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 | d1a8pa1 | 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 <-- 1.223 --> HitDALI alignment (Z-score: 2.5 Raw score:232.90) d1knwa1 1 phslfstdtdltaenllrlpaefgcpvwVYVLITQVRSVKQMG-SRHFVLVDAGfNDLMR 59 ::::::::::::::: :::::::::: ::::: d1a8pa1 1 ----------------------------SNLNVERVLSVHHWNdTLFSFKTTRN-PSLRF 31 d1knwa1 60 paMYGSYHHISAlaadgrsLEHAptvetvvagplcesgdvFTQQ-----------eggnv 108 :::::::::: :::: :::: d1a8pa1 32 --ENGQFVMIGL-------EVDG---------rplmraysIASPnyeehleffsikvqng 73 d1knwa1 109 etrALPE-VKAGDYLVLHDTgaygasmssnynsrpllpevlfdngqarlirrrqtieell 167 :::: :::::::::::: d1a8pa1 74 pltSRLQhLKEGDELMVSRK---------------------------------------- 93 d1knwa1 168 alellhh 174 d1a8pa1 94 -ptgtlv 99 FAST alignment (Normalized score: 2.55 Raw score:335.00) d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWV-YVLITQVRSVKQM-GSRHFVLVDAGFNDLM 58 ::::::::::::: :::::::: :::::: d1a8pa1 1 -----------------------------SNLNVERVLSVHHWNDTLFSFKT-TRNPSL- 29 d1knwa1 59 RP-AMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA----- 112 ::::::::::: d1a8pa1 30 --RFENGQFVMIGL-----------------------------------------EVDGR 46 d1knwa1 113 --------------------------------LPEVKAGDYLVLHDTGAYGASMSSNYNS 140 :::::::::::: d1a8pa1 47 PLMRAYSIASPNYEEHLEFFSIKVQNGPLTSRLQHLKEGDELMV---------------- 90 d1knwa1 141 RPLLPEVLFDNGQARLIRRRQTIEELLALELLHH--------- 174 d1a8pa1 91 ----------------------------------SRKPTGTLV 99 TMalign alignment (TM-score: 0.31 Raw score:54.27) d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYVLITQVRSVKQMGS--RHFVLVDAGFND-L 57 : :::::::::::: :: ::::::::: : : d1a8pa1 1 ----------S------------------NLNVERVLSVHH-WNDTLFSFKTTRN--PSL 29 d1knwa1 58 MRPAMYGSYHHISALAADGRSLE------HAPTVETVVAGPLCESG--D--VFTQQEGGN 107 :: ::::::::::: ::: :::: :: : ::: d1a8pa1 30 RF--ENGQFVMIGLE-----VDGRPLMRA------YSIA-----SPNYEEHLEF------ 65 d1knwa1 108 VETR------AL--PE-VKAGDYLVLHDTGAY-----GASMSSNYNSRPLLPEVLFDNGQ 153 ::: :: :: :::::::::: : :: d1a8pa1 66 -FSIKVQNGPLTSRLQHLKEGDELMVS-R-KPTGTLV----------------------- 99 d1knwa1 154 ARLIRRRQTIEELLALELLHH 174 d1a8pa1 100 --------------------- 100 HHsearch alignment (Probability: 0.07 E-value:0.12) d1knwa1 30 YVLITQVRSVKQMGSRHFVLV-DAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETV 88 ::::::::::::::::::::: :::::::::: :::::::::::: :::::::: d1a8pa1 2 NLNVERVLSVHHWNDTLFSFKTTRNPSLRFEN----GQFVMIGLEVDG----RPLMRAYS 53 d1knwa1 89 VAGPLCE-SGDVFTQQE-GGNVETRALPEVKAGDYLVLH 125 ::::::: ::::::::: ::::: ::::::::::::::: d1a8pa1 54 IASPNYEEHLEFFSIKVQNGPLT-SRLQHLKEGDELMVS 91