: :::: d7odca2 110 LRIAT-KFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPDTFVQAVSDARC-VFDM 167 query 172 IA----RVDWVSLGGGIHFTG----DDYP-VDAFSARLRAFSDR-YGVQIYLEPGEASIT 221 :: ::::::::::::::: :::: :::::::::::::: ::::::::::::::: d7odca2 168 ATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYVA 227 query 222 KSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAG 281 :: d7odca2 228 SA---------------------------------------------------------- 229 query 282 DVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYA 341 d7odca2 230 ------------------------------------------------------------ 230 query 342 DYEQSLS 348 d7odca2 230 ------- 230 HHsearch alignment (Probability: 1.00 E-value:0.00) query 10 DKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRER 69 :::::::::::::::: :::::::::::::::::::::::::::::::::::::::::: d7odca2 1 DLGDILKKHLRWLKAL--PRVTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTEIQLVQGL 58 query 70 FGKETHAYSVA--YGDNEIDEVVSHAD-KIIFNSISQLERFADKAAGIARGLRLNPQRLG 126 ::::::::::: :::::::::::::: :::::::::::::::::::::::::::: ::: d7odca2 59 GVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVARAHPKAKLVLRIAT-KFG 117 query 127 EWDVPKVERVMDR------INGFMIHNNCENKDFGLFDRMLGEIEE---RFGALIARVDW 177 ::::::::::::: ::::::::::::::::::::::::::: ::::::::::: d7odca2 118 ATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPDTFVQAVSDARCVFDMATEVGFSMHL 177 query 178 VSLGGGIHFTGDD-YPVDAFSARLRAFSDRY-----GVQIYLEPGEASITKS 223 ::::::::::::: ::::::::::::::::: :::::::::::::::: d7odca2 178 LDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYVASA 229
Intermediate <-- 0.966 --> HitDALI alignment (Z-score: 7.7 Raw score:813.30) d7odca2 1 dlgdilkkhLRWLkalprvTPFYAVKCND----------------SRAIVSTLAAIGT-G 43 :::: :::::::::: ::::::::::::: : d1muwa_ 1 --------sYQPT---pedRFTFGLWTVGwqgrdpfgdatrpaldPVETVQRLAELGAhG 49 d7odca2 44 FDCASkTEIQL-------------vQGLGV---paeRVIYAN------------------ 69 ::::: ::::: ::::: :::::: d1muwa_ 50 VTFHD-DDLIPfgssdtereshikrFRQALdatgmtVPMATTnlfthpvfkdggftandr 108 d7odca2 70 --pckQVSQIKYAASNGV----QMMTF--------------------dSEIELMKVARAH 103 ::::::::::::: ::::: :::::::::::: d1muwa_ 109 dvrryALRKTIRNIDLAVelgaKTYVAwggregaesgaakdvrvaldrMKEAFDLLGEYV 168 d7odca2 104 P----KAKLVLRIA------tKFGAT-LKTSRLLLERAKelniDVIGVSFHVG--sGCTD 150 : ::::::::: ::::: :::::::::::: :::::::::: :::: d1muwa_ 169 TsqgyDIRFAIEPKpneprgdILLPTvGHALAFIERLER---pELYGVNPEVGheqMAGL 225 d7odca2 151 pdTFVQAVSDARCVFdmatevgfsmhLLDIGGGFP------gsedtkLKFEEITSVINPA 204 ::::::::::::: ::::::::: ::::::::::::: d1muwa_ 226 --NFPHGIAQALWAG----------kLFHIDLNGQsgikydqdlrfgAGDLRAAFWLVDL 273 d7odca2 205 LDKYFpsdsgVRIIAEPGRyyVASA----------------------------------- 229 ::::: ::::::::: :::: d1muwa_ 274 LESAG-----YEGPRHFDF--KPPRtedidgvwasaagcmrnylilkeraaafradpevq 326 d7odca2 230 ------------------------------------------------------------ 230 d1muwa_ 327 ealrasrldelaqptaadgvqelladrtafedfdvdaaaargmaferldqlamdhllgar 386 FAST alignment (Normalized score: 3.91 Raw score:1164.00) d7odca2 1 DLGDILKKHLRWLKALPR-------VTPFYAVKCND------------------SRAIVS 35 ::::::::: :::::: d1muwa_ 1 ------------------SYQPTPEDRFTFGLWT--VGWQGRDPFGDATRPALDPVETVQ 40 d7odca2 36 TLAAIGT-GFDCA------------------SKTEIQLVQGLGVPAERVIYANPCK---- 72 ::::::: :::: :::::::::::::: d1muwa_ 41 RLAELGAHGVTF-HDDDLIPFGSSDTERESHIKRFRQALDATGMT-----------VPMA 88 d7odca2 73 -----------------------------QVSQIKYAASNGVQMMTFD------------ 91 :::::::::::::::::: d1muwa_ 89 TTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVA-WGGREGAESGAA 147 d7odca2 92 ------SEIELMKVARAH---------PKAKLVLRIATKFGATLK-------------TS 123 :::::::::: :::::::: :: d1muwa_ 148 KDVRVALDRMKEAFDL--LGEYVTSQGYDIRFAIE----------PKPNEPRGDILLPTV 195 d7odca2 124 RLLLERAKELNIDV-----IGVSFHVGSGCTDPDTFVQAVS---------DARCVFDMAT 169 :::::::::: :::::: :::::::::: d1muwa_ 196 GHALAFIERL----ERPELYGVNPE----------------VGHEQMAGLNFPHGIAQAL 235 d7odca2 170 EVGFSMHLLDIGGGFPGSEDTKLK------------------FEEITSVINPALDKYFPS 211 ::: :::::: :::::::::::::: d1muwa_ 236 WAG-KLFHID--------------LNGQSGIKYDQDLRFGAGDLRAAFWLVDLLES---- 276 d7odca2 212 -DSGVRIIAEPGRYYVASA----------------------------------------- 229 :::::::::: d1muwa_ 277 AGYEGPRHFDF--------KPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEA 328 d7odca2 230 ---------------------------------------------------------- 230 d1muwa_ 329 LRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 386 TMalign alignment (TM-score: 0.63 Raw score:143.40) d7odca2 1 DLGDILKKHLRWLK-ALPRVTPFYAV--KC------------NDS-RAIVSTLAAIGT-G 43 ::::: ::::::::: :: ::: :::::::::::: : d1muwa_ 1 ---------SYQPTP--EDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHG 49 d7odca2 44 FDCASKTEI------------Q-LVQGLGV--PAERVIYANPC----------------- 71 ::::::::: : ::::::: ::::::::::: d1muwa_ 50 VTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRD 109 d7odca2 72 ----K--Q-VSQIKYAASNGVQMMTF-D-------------------SEIELMKVARAHP 104 : : ::::::::::::::::: : ::::::::::::: d1muwa_ 110 VRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVT 169 d7odca2 105 ----KAKLVLRIAT---K--FGATL-KTSRLLLERAKELNIDVIGVSFHVG-SGCTDPDT 153 :::::::::: : ::::: :::::::::: :::::::::::::: :: d1muwa_ 170 SQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERL-ERPELYGVNPEVGHE------QM 222 d7odca2 154 -FVQAVSDARCVFDMATEVGFSMHLLDIGG--------GFPGSEDTKLKFEEITSVINPA 204 ::::::::::::: : :::::::::: ::: ::::::::::: d1muwa_ 223 AGLNFPHGIAQALW--A---GKLFHIDLNGQSGIKYDQDLR--------FGAGDLRAAFW 269 d7odca2 205 LDKYFPSDSGV-R-IIAEPGRYYVASA--------------------------------- 229 ::: ::::::: : ::::::::::::: d1muwa_ 270 LVD-LLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEA 328 d7odca2 230 ---------------------------------------------------------- 230 d1muwa_ 329 LRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 386 HHsearch alignment (Probability: 0.96 E-value:0.00) d7odca2 90 FDSEIELMKVARAHPKAKLVLRIA-TKFGATL----KTSRLLLERAKELNIDVIGVSFHV 144 :::::::::::::::::::::::: ::::::: :::::::::::::::::::::::: d1muwa_ 33 LDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNL 92 d7odca2 145 ---------GSGCTDPDTFVQAVSDARCVFDMATEVGFSMHLLDIGGGFPGSEDTKLKFE 195 :::::::::::::::::::::::::::::: :::::::::::::::::::: d1muwa_ 93 FTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAK-TYVAWGGREGAESGAAKDVR 151 d7odca2 196 EITSVINPALDKYF----PSDSGVRIIAEPG 222 :::::::::::::: ::::::::::::: d1muwa_ 152 VALDRMKEAFDLLGEYVTSQGYDIRFAIEPK 182