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 | d1knwa1 | Diaminopimelate decarboxylase LysA | 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: 21.2 Raw score:1483.30) d1twia1 1 mlgNDTVEIKdgrffIDGYDAIELAEKFGTPLYVMgYLLGKVHHIKETPVTKWVMIDAGM 60 ::::::: :::::::::::::::::::: :::::::::::::::::::::::: d1knwa1 1 ---PHSLFST--dtdLTAENLLRLPAEFGCPVWVY-VLITQVRSVKQMGSRHFVLVDAGF 54 d1twia1 61 NDMMRPAMYEAYHHIINCK-----VKNE-KEVVSIAGGLCESSDVFG-------RDRELD 107 ::::::::::::::::::: :::: :::::::::::::::::: :::::: d1knwa1 55 NDLMRPAMYGSYHHISALAadgrsLEHApTVETVVAGPLCESGDVFTqqeggnvETRALP 114 d1twia1 108 KVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIVPp 167 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa1 115 EVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELLH- 173 d1twia1 168 hll 170 d1knwa1 174 --h 174 FAST alignment (Normalized score: 18.25 Raw score:3139.00) d1twia1 1 MLGN--------DTVEIKDGRFFIDGY--DAIELAEKFGTPLYVMGYLLGKVHHIKETPV 50 :::: ::::::::::::::: ::::::::::::::: d1knwa1 1 ----PHSLFSTDTDLT-----------AENLLRLPAEFGCPVWV-YVLITQVRSVKQMGS 44 d1twia1 51 TKWVMIDAGMNDMMRPAMYEAYHHIINCKVK----------NEKEVVSIAGGLCESSDVF 100 ::::::::::::::::::::::::::: ::::::::::::::::::: d1knwa1 45 RHFVLVDAGFNDLMRPAMYGSYHHISA----LAADGRSLEHAPTVETVVAGPLCESGDVF 100 d1twia1 101 G--------RDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRE 152 ::::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa1 101 -TQQEGGNVETRALPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRR 159 d1twia1 153 RETYADLIAKDIVPPHLL--- 170 :::::::::::: d1knwa1 160 RQTIEELLALEL------LHH 174 TMalign alignment (TM-score: 0.84 Raw score:143.54) d1twia1 1 MLGNDTVEIKD--GRFFIDGYDAIELAEKFGTPLYVMGYLLGKVHHIKETPVTKWVMIDA 58 : : ::::: ::::::::::::::::::::: :::::::::::::::::::::: d1knwa1 1 P--H--SLFSTDT---DLTAENLLRLPAEFGCPVWVY-VLITQVRSVKQMGSRHFVLVDA 52 d1twia1 59 GMNDMMRPAMYEAYHHIINCK----VK--NEKEVVSIAGGLCESSDVFG-------RDRE 105 ::::::::::::::::::::: :: :::::::::::::::::::: :::: d1knwa1 53 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA 112 d1twia1 106 LDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIV 165 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa1 113 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 172 d1twia1 166 PPHLL 170 : : d1knwa1 173 H---H 174 HHsearch alignment (Probability: 1.00 E-value:0.00) d1twia1 19 YDAIELAEKFGTPLYVMGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINC 78 :::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::: d1knwa1 14 ENLLRLPAEFGCPVWV-YVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHISAL 72 d1twia1 79 KV------KNEKEVVSIAGGLCESSDVFGRD-------RELDKVEVGDVLAIFDVGAYGI 125 :: ::::::::::::::::::::::: :::::::::::::::::::::: d1knwa1 73 AADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLHDTGAYGA 132 d1twia1 126 SMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIV 165 :::::::::::::::::::::::::::::::::::::::: d1knwa1 133 SMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 172