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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1m6ia2 | Apoptosis-inducing factor (AIF) | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1f14a2 | Short chain L-3-hydroxyacyl CoA dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.321 --> IntermediateDALI alignment (Z-score: 3.4 Raw score:307.80) query 1 -------------------------------GMEN--KKMNLLLfsgdydkALASLIIAN 27 :::: ::::::: ::::::::: d1m6ia2 1 prslsaidragaevksrttlfrkigdfrsleKISRevKSITIIG------gGFLGSELAC 54 query 28 AAREME----IEVTIFCafwGLLLlrdpekasqedkslyeqafssltpreAEELPlskmn 83 :::::: ::::::: :::: ::::: d1m6ia2 55 ALGRKAralgTEVIQLF---PEKG------------------------nmGKILP----- 82 query 84 lggigkkmllemmkeekapKLSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqi 141 ::::::::::::::::: :::: d1m6ia2 83 -----------------eyLSNWTMEKVRREGVKVMpnAIVQ-----svgvssgkllikl 120 query 142 mDVKEYlknalESDLQLF---i 160 ::::: ::::::: d1m6ia2 121 kDGRKV-----ETDHIVAavgl 137 FAST alignment (Normalized score: 3.45 Raw score:510.50) query 1 GME------------------------------------NKKMNLLLFSGDYDKALASLI 24 :::::: ::::::::::::: d1m6ia2 1 ---PRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITI--IGGGFLGSELACA 55 query 25 IANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNL 84 :::::::::::::::: d1m6ia2 56 LGRKARALGTEVIQLF-------------------------------------------- 71 query 85 GGIGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFK 131 ::::::::::::::::: d1m6ia2 72 ------------------PEKGNMGKILPEYLSNWTMEKVRREGVKVM------------ 101 query 132 KEELFPEVQIMDVKEYLKNA-------------------LESDLQLFI----- 160 ::::: ::::::: d1m6ia2 102 --------PNAIV-------QSVGVSSGKLLIKLKDGRKVETDHIV--AAVGL 137 TMalign alignment (TM-score: 0.37 Raw score:59.83) query 1 -------------GMENK-KMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLL 46 : :::::: ::::::::::::::::::::::::::::: d1m6ia2 1 PRSLSAIDRAGAE----VKSRTTLF------RKIGDFRSLEKISREVKSITIIGGGFLGS 50 query 47 LLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSD 106 ::: : : d1m6ia2 51 ELA------------------------C------------------------------A- 55 query 107 LLSGARKK-EVKFYAXQLSV--EI-M-G--FK--KEELFP--EVQIM-DVKEYLKNALE- 153 :::::::: ::::::::::: :: : : :: :::::: ::::: ::: :: ::: d1m6ia2 56 LGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIV--QS-VGVS 112 query 154 ---S------------DLQLFI--- 160 : :::::: d1m6ia2 113 SGKLLIKLKDGRKVETDHIVAAVGL 137 HHsearch alignment (Probability: 0.03 E-value:0.11) query 4 NKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 :::::::::::::::::::::::::::::::::::: d1m6ia2 35 REVKSITIIGGGFLGSELACALGRKARALGTEVIQL 70
Intermediate <-- 1.144 --> HitDALI alignment (Z-score: 3.0 Raw score:329.00) d1m6ia2 1 prslsaidragaevksrttlfrkigdfrslekisrEVKSITIIGGGFLGSELACALGRKA 60 ::::::::::::::::::::::::: d1f14a2 1 ---------------------------------kiIVKHVTVIGGGLMGAGIAQVAAATG 27 d1m6ia2 61 ralgtEVIQLFP-EKGNmgkilpeylsNWTMEKV-------------------------r 94 ::::::: :::: ::::::: d1f14a2 28 ----hTVVLVDQtEDIL----------AKSKKGIeeslrkvakkkfaenpkagdecvekt 73 d1m6ia2 95 REGVKVMPnaivqsvgvssgklliklkdgRKVE--TDHIVAAVGL--------------- 137 :::::::: :::: :::::::::: d1f14a2 74 LSTIATST-------------------daASVVhsTDLVVEAIVEnlkvknelfkrldkf 114 d1m6ia2 138 ------------------------------------------------------------ 138 d1f14a2 115 aaehtifasntsslqitsianattrqdrfaglhffnpvpvmklveviktpmtsqktfesl 174 d1m6ia2 138 ------------------ 138 d1f14a2 175 vdfskalgkhpvsckdtp 192 FAST alignment (Normalized score: 3.67 Raw score:594.50) d1m6ia2 1 PRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISR--EVKSITIIGGGFLGSELACALGR 58 ::::::::::::::::::::::: d1f14a2 1 -----------------------------------KIIVKHVTVIGGGLMGAGIAQVAAA 25 d1m6ia2 59 KARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRR----------------------- 95 :::::::::: :::::::::: d1f14a2 26 ----TGHTVVLVDQ-------------TEDILAKSKKGIEESLRKVAKKKFAENPKAGDE 68 d1m6ia2 96 ------EGVKVMPNAIVQSVGVSSGKLLIKLKDGRK------VETDHIVAAVGL------ 137 ::::::: ::::::::::: d1f14a2 69 CVEKTLSTIATST-----------------------DAASVVHSTDLVVEAIV-ENLKVK 104 d1m6ia2 138 ------------------------------------------------------------ 138 d1f14a2 105 NELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPVMKLVEVIKTP 164 d1m6ia2 138 ---------------------------- 138 d1f14a2 165 MTSQKTFESLVDFSKALGKHPVSCKDTP 192 TMalign alignment (TM-score: 0.49 Raw score:66.65) d1m6ia2 1 ----------PRSLSAIDR-AG-AEV----KSRTTLFRKI-------------------- 24 ::::::::: :: :: ::::: ::: d1f14a2 1 KIIVKHVTVIGGGLMGAGIAQVA-AATGHT-VVLVD-QTEDILAKSKKGIEESLRKVAKK 57 d1m6ia2 25 ----------------------GDFRSLEKISREVKSITIIG-GG-FLGSELACALGRKA 60 ::: ::::::::::::::: :: :::::::::::::: d1f14a2 58 KFAENPKAGDECVEKTLSTIATSTD--AASVVHSTDLVVEAIVENLKVKNELFKRLDKFA 115 d1m6ia2 61 RALG-TEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGV--KVMPNAIVQ-SVG-VSSGK 115 :: :::::::::::: : ::::: :::: :::: :::: ::: d1f14a2 116 --AEHTIFASNTSSLQI----------T-SIANA-TTRQDRFAGL-HFFNPVPVM----- 155 d1m6ia2 116 LLIKLKDGR-------------KV-ET--------------DHIVAAVGL 137 ::: : : :: :: d1f14a2 156 --KLV-E-VIKTPMTSQKTFESLVDFSKALGKHPVSCKDTP--------- 192 HHsearch alignment (Probability: 0.97 E-value:0.00) d1m6ia2 37 VKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRR 95 ::::::::::::::::::::: ::::::::::::::::::: :::::::::::::: d1f14a2 4 VKHVTVIGGGLMGAGIAQVAA----ATGHTVVLVDQTEDILAKS-KKGIEESLRKVAKK 57