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 | d1twia1 | Diaminopimelate decarboxylase LysA | Alanine racemase C-terminal domain-like | Domain of alpha and beta subunits of F1 ATP synthase-like | All β |
| Hit | d7odca1 | Eukaryotic ornithine decarboxylase (ODC) | Alanine racemase C-terminal domain-like | Domain of alpha and beta subunits of F1 ATP synthase-like | All β |
Query <-- 1.000 --> IntermediateDALI alignment (Z-score: 15.7 Raw score:1022.10) query 1 --------------------------MIETPYYLIdkakltrnmeriahvreksgakall 34 ::::::::: d1twia1 1 mlgndtveikdgrffidgydaielaeKFGTPLYVM------------------------- 35 query 35 alkcfatwsvfdlmrdymdgttssslfevrlgrerfgkethaysvaygdneidevvshad 94 d1twia1 36 ------------------------------------------------------------ 36 query 95 kiifnsisqlerfadkaagiarglrlnpqrlgewdvpkvervmdringfmihnncenkdf 154 d1twia1 36 ------------------------------------------------------------ 36 query 155 glfdrmlgeieerfgaliarvdwvslgggihftgddypvdafsarlrafsdrygvqiyle 214 d1twia1 36 ------------------------------------------------------------ 36 query 215 pgeasitksTTLEVTVLDTLYN--KNLAIVDSSIeAHMLDLLIYRETAKVL---pneGSH 269 ::::::::::::: :::::::::: :::::::::::::::: ::: d1twia1 36 ---------GYLLGKVHHIKETpvTKWVMIDAGM-NDMMRPAMYEAYHHIInckvknEKE 85 query 270 SYMICGKSCLAGDVFGE-FRFAeELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIREL 328 ::::::::::::::::: :::: ::::::::::::::::::::::::::::::::::::: d1twia1 86 VVSIAGGLCESSDVFGRdRELD-KVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSK 144 query 329 DgSVRTVRE-FTYADYeQSLS------- 348 : ::::::: :::::: :::: d1twia1 145 K-GVFLIRErETYADL-IAKDivpphll 170 FAST alignment (Normalized score: 8.50 Raw score:2067.00) query 1 --------------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALL 34 ::::::: d1twia1 1 MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLY--------------------------- 33 query 35 ALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHAD 94 d1twia1 34 ------------------------------------------------------------ 34 query 95 KIIFNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDF 154 d1twia1 34 ------------------------------------------------------------ 34 query 155 GLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLE 214 d1twia1 34 ------------------------------------------------------------ 34 query 215 PGEASITKS--TTLEVTVLDTLY---NKNLAIVDSSIEAHMLDLLIYRETAKVLPNEG-- 267 ::::::::::: :::::::::: ::::::::::::::: d1twia1 34 ---------VMGYLLGKVHHIK-ETPVTKWVMIDAG-MNDMMRPAMYEAYHH------II 76 query 268 -------SHSYMICGKSCLAGDVF-GEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVK 319 ::::::::::::::::: ::::: ::::::::::::::::::::::::::::: d1twia1 77 NCKVKNEKEVVSIAGGLCESSDVFGRDREL-DKVEVGDVLAIFDVGAYGISMANNYNARG 135 query 320 MPAIAIRELDGSVRTV-REFTYADYEQSLS------- 348 ::::::::: :::::: :::::::::::: d1twia1 136 RPRMVLTSK-KGVFLIRERETYADLIAKD-IVPPHLL 170 TMalign alignment (TM-score: 0.35 Raw score:122.00) query 1 --------------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALL 34 ::::::::: d1twia1 1 MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVM------------------------- 35 query 35 ALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHAD 94 d1twia1 36 ------------------------------------------------------------ 36 query 95 KIIFNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDF 154 d1twia1 36 ------------------------------------------------------------ 36 query 155 GLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLE 214 d1twia1 36 ------------------------------------------------------------ 36 query 215 PGEASITKSTTLEVTVLDTLYN--KNLAIVDSSIEAHMLDLLIYRETAKVLP--NE--GS 268 ::::::::::::: :::::::::: ::::::::::::::::: : :: d1twia1 36 ---------GYLLGKVHHIKETPVTKWVMIDAGM-NDMMRPAMYEAYHHIINCK-VKNEK 84 query 269 HSYMICGKSCLAGDVFGE-FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRE 327 :::::::::::::::::: ::::: ::::::::::::::::::::::::::::::::::: d1twia1 85 EVVSIAGGLCESSDVFGRDRELDK-VEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTS 143 query 328 LDGSVRTVREF-TYADYEQSLS------ 348 :: :::::::: :::::::::: d1twia1 144 KK-GVFLIRERETYADLIAKDIVPPHLL 170 HHsearch alignment (Probability: 1.00 E-value:0.00) query 208 GVQIYLEPGEASITKSTTLEVTVLDTLY--NKNLAIVDSSIEAHMLDLLIYRETAKVLP- 264 :::::::::::::: ::::::::::::: :::::::::::: :::::::::::::::: d1twia1 21 AIELAEKFGTPLYV-MGYLLGKVHHIKETPVTKWVMIDAGMN-DMMRPAMYEAYHHIINC 78 query 265 --NEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPA 322 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1twia1 79 KVKNEKEVVSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPR 138 query 323 IAIRELDGSVRTVREFTYADYEQS 346 :::::::::::::::::::::::: d1twia1 139 MVLTSKKGVFLIRERETYADLIAK 162
Intermediate <-- 1.000 --> HitDALI alignment (Z-score: 13.3 Raw score:906.10) d1twia1 1 -mlgndtveikdgrffiDGYD-AIELAEkfGTPLYVMGYLLGKVHHIKETP-VTKWVMID 57 :::: :::::: ::::::::::::::::::::: :::::::: d7odca1 1 ssftkdefdchildegfTAKDiLDQKIN-dKDAFYVAFTLAVNIIAKKTVWeQTFMYYVN 59 d1twia1 58 AGMNDM-MRPAMYEAYHHIINCKVK---NEKEVVSIAGGLCESSDVFGRDRELDKVEVGD 113 :::::: :::::::::::::::::: :::::::::::::::::::::::::::::::: d7odca1 60 DGVYGSfNCILYDHAHVKALLQKRPkpdEKYYSSSIWGPTCDGLDRIVERCNLPEMHVGD 119 d1twia1 114 VLAIFDVGAYGISMANNYNARGRPRMVLTSKKgvflireretyadliakdivpphll 170 :::::::::::::::::::::::::::::::: d7odca1 120 WMLFENMGAYTVAAASTFNGFQRPNIYYVMSR------------------pmwqlmk 158 FAST alignment (Normalized score: 12.05 Raw score:1974.00) d1twia1 1 MLGNDTVEIKDGRFFIDGY-----------------DAIELAEKF----GTPLYVMGYLL 39 :::::::: ::::::::::: d7odca1 1 -------------------SSFTKDEFDCHILDEGFTAKDILDQ-KINDKDAFYVAFTLA 40 d1twia1 40 GKVHHIKET-PVTKWVMIDAGMN-DMMRPAMYEAYHHIINC-KVK--NEKEVVSIAGGLC 94 ::::::::: ::::::::::::: ::::::::::::::::: ::: ::::::::::::: d7odca1 41 VNIIAKKTVWEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDEKYYSSSIWGPTC 100 d1twia1 95 ESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERE 154 ::::::::::::::::::::::::::::::::::::::::::::::::: d7odca1 101 DGLDRIVERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYYVM----------- 149 d1twia1 155 TYADLIAKDIVPPHLL--------- 170 d7odca1 150 ----------------SRPMWQLMK 158 TMalign alignment (TM-score: 0.64 Raw score:109.64) d1twia1 1 ----------------MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMGYLLGKVHH 44 :::::::::::: ::::::::::::::::: d7odca1 1 SSFTKDEFDCHILDEG--------------FTAKDILDQKIN-DKDAFYVAFTLAVNIIA 45 d1twia1 45 IKETP-VTKWVMIDAGMNDM-MRPAMYEAYHHIINCKVKN--E-KEVVSIAGGLCESSDV 99 ::::: :::::::::::::: ::::::::::::::::::: : :::::::::::::::: d7odca1 46 KKTVWEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDEKYYSSSIWGPTCDGLDR 105 d1twia1 100 FGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKK-------GVFLIRE 152 :::::::::::::::::::::::::::::::::::::::::::::: d7odca1 106 IVERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYYVMSRPMWQLMK------- 158 d1twia1 153 RETYADLIAKDIVPPHLL 170 d7odca1 159 ------------------ 159 HHsearch alignment (Probability: 1.00 E-value:0.00) d1twia1 12 GRFFIDGYDAIELAEKFGTPLYVMGYLLGKVHHIKETPVTKWV-MIDAGMNDMMRPAMYE 70 ::::::::::::::::::::::: ::::::::::::::::::: :::::::::::::::: d7odca1 14 DEGFTAKDILDQKINDKDAFYVA-FTLAVNIIAKKTVWEQTFMYYVNDGVYGSFNCILYD 72 d1twia1 71 AYHHIINCKV----KNEKEVVSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGIS 126 :::::::::: :::::::::::::::::::::::::::::::::::::::::::::: d7odca1 73 HAHVKALLQKRPKPDEKYYSSSIWGPTCDGLDRIVERCNLPEMHVGDWMLFENMGAYTVA 132 d1twia1 127 MANNYNARGRPRMVLTSKK 145 ::::::::::::::::::: d7odca1 133 AASTFNGFQRPNIYYVMSR 151