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 | d1ur3m_ | Hypothetical oxidoreductase YdhF | NAD(P)-linked oxidoreductase | 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 <-- 1.311 --> HitDALI alignment (Z-score: 12.0 Raw score:1209.10) d1tqja_ 1 ------------KNIVVAPSILS---ADFS--RLGEEIKAVDEAGADWIHVDVMdgrfvp 43 ::::::::::: :::: :::::::::::::::::::::: d1ur3m_ 1 lvqritiapqgpEFSRFVMGYWRlmdWNMSarQLVSFIEEHLDLGVTTVDHADI-----y 55 d1tqja_ 44 NITIGPLIVDAIR----PLTK-KTLDVHLMIV-----------------EPEKYVEDFAK 81 ::::::::::::: :::: :::::::::: ::::::::::: d1ur3m_ 56 GGYQCEAAFGEALklapHLRErMEIVSKCGIAttareenvighyitdrdHIIKSAEQSLI 115 d1tqja_ 82 A----GADIISVHVEHNasPHLHRTLCQIRELG-----KKAGAVLnpsTPLDFLEYVL-- 130 : :::::::::::: :::::::::::::: ::::::: :::::::::: d1ur3m_ 116 NlatdHLDLLLIHRPDP-lMDADEVADAFKHLHqsgkvRHFGVSN---FTPAQFALLQsr 171 d1tqja_ 131 --PVCDLILIMSvnpqSFIPEVLP--KIRALRQMCdergldPWIEVDGGL---------- 176 :::::::::: :::::::: ::::::::: ::::::::: d1ur3m_ 172 lpFTLATNQVEI---sPVHQPLLLdgTLDQLQQLR------VRPMAWSCLgggrlfnddy 222 d1tqja_ 177 --------------------KPNNTWQVLEA-GANAIVAGSavFNAPNYAEAIAGvrNSK 215 ::::::::::: ::::::::: :::::::::::: ::: d1ur3m_ 223 fqplrdelavvaeelnagsiEQVVNAWVLRLpSQPLPIIGS--GKIERVRAAVEA--ETL 278 d1tqja_ 216 R------------------ 216 : d1ur3m_ 279 Kmtrqqwfrirkaalgydv 297 FAST alignment (Normalized score: 8.24 Raw score:2088.00) d1tqja_ 1 KNI---------------VVAPSILS-----ADFSRLGEEIKAVDEAGADWIHVDVMDGR 40 :::::::: :::::::::::::::::::::::: d1ur3m_ 1 ---LVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHA----- 52 d1tqja_ 41 FVPNIT---IGPLIVDAIRPLT----------KKTLDVHLMIV----------------- 70 ::::::::::: ::::::: d1ur3m_ 53 ------DIYGGYQCEAAFGE--ALKLAPHLRERMEIVSK----CGIATTAREENVIGHYI 100 d1tqja_ 71 ----EPEKYVEDFAK----AGADIIS-VHVEHNAS---PHLHRTLCQIRELG--KKAGAV 116 ::::::::::: ::::::: :::::: :::::::::::::: ::::: d1ur3m_ 101 TDRDHIIKSAEQSLINLATDHLDLLLIHRPDPL--MDADEVADAFKHLHQSGKVRHFGV- 157 d1tqja_ 117 LNP-STPLDFLEYVLP----VCDLILIMSVNPQS---FIPEVLPKIRALRQMCDERGLDP 168 :::::::::::: :::::::: ::::::: ::::::::: ::: d1ur3m_ 158 ---SNFTPAQFALLQSRLPFTLATNQVE------ISPVHQPLLL--DGTLDQLQQ--LRV 204 d1tqja_ 169 WIEVDGGL-------------------------------KPNNTWQVLEAGA-NAIVAGS 196 ::::::: ::::::::::::: ::::: d1ur3m_ 205 RPMAWSC-LGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVNAWVLRLPSQPLPII-- 261 d1tqja_ 197 AVFNAPN---YAEAIAGVRNSKR------------------------ 216 ::::::::: d1ur3m_ 262 -------GSGKIERVRAAV----EAETLKMTRQQWFRIRKAALGYDV 297 TMalign alignment (TM-score: 0.56 Raw score:119.94) d1tqja_ 1 ---K----------N------------------------------IVVAPSI--L----S 11 : : ::::::: : : d1ur3m_ 1 LVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQC 60 d1tqja_ 12 ADFSRLGEEIKAVDEAG-ADWIHVDV-MDGR------FVPNITI---GP-LIVDA-IR-- 56 ::: :: :::::::::: :::::::: :::: :::::: :: ::::: :: d1ur3m_ 61 EAA-FG-EALKLAPHLRERMEIVSKCGIATTAREENV-IGHYITDRDHIIKSAEQSLINL 117 d1tqja_ 57 PLTKKTLDVHLMIVEPEKY--VEDFAK-AG----A-DIISVHVEHNASPHLHRTLCQIRE 108 ::::::::::::::::::: :::::: :: : ::::::: ::::::::::: : d1ur3m_ 118 ATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNF----TPAQFALLQSR-L 172 d1tqja_ 109 LGKKAGAVLNP--STP-LD---FLEYVLPVCDLILIMSVNPQSFIP-------------- 148 ::::::::::: ::: :: :::::::::::::::::: ::::: d1ur3m_ 173 PFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCL-GGGRLFNDDYFQPLRDELA 231 d1tqja_ 149 ----------EVLPKIRALRQMCDERGLDPWIEVDGGLKPNNTWQVLEAG---------- 188 ::::::::::::: : ::::::::::::::::::::: d1ur3m_ 232 VVAEELNAGSIEQVVNAWVLRLP----S-QPLPIIGSGKIERVRAAVEAETLKMTRQQWF 286 d1tqja_ 189 -----------ANAIVAGSAVFNAPNYAEAIAGVRNSKR 216 d1ur3m_ 287 RIRKAALGYDV---------------------------- 297 HHsearch alignment (Probability: 0.03 E-value:0.03) d1tqja_ 12 ADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITI--GPLIVDA-IRPLTKKTLDVHLM 68 :::::::::::::::::::: ::::: :::: ::::::: :::::::::::::: d1ur3m_ 29 MSARQLVSFIEEHLDLGVTT--VDHAD-----IYGGYQCEAAFGEALKLAPHLRERMEIV 81 d1tqja_ 69 IVE------------------PEKYV----EDFAKAG---ADIISVHVE--HNASPHLHR 101 ::: ::::: ::::::: ::::::::: ::::::::: d1ur3m_ 82 SKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVAD 141 d1tqja_ 102 TLCQIRELGK--KAGAVLNPSTPLDFLEY 128 :::::::::: ::::::::::::::::: d1ur3m_ 142 AFKHLHQSGKVRHFGVSNFTPAQFALLQS 170