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 | d1knwa1 | Diaminopimelate decarboxylase LysA | Alanine racemase C-terminal domain-like | Domain of alpha and beta subunits of F1 ATP synthase-like | All β |
| Hit | d1fdra1 | Ferredoxin reductase (flavodoxin reductase) N-terminal domain | Riboflavin synthase domain-like | Reductase/isomerase/elongation factor common domain | All β |
Query <-- 1.321 --> IntermediateDALI alignment (Z-score: 15.0 Raw score:988.00) query 1 ---------------------MIETPYYLIdkakltrnmeriahvreksgakallalkcf 39 ::::::::: d1knwa1 1 phslfstdtdltaenllrlpaEFGCPVWVY------------------------------ 30 query 40 atwsvfdlmrdymdgttssslfevrlgrerfgkethaysvaygdneidevvshadkiifn 99 d1knwa1 31 ------------------------------------------------------------ 31 query 100 sisqlerfadkaagiarglrlnpqrlgewdvpkvervmdringfmihnncenkdfglfdr 159 d1knwa1 31 ------------------------------------------------------------ 31 query 160 mlgeieerfgaliarvdwvslgggihftgddypvdafsarlrafsdrygvqiylepgeas 219 d1knwa1 31 ------------------------------------------------------------ 31 query 220 itkstTLEVTVLDTLYN--KNLAIVDSSIeAHMLDLLIYRETAKVL---------pneGS 268 :::::::::::: :::::::::: :::::::::::::::: :: d1knwa1 31 -----VLITQVRSVKQMgsRHFVLVDAGF-NDLMRPAMYGSYHHISalaadgrslehaPT 84 query 269 HSYMICGKSCLAGDVFG--------EFRFaEELKVGDRISFQDAAGYTMVKKNWFNGVKM 320 ::::::::::::::::: :::: :::::::::::::::::::::::::::::: d1knwa1 85 VETVVAGPLCESGDVFTqqeggnveTRAL-PEVKAGDYLVLHDTGAYGASMSSNYNSRPL 143 query 321 PAIAIRELdGSVRTVREFTYadYEQSLS------ 348 :::::::: ::::::::::: :::::: d1knwa1 144 LPEVLFDN-GQARLIRRRQT--IEELLAlellhh 174 FAST alignment (Normalized score: 8.04 Raw score:1978.00) query 1 ---------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF 39 ::::::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVW-------------------------------- 28 query 40 ATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFN 99 d1knwa1 29 ------------------------------------------------------------ 29 query 100 SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDR 159 d1knwa1 29 ------------------------------------------------------------ 29 query 160 MLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 d1knwa1 29 ------------------------------------------------------------ 29 query 220 ITKS-TTLEVTVLDTLYN----KNLAIVDSSIEAHMLDLLIYRETAKVLPNEG------- 267 ::::::::::: ::::::::: :::::::::::::::: d1knwa1 29 ----VYVLITQVRSVK--QMGSRHFVLVDAG-FNDLMRPAMYGSYHHI-----SALAADG 76 query 268 -------SHSYMICGKSCLAGDV--------FGEFRFAEELKVGDRISFQDAAGYTMVKK 312 :::::::::::::::: :::::: :::::::::::::::::::::: d1knwa1 77 RSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRAL-PEVKAGDYLVLHDTGAYGASMS 135 query 313 NWFNGVKMPAIAIRELDGSVRTV-REFTYADYEQSLS----- 348 ::::::::::::::: ::::::: ::::::::::: d1knwa1 136 SNYNSRPLLPEVLFD-NGQARLIRRRQTIEELLAL--ELLHH 174 TMalign alignment (TM-score: 0.35 Raw score:120.59) query 1 ---------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF 39 ::::::::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVY------------------------------ 30 query 40 ATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFN 99 d1knwa1 31 ------------------------------------------------------------ 31 query 100 SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDR 159 d1knwa1 31 ------------------------------------------------------------ 31 query 160 MLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 d1knwa1 31 ------------------------------------------------------------ 31 query 220 ITKSTTLEVTVLDTLYN--KNLAIVDSSIEAHMLDLLIYRETAKVLP--------NE-GS 268 :::::::::::: :::::::::: ::::::::::::::::: :: :: d1knwa1 31 -----VLITQVRSVKQMGSRHFVLVDAGF-NDLMRPAMYGSYHHISALAADGRSLEHAPT 84 query 269 HSYMICGKSCLAGDVFG--------EFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKM 320 ::::::::::::::::: ::::: ::::::::::::::::::::::::::::: d1knwa1 85 VETVVAGPLCESGDVFTQQEGGNVETRALP-EVKAGDYLVLHDTGAYGASMSSNYNSRPL 143 query 321 PAIAIRELDGSVRTVRE-FTYADYEQSLS--- 348 :::::::: :::::::: ::::::::::: d1knwa1 144 LPEVLFDN-GQARLIRRRQTIEELLALELLHH 174 HHsearch alignment (Probability: 1.00 E-value:0.00) query 193 VDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLD 252 ::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYVLITQVRSVKQMGSRHFVLVDAGFN-DLMR 59 query 253 LLIYRETAKVLP---------NEGSHSYMICGKSCLAGDVFGEF-------RFAEELKVG 296 :::::::::::: ::::::::::::::::::::::: ::::::::: d1knwa1 60 PAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAG 119 query 297 DRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 :::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa1 120 DYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLAL 169
Intermediate <-- 0.926 --> HitDALI alignment (Z-score: 2.0 Raw score:215.30) d1knwa1 1 phslfstdtdltaenllrlpaefgcpvwVYVLITQVRSVKQMGS-RHFVLVDAgfnDLMR 59 :::::::::::::::: :::::::: :::: d1fdra1 1 ----------------------------ADWVTGKVTKVQNWTDaLFSLTVHA--pVLPF 30 d1knwa1 60 paMYGSYHHISAlaadgrslehaptvetvvagplcesgdvFTQQ----------eggnve 109 :::::::::: :::: d1fdra1 31 --TAGQFTKLGL-------------------eirvqraysYVNSpdnpdlefylvtvpdg 69 d1knwa1 110 tRALP--EVKAGDYLVLHDTgaygasmssnynsrpllpevlfdngqarlirrrqtieell 167 :::: ::::::::::::: d1fdra1 70 kLSPRlaALKPGDEVQVVSE---------------------------------------- 89 d1knwa1 168 alellhh 174 d1fdra1 90 aagffvl 96 FAST alignment (Normalized score: 2.17 Raw score:279.90) d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWV-YVLITQVRSVKQM-GSRHFVLVDAGFNDLM 58 ::::::::::::: ::::::::: d1fdra1 1 -----------------------------ADWVTGKVTKVQNWTDALFSLTVH------- 24 d1knwa1 59 RP-----AMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRAL 113 ::::::::::: d1fdra1 25 --APVLPFTAGQFTKLGL------------------------------------------ 40 d1knwa1 114 -----------------------------------PEVKAGDYLVLHDTGAYGASMSSNY 138 :::::::::: d1fdra1 41 EIRVQRAYSYVNSPDNPDLEFYLVTVPDGKLSPRLAALKPGDEVQ--------------- 85 d1knwa1 139 NSRPLLPEVLFDNGQARLIRRRQTIEELLALELLHH----------- 174 d1fdra1 86 ------------------------------------VVSEAAGFFVL 96 TMalign alignment (TM-score: 0.30 Raw score:52.63) d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYVLITQVRSVKQMG-SRHFVLVDAGFNDLMR 59 : :::::::::::::: :::::::::: :::: d1fdra1 1 A----------------------------DWVTGKVTKVQNWTDALFSLTVHAP--VLPF 30 d1knwa1 60 PAMYGSYHHISALAADGRSLE-----HAPTVETVVAGPLCESG--D--VFTQQEGGNVET 110 :::::::::: :: :::: :: : ::: :: d1fdra1 31 --TAGQFTKLGL-------EIRVQRA------YSYV-----NSPDNPDLEF-------YL 63 d1knwa1 111 R------AL-P--EVKAGDYLVLHDTGAY------GASMSSNYNSRPLLPEVLFDNGQAR 155 : :: : ::::::::::: : :: d1fdra1 64 VTVPDGKLSPRLAALKPGDEVQVV-S-EAAGFFVL------------------------- 96 d1knwa1 156 LIRRRQTIEELLALELLHH 174 d1fdra1 97 ------------------- 97 HHsearch alignment (Probability: 0.02 E-value:0.59) d1knwa1 29 VYVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETV 88 ::::::::::::::::::::::::::: :::::::::::::: :::::::: d1fdra1 1 ADWVTGKVTKVQNWTDALFSLTVHAPV-----LPFTAGQFTKLGLE------IRVQRAYS 49 d1knwa1 89 VAGPLCE-SGDVFTQQ-EGGNVETRALPEVKAGDYLVLHD 126 ::::::: :::::::: :::::: :::::::::::::::: d1fdra1 50 YVNSPDNPDLEFYLVTVPDGKLS-PRLAALKPGDEVQVVS 88