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 <-- 1.745 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1o5ia_) 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 d1o5ia_ beta-​keto acyl carrier protein reductaseNAD(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 <-- 1.745 --> Hit
DALI alignment (Z-score: 8.2 Raw score:701.30) d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 :::: :::::::: :::::::::::::::::::::: d1o5ia_ 1 ---------------GIRD----------KGVLVLAAsRGIGRAVADVLSQEGAEVTICA 35 d1l7da1 60 VRAATKEQVEslgGKFIT--vkKQAEAVLKELVKTDIAITTALIPG-------------- 103 :::::::::: ::::: :::::::::::::::::::::::: d1o5ia_ 36 RNEELLKRSG---HRYVVcdlrKDLDLLFEKVKEVDILVLNAGGPKagffdeltnedfke 92 d1l7da1 104 -KPAP--VLIT-EEMVTKMKP---GSVIIDLA----------------vEAGGncpLSEP 140 :::: :::: ::::::::: :::::::: :::: :::: d1o5ia_ 93 aIDSLflNMIKiVRNYLPAMKekgWGRIVAITsfsvispienlytsnsaRMAL-tgFLKT 151 d1l7da1 141 gkIVVK--hGVKIVG--------------------------------------------- 153 :::: :::::: d1o5ia_ 152 -lSFEVapyGITVNCvapgwtetervkellseekkkqvesqipmrrmakpeeiasvvafl 210 d1l7da1 154 ----------HTNVPS-------r 160 :::::: d1o5ia_ 211 csekasyltgQTIVVDgglskfpl 234 FAST alignment (Normalized score: 5.46 Raw score:1057.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP---PARVLVF-GVGVAGLQAIATAKRLGAVVM 56 ::::::: ::::::::::::::::::::: d1o5ia_ 1 ----------------------------GIRDKGVLVLAASRGIGRAVADVLSQEGAEVT 32 d1l7da1 57 ATDVRAATKEQVESLGGKFITVK------KQAEAVLKELVKTDIAITTALIPGKPAPVLI 110 ::::: ::::::::::: ::::::::::::::::::: d1o5ia_ 33 ICARN---EELLKRSGHRY----VVCDLRKDLDLLFEKVKEVDILVLN------------ 73 d1l7da1 111 ---------------------------TEEMVTK------MKPGSVIIDLAVEAGGNCPL 137 ::::::: ::::::::: d1o5ia_ 74 AGGPKAGFFDELTNEDFKEAIDSLFLNMIKIVRNYLPAMKEKGWGRIVA----------- 122 d1l7da1 138 SEPGKIVVK------------------------------------HGVKIVGHTNVPSR- 160 :::::::: d1o5ia_ 123 ---------ITSFSVISPIENLYTSNSARMALTGFLKTLSFEVAPYGITVNCV------A 167 d1l7da1 161 ------------------------------------------------------------ 161 d1o5ia_ 168 PGWTETERVKELLSEEKKKQVESQIPMRRMAKPEEIASVVAFLCSEKASYLTGQTIVVDG 227 d1l7da1 161 ------- 161 d1o5ia_ 228 GLSKFPL 234 TMalign alignment (TM-score: 0.63 Raw score:100.74) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 ::: ::::::::: :::::::::::::::::::::: d1o5ia_ 1 ---------------GIR----------DKGVLVLAASRGIGRAVADVLSQEGAEVTICA 35 d1l7da1 60 VRAATKEQVESLGGKFITVK--KQAEAVLK-ELVKTDIAITTALIP-G----------K- 104 :::::::::: ::::::: :::::::: : ::::::::::::: : : d1o5ia_ 36 RNEELLKRSG---HRYVVCDLRKDLDLLFEKV-KEVDILVLNAGGPKAGFFDELTNEDFK 91 d1l7da1 105 -P--APV-LIT--EEMVTKMKP---GSVIIDLAV--E----------A--GGNCP-LSEP 140 : ::: ::: ::::::::: ::::::::: : : ::::: ::: d1o5ia_ 92 EAIDSLFLNMIKIVRNYLPAMKEKGWGRIVAITSFSVISPIENLYTSNSARMALTGFLK- 150 d1l7da1 141 GKIVVKH--G-VKIVG-------------------------------------------- 153 :::::: : ::::: d1o5ia_ 151 -TLSFEVAPYGITVNCVAPGWTETERVKELLSEEKKKQVESQIPMRRMAKPEEIASVVAF 209 d1l7da1 154 ------------HTNVPSR------ 160 ::::::: d1o5ia_ 210 LCSEKASYLTGQTIVVDGGLSKFPL 234 HHsearch alignment (Probability: 0.97 E-value:0.00) d1l7da1 26 TVPPARVLVFG-VGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVKKQAEA 84 ::::::::::: ::::::::::::::::::::::::::::::::::::: :::::::::: d1o5ia_ 1 GIRDKGVLVLAASRGIGRAVADVLSQEGAEVTICARNEELLKRSGHRYV-VCDLRKDLDL 59 d1l7da1 85 VLKELVKTDIAITTALIPGKP-------------------APVLITEEMVTKMKP--GSV 123 ::::::::::::::::::::: ::::::::::::::: ::: d1o5ia_ 60 LFEKVKEVDILVLNAGGPKAGFFDELTNEDFKEAIDSLFLNMIKIVRNYLPAMKEKGWGR 119 d1l7da1 124 IIDLAVEA 131 :::::::: d1o5ia_ 120 IVAITSFS 127