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 | d1luca_ | Bacterial luciferase alpha chain, LuxA | Bacterial luciferase-like | 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 <-- 1.347 --> HitDALI alignment (Z-score: 12.2 Raw score:1266.80) d1tqja_ 1 knIVVAPSILS---------aDFSRLGEEIKAVDEAGADWIHVDVMDGRfvPNITIG-PL 50 ::::::::: :::::::::::::::::::::::::::: :::::: :: d1luca_ 1 --MKFGNFLLTyqppelsqteVMKRLVNLGKASEGCGFDTVWLLEHHFT-eFGLLGNpYV 57 d1tqja_ 51 IVDAIRPLT-KKTLDV-HLMIVEPEK--YVEDFAKAG-----aDIISVHVEH-------- 93 ::::::::: :::::: ::::::::: ::::::::: ::::::::: d1luca_ 58 AAAHLLGATeTLNVGTaAIVLPTAHPvrQAEDVNLLDqmskgrFRFGICRGLydkdfrvf 117 d1tqja_ 94 -----nASPHLHRTLCQIRE----------------------------LGKKAGAVLnps 120 :::::::::::::: ::::::::: d1luca_ 118 gtdmdnSRALMDCWYDLMKEgfnegyiaadnehikfpkiqlnpsaytqGGAPVYVVA--- 174 d1tqja_ 121 TPLDFLEYVLPVCDLILIMSVnpqsfipEVLPKIRALRQMCDE------RGLD-PWIEVD 173 ::::::::::::::::::::: ::::::::::::::: :::: :::::: d1luca_ 175 ESASTTEWAAERGLPMILSWI-------INTHEKKAQLDLYNEvatehgYDVTkIDHCLS 227 d1tqja_ 174 GGL-----------------------------------------------KPNNTWQVLE 186 ::: :::::::::: d1luca_ 228 YITsvdhdsnrakdicrnflghwydsyvnatkifridysyeinpvgtpeeCIAIIQQDID 287 d1tqja_ 187 AG-ANAIVAGSA-----vfNAPNYAEAIA-GVRNSK--r 216 :: ::::::::: :::::::::: :::::: d1luca_ 288 ATgIDNICCGFEangseeeIIASMKLFQSdVMPYLKekq 326 FAST alignment (Normalized score: 8.23 Raw score:2185.00) d1tqja_ 1 KNIVVAPSILSA-------------DFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITI 47 :::::: ::::::::::::::::::::::::: d1luca_ 1 --MKFGNF----LLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEH---------- 44 d1tqja_ 48 ----------GPLIVDAIRPLT-KKTLDVHLMIV-----------EPEKYVEDFAKAGA- 84 :::::::::::: :::::: ::::::::::: d1luca_ 45 HFTEFGLLGNPYVAAAHLLGATETLNVGT-----AAIVLPTAHPVRQAEDVNLLDQ---M 96 d1tqja_ 85 ----DIISVHVEH----------------NASPHLHRTLCQIREL--------------- 109 :::::: ::::::::::::::: d1luca_ 97 SKGRFRFGIC---RGLYDKDFRVFGTDMDNSRALMDCWYDLMKE-GFNEGYIAADNEHIK 152 d1tqja_ 110 --------------GKKAGAVLNPSTPLDFLEYVLPV-CDLILIMSVNPQSFIPE---VL 151 :::::::: ::::::::::: ::::::: :: d1luca_ 153 FPKIQLNPSAYTQGGAPVYVVA---ESASTTEWAAE-RGLPMILS----------WIINT 198 d1tqja_ 152 PKIRALRQMCDERG---------LDPWIEVDGGL-------------------------- 176 :::::::::::: ::::::::::: d1luca_ 199 HEKKAQLDLYNE--VATEHGYDVTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVN 256 d1tqja_ 177 ---------------------KPNNTWQVLE-AGANAIVAGSA-VFNA---PNYAEAIAG 210 :::::::::: :::::::: :::: ::::::::: d1luca_ 257 ATKIFRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICC---GFEANGSEEEIIASMKL 313 d1tqja_ 211 VRNSKR----------- 216 :: d1luca_ 314 FQ----SDVMPYLKEKQ 326 TMalign alignment (TM-score: 0.73 Raw score:157.01) d1tqja_ 1 KNIVVAPSILSA---------DFSRLGEEIKAVDEAGADWIHVDVMDGR-FVPNITIG-P 49 :::::::::: :::::::::::::::::::::::::::: :::::: : d1luca_ 1 --MKFGNFLLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEHHFTE--FGLLGNPY 56 d1tqja_ 50 LIVDAIRPLT-KKTLDVHLMIVE-P-E-KYVEDFAKA---G--ADIISVHV--------- 91 :::::::::: :::::::::::: : : ::::::::: : :::::::: d1luca_ 57 VAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFRFGICRGLYDKDFRV 116 d1tqja_ 92 -------EHNASPHLHRTLCQIRE---------------------L-G---KKAGAVLNP 119 ::::::::::::::::: : : :::::::: d1luca_ 117 FGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNPSAYTQGGAPVYVVAE- 175 d1tqja_ 120 STP-LDFLEYVLPVCDLILIMSVNPQSFIP--EVLPKIRALRQMCDE-RGL--DPWIEVD 173 ::: :::::::: : :::::: ::: ::::::::::::::: ::: ::::::: d1luca_ 176 SASTTEWAAERG--L--PMILSW----IINTHEKKAQLDLYNEVATEHGYDVTKIDHCLS 227 d1tqja_ 174 GG----------------------------------------LK------PN-NTWQVLE 186 :: :: :: ::::::: d1luca_ 228 YITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFRIDYSYEINPVGTPEECIAIIQQDID 287 d1tqja_ 187 -AGANAIVAGSAVF-----NAPNYAEAIA-GVRNSK---R 216 ::::::::::::: :::::::::: :::::: d1luca_ 288 ATGIDNICCGFEANGSEEEIIASMKLFQSDVMPYLKEKQ- 326 HHsearch alignment (Probability: 0.02 E-value:0.06) d1tqja_ 180 NTWQVLE-AGANAIVAG 195 ::::::: ::::::::: d1luca_ 281 IIQQDIDATGIDNICCG 297