HorA Server Transitive Detail

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


Query <-- 1.100 --> Intermediate <-- 1.506 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1qmga2) through the intermediate protein (d1l7da1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1l7da1 Nicotinamide nucleotide transhydrogenase dI componentNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1qmga2 Class II ketol-​acid reductoisomerase (KARI)NAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.100 --> Intermediate
DALI 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 <-- 1.506 --> Hit
DALI alignment (Z-score: 6.9 Raw score:606.50) d1l7da1 1 ----------------------------agyravidgayeFARAfpmmmtaagtvppARV 32 :::: ::: d1qmga2 1 sattfdfdssvfkkekvtlsghdeyivrggrnlfpllpdaFKGI-------------KQI 47 d1l7da1 33 LVFGVGVAGLQAIATAKRLG------AVVMATDV-rAATKEQVESLGG-----KFITvkk 80 :::::::::::::::::::: :::::::: :::::::::::: :::: d1qmga2 48 GVIGWGSQAPAQAQNLKDSLteaksdVVVKIGLRkgSNSFAEARAAGFseengTLGD--- 104 d1l7da1 81 qaeaVLKELVKTDIAITTALipgkpAPVL--iTEEMVTKMKPGSVIIDLAVEaggncplS 138 :::::::::::::::: :::: :::::::::::::::::::: : d1qmga2 105 ----MWETISGSDLVLLLIS-----DSAQadnYEKVFSHMKPNSILGLSHGF-------L 148 d1l7da1 139 EPG----kiVVKHGVKIVGhtnVPSR---------------------------------- 160 ::: :::::::::: :::: d1qmga2 149 LGHlqslgqDFPKNISVIA--vCPKGmgpsvrrlyvqgkevngaginssfavhqdvdgra 206 d1l7da1 161 -------------------- 161 d1qmga2 207 tdvalgwsialgspftfatt 226 FAST alignment (Normalized score: 5.48 Raw score:1042.00) d1l7da1 1 AGYRAVID------------------------------------GAYEFARAFPMMMTAA 24 ::::: d1qmga2 1 --------SATTFDFDSSVFKKEKVTLSGHDEYIVRGGRNLFPLLPDAF----------- 41 d1l7da1 25 GTVPP---ARVLVFGVGVAGLQAIATAKR------LGAVVMATDVR----AATKEQVESL 71 ::::::::::::::::::::: :::::::: :::::::::: d1qmga2 42 -----KGIKQIGVIGWGSQAPAQAQNLKDSLTEAKSDVVVKIG---LRKGSNSFAEARAA 93 d1l7da1 72 GGKFITVKKQAE--------AVLKELVKTDIAITTALIPGKPAPVLI---------TEEM 114 :: ::::::::::::::: :::: d1qmga2 94 GF----------SEENGTLGDMWETISGSDLVLLL------------ISDSAQADNYEKV 131 d1l7da1 115 VTKMKPGSVIIDLAVEAGGNCPLSEPGKIVV-------------KHGVKIVGHTNVPSR- 160 ::::::::::::::: ::::::::: d1qmga2 132 FSHMKPNSILGLSHG----------------FLLGHLQSLGQDFPKNISVIAV------C 169 d1l7da1 161 --------------------------------------------------------- 161 d1qmga2 170 PKGMGPSVRRLYVQGKEVNGAGINSSFAVHQDVDGRATDVALGWSIALGSPFTFATT 226 TMalign alignment (TM-score: 0.55 Raw score:87.89) d1l7da1 1 ----------------------------AGYR----AVI--DGAYEFARAFPMMMTAAGT 26 : : :::::::: d1qmga2 1 SATTFDFDSSVFKKEKVTLSGHDEYIVR---GGRNL--FPL-LPDAFKGI---------- 44 d1l7da1 27 VPPARVLVFGVGVAGLQAIATAKR-L------GAVVMATD-VRAATKEQVESLGGK---- 74 ::::::::::::::::::::: : :::::::: ::: ::::::::::: d1qmga2 45 ---KQIGVIGWGSQAPAQAQNLKDSLTEAKSDVVVKIGLRKGSN-SFAEARAAGFSEENG 100 d1l7da1 75 -FITVKKQAEAVLKELVKTDIAITTALIPGKPAPV-LITEEMVTKMKPGSVIIDLAVEAG 132 :: ::::::::::::::::: :::: ::::::::::::::::::::: : d1qmga2 101 TLG-------DMWETISGSDLVLLLIS----DSAQADNYEKVFSHMKPNSILGLSHG--F 147 d1l7da1 133 GNCPLS----EPGKIVVKHGVKIVGHTNVP---------------------SR------- 160 :::::: ::::::::::: ::: :: d1qmga2 148 LLGHLQSLGQ-----DFPKNISVIAV-CPKGMGPSVRRLYVQGKEVNGAGINSSFAVHQD 201 d1l7da1 161 ------------------------- 161 d1qmga2 202 VDGRATDVALGWSIALGSPFTFATT 226 HHsearch alignment (Probability: 0.96 E-value:0.00) d1l7da1 28 PP-ARVLVFGVGVAGLQAIATAKRL------GAVVMATDVRA-ATKEQVESLGGKFITVK 79 :: :::::::::::::::::::::: ::::::::::: :::::::::::: ::: d1qmga2 42 KGIKQIGVIGWGSQAPAQAQNLKDSLTEAKSDVVVKIGLRKGSNSFAEARAAGFS--EEN 99 d1l7da1 80 KQAEAVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVII 125 ::::::::::::::::: :::::::: :::::::::::::::::: d1qmga2 100 GTLGDMWETISGSDLVL--LLISDSAQ-ADNYEKVFSHMKPNSILG 142