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 | d1l7da1 | Nicotinamide nucleotide transhydrogenase dI component | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1j3va2 | Hydroxyisobutyrate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.100 --> IntermediateDALI alignment (Z-score: 5.1 Raw score:345.40) query 1 ---------------GMEN----------KKMNLLLfsgdydkALASLIIANAAREMEIE 35 :::: ::::::: ::::::::::::::::: d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFG------vGVAGLQAIATAKRLGAV 54 query 36 VTIFCafwgLLLLrdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllem 95 ::::: :::: d1l7da1 55 VMATD----VRAA----------------------------------------------- 63 query 96 mkeekapklsdllSGARKKEVKFYAXQLsveimgfkkeelfpevqimDVKEYLKNALESD 155 ::::::::::::::: ::::::::::::: d1l7da1 64 -----------tkEQVESLGGKFITVKK-------------------QAEAVLKELVKTD 93 query 156 LQLFI------------------------------------------------------- 160 ::::: d1l7da1 94 IAITTalipgkpapvliteemvtkmkpgsviidlaveaggncplsepgkivvkhgvkivg 153 query 161 ------- 161 d1l7da1 154 htnvpsr 160 FAST alignment (Normalized score: 3.90 Raw score:624.80) query 1 GME----------------------------NKKMNLLLFSGDYDK---ALASLIIANAA 29 :::::: ::::::::::: d1l7da1 1 ---AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLV---------FGVGVAGLQAIATA 48 query 30 REMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGK 89 :::::::::: d1l7da1 49 KRLGAVVMAT-------------------------------------------------- 58 query 90 KMLLEMMKEEKAPKLSD-----LLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-- 142 :::::::::::::: d1l7da1 59 -----------------DVRAATKEQVESLGGKFIT----------------------VK 79 query 143 -DVKEYLKNALESDLQLFI----------------------------------------- 160 :::::::::::::::: d1l7da1 80 KQAEAVLKELVKTDIAI--TTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPL 137 query 161 ----------------------- 161 d1l7da1 138 SEPGKIVVKHGVKIVGHTNVPSR 160 TMalign alignment (TM-score: 0.23 Raw score:37.44) query 1 ------------------------------GMENKKMNLLLFSGDYDKALASLIIANAAR 30 d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPA------------------------------ 30 query 31 EMEIEVTIFCAFWGLLLLRDPEK--AS--QEDKSLYEQAFSSLTPREAE----------- 75 :: ::: ::::: :: :::::: : :: :: ::: d1l7da1 31 -----------RV-LVF-GVGVAGLQAIATAKRLG-A--VV--MA-TDVRAATKEQVESL 71 query 76 ---ELPL-SK-----------------MNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK 114 :::: :: ::::::: d1l7da1 72 GGKFITVKKQAEAVLKELVKTDIAITT--------------------------ALIPGKP 105 query 115 EVKFYA---X----QLSVEIMGFKKEELFPE---V----Q----IMDVKEY--------- 147 :::::: : :::: : : :::: : : ::::::: d1l7da1 106 APVLITEEMVTKMKPGSV----I-I--DLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVP 158 query 148 --LKNALESDLQLFI 160 d1l7da1 159 SR------------- 160 HHsearch alignment (Probability: 0.09 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1l7da1 40 AGLQAIATAKRLGAVVMAT 58
Intermediate <-- 2.084 --> HitDALI alignment (Z-score: 9.0 Raw score:632.60) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFGVGVAGLQAIATAKRlGAVVMATDV 60 ::::::::::::::::::::: ::::::::: d1j3va2 1 -----------------------------EKVAFIGLGAMGYPMAGHLAR-RFPTLVWNR 30 d1l7da1 61 RAATKEQVES-LGGKFItvkkqaeAVLKELvKTDIAITTALIpgkpAPVL--ITEEMVTK 117 :::::::::: :::::: :::::: ::::::::::: :::: :::::::: d1j3va2 31 TFEKALRHQEeFGSEAV-------PLERVA-EARVIFTCLPT----TREVyeVAEALYPY 78 d1l7da1 118 MKPGSVIIDLAVEAG-gncPLSEpgkivVKHGVKIVGHtnVPSR---------------- 160 ::::::::::::::: :::: :::::::::: :::: d1j3va2 79 LREGTYWVDATSGEPeasrRLAE---rlREKGVTYLDA-pVSGGtsgaeagtltvmlggp 134 d1l7da1 161 ---------------------- 161 d1j3va2 135 eeavervrpflayakkvvhvgp 156 FAST alignment (Normalized score: 5.89 Raw score:931.20) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDV 60 ::::::::::::::::::::: ::::::::: d1j3va2 1 -----------------------------EKVAFIGLGAMGYPMAGHLAR-RFPTLVWNR 30 d1l7da1 61 RAATKEQVE-SLGGKFITVKKQAEAVL---KELVKTDIAITTALIPGKPAPVLITEEMV- 115 ::::::::: :::::: :::::::::::: d1j3va2 31 TFEKALRHQEEFGSEA-----------VPLERVAEARVIFTC-----------------L 62 d1l7da1 116 --------------TKMKPGSVIIDLAVEAGGNCPLSEPGKI--------------VVKH 147 :::::::::::: :::: d1j3va2 63 PTTREVYEVAEALYPYLREGTYWVDA----------------TSGEPEASRRLAERLREK 106 d1l7da1 148 GVKI--VGHTNVPSR---------------------------------------- 160 :::: :::: d1j3va2 107 GVTYLDAPVS-----GGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGP 156 TMalign alignment (TM-score: 0.56 Raw score:90.32) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDV 60 :::::::::::::::::::::: :::::::: d1j3va2 1 -----------------------------EKVAFIGLGAMGYPMAGHLARR-FPTLVWNR 30 d1l7da1 61 RAAT-KEQVESLGGKFITVKKQAEAVLKELVKTDIAITTALIPGKPAP--VLITEEMVTK 117 :::: :::::::::::: ::: :::::::::::::: ::: :::: ::::: d1j3va2 31 TFEKALRHQEEFGSEAV-------PLE-RVAEARVIFTCLPT---TREVYEVAE-ALYPY 78 d1l7da1 118 MKPGSVIIDLAVEA--GGNCPLSEPGKIVVK-HGVKIVGHTNVP-----------SR--- 160 :::::::::::::: :: ::::: ::: :::::::: ::: :: d1j3va2 79 LREGTYWVDATSGEPEAS-RRLAE----RLREKGVTYLDA-PVSGGTSGAEAGTLTVMLG 132 d1l7da1 161 ------------------------ 161 d1j3va2 133 GPEEAVERVRPFLAYAKKVVHVGP 156 HHsearch alignment (Probability: 0.98 E-value:0.00) d1l7da1 31 RVLVFGVGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVKKQAEAVLKELV 90 :::::::::::::::::::::::::::::::::::::::::::: :::::::: d1j3va2 2 KVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSE--------AVPLERVA 53 d1l7da1 91 KTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAV 129 :::::::: ::::::::::::::::::::::::::::: d1j3va2 54 EARVIFTC--LPTTREVYEVAEALYPYLREGTYWVDATS 90