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 | d1np3a2 | Class I ketol-acid reductoisomerase (KARI) | 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 <-- 2.143 --> HitDALI alignment (Z-score: 8.8 Raw score:664.50) d1l7da1 1 agyravidgayefaRAFPmmmtaagtvppARVLVFGVGVAGLQAIATAKRLGAVVMATDV 60 :::: ::::::::::::::::::::::::::::::: d1np3a2 1 ---mrvfydkdcdlSIIQ----------gKKVAIIGYGSQGHAHACNLKDSGVDVTVGLR 47 d1l7da1 61 -RAATKEQVESLGGKFItvkkqaeAVLKELVKTDIAITTALipgkpAPVL--ITEE-MVT 116 :::::::::::::::: ::::::::::::::::: :::: :::: ::: d1np3a2 48 sGSATVAKAEAHGLKVA-------DVKTAVAAADVVMILTP-----DEFQgrLYKEeIEP 95 d1l7da1 117 KMKPGSVIIDLAVEaggncplSEPG-kiVVKHGVKIVGhtnVPSR--------------- 160 :::::::::::::: :::: :::::::::: :::: d1np3a2 96 NLKKGATLAFAHGF-------SIHYnqvVPRADLDVIM--iAPKApghtvrsefvkgggi 146 d1l7da1 161 ------------------------------------ 161 d1np3a2 147 pdliaiyqdasgnaknvalsyacgvgggrtgiiett 182 FAST alignment (Normalized score: 7.18 Raw score:1226.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP---------------PARVLVFGVGVAGLQAI 45 ::::::::::::::::: d1np3a2 1 ----------------------------MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHA 32 d1l7da1 46 ATAKRLGAVVMATDVR-AATKEQVESLGGKFITVKKQAE-AVLKELVKTDIAITTALIPG 103 :::::::::::::::: :::::::::::::: ::::::::::::::: d1np3a2 33 CNLKDSGVDVTVGLRSGSATVAKAEAHGLKV--------ADVKTAVAAADVVMIL----- 79 d1l7da1 104 KPAPVLI---------TEEM-VTKMKPGSVIIDLAVEAGGNCPLSEPGKIVV-------- 145 :::: :::::::::::::::: d1np3a2 80 -------TPDEFQGRLYKEEIEPNLKKGATLAFAHGF---------------SIHYNQVV 117 d1l7da1 146 -KHGVKIVGHTNVPSR-------------------------------------------- 160 ::::::::: d1np3a2 118 PRADLDVIMI------APKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGV 171 d1l7da1 161 ----------- 161 d1np3a2 172 GGGRTGIIETT 182 TMalign alignment (TM-score: 0.58 Raw score:92.38) d1l7da1 1 -----AGYRAVI--DGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGA 53 : ::: :::: ::::::::::::::::::::::::: d1np3a2 1 MRVFY------DKD---CDL-SIIQ----------GKKVAIIGYGSQGHAHACNLKDSGV 40 d1l7da1 54 VVMATDV-RAATKEQVESLGGKFITVKKQAEAVLKELVKTDIAITTALIPGKPAPV--LI 110 ::::::: ::::::::::::::::: :::::::::::::::: :::: :: d1np3a2 41 DVTVGLRSGSATVAKAEAHGLKVAD-------VKTAVAAADVVMILTP----DEFQGRLY 89 d1l7da1 111 TE-EMVTKMKPGSVIIDLAVEAGG---NCPLSEPGKIVVKHGVKIVGHTNVP-------- 158 :: :::::::: ::::::::: :: :::: ::::::::: ::: d1np3a2 90 KEEIEPNLKKG-ATLAFAHGF-SIHYN-QVVP-------RADLDVIMI-APKAPGHTVRS 138 d1l7da1 159 ---------SR--------------------------------- 160 :: d1np3a2 139 EFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGIIETT 182 HHsearch alignment (Probability: 0.99 E-value:0.00) d1l7da1 25 GTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAA-TKEQVESLGGKFITVKKQAE 83 ::::::::::::::::::::::::::::::::::::::: :::::::::::: : d1np3a2 12 SIIQGKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSATVAKAEAHGLKV-------A 64 d1l7da1 84 AVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIID---LAVEAGGNCPLS 138 ::::::::::::: :::::::::::::::::::::::::::: :::::::::::: d1np3a2 65 DVKTAVAAADVVM--ILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120