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 <-- 1.461 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1gr0a1) 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 d1gr0a1 Myo-​inositol 1-​phosphate synthaseNAD(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 <-- 1.461 --> Hit
DALI alignment (Z-score: 5.7 Raw score:542.80) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFGVGVAGLQAIATA------------ 48 ::::::::::::::::::: d1gr0a1 1 ---------------------------teVRVAIVGVGNCASSLVQGVeyyynaddtstv 33 d1l7da1 49 -----------kRLGAVV-MATDVRAATK-EQVES-----------------LGGKFIT- 77 :::::: :::::::::: ::::: ::::::: d1gr0a1 34 pglmhvrfgpyhVRDVKFvAAFDVDAKKVgFDLSDaifasenntikiadvapTNVIVQRg 93 d1l7da1 78 -----------------vKKQAEaVLKELV--KTDIAITTALIpgkPAPVL---ITEEMV 115 ::::: :::::: ::::::::::: ::::: :::::: d1gr0a1 94 ptldgigkyyadtielsdAEPVD-VVQALKeaKVDVLVSYLPV---GSEEAdkfYAQCAI 149 d1l7da1 116 TKMkpgSVIIDLAVEaggncPLSEpgkIVVK---HGVKIVGHTNVP-------------- 158 ::: ::::::::: :::: :::: :::::::::::: d1gr0a1 150 DAG---VAFVNALPV-----FIASdpvWAKKftdARVPIVGDDIKSpnsagviidavraa 201 d1l7da1 159 ----------------------------------------sr 160 d1gr0a1 202 kiakdrgiggpvipasaylmksppeqlpddiaraqleefiig 243 FAST alignment (Normalized score: 4.23 Raw score:834.70) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKR---------- 50 ::::::::::::::::::::::: d1gr0a1 1 ---------------------------TEVRVAIVGVGNCASSLVQGVEYYYNADDTSTV 33 d1l7da1 51 -------------LGAV-VMATDVRAATKEQVE---------------------SLGGKF 75 :::: :::::::::::: :::::: d1gr0a1 34 PGLMHVRFGPYHVRDVKFVAAFDVDAKKVG---FDLSDAIFASENNTIKIADVAPTNVIV 90 d1l7da1 76 ITV---------------------KKQAEAVLKELV--KTDIAITTALIPGKPAPVLIT- 111 :::: ::::::: :::::::: :::: d1gr0a1 91 ---QRGPTLDGIGKYYADTIELSDAEPV-DVVQALKEAKVDVLVSY-LPVG--------S 137 d1l7da1 112 -------EEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVV----------------KHG 148 :::::: :::::::: ::: d1gr0a1 138 EEADKFYAQCAID--AGVAFVNA------------------LPVFIASDPVWAKKFTDAR 177 d1l7da1 149 VKIVGHTNVPSR------------------------------------------------ 160 :::: d1gr0a1 178 VPIV--------GDDIKSPNSAGVIIDAVRAAKIAKDRGIGGPVIPASAYLMKSPPEQLP 229 d1l7da1 161 -------------- 161 d1gr0a1 230 DDIARAQLEEFIIG 243 TMalign alignment (TM-score: 0.45 Raw score:71.32) d1l7da1 1 ------------AGYRAV-ID---GA--------------YE-FA---RAFPMMMTAAGT 26 :::::: :: : :: :: ::: d1gr0a1 1 TEVRVAIVGVGNCASSLVQGVEYY-YNADDTSTVPGLMHVRFGPYHVRDVK--------- 50 d1l7da1 27 VPPARVLVFGVG--VAG---LQAIAT-----------AKRLGAVVMA-TDV---R----- 61 ::::::::: : :::::: ::::::::: ::: : d1gr0a1 51 ---FVAAFDVDAKK--VGFDLSDAIFASENNTIKIAD-VAPTNVIVQRGPTLDGIGKYYA 104 d1l7da1 62 --AATKEQVESLGGKFITVKKQAEAVLKELVKT-D-IAITTALIPGKPAP--VLITEEMV 115 ::::: : : : :::::::::: : :::::::: :::: ::::: :: d1gr0a1 105 DTIELSD--------A-E---P-VDVVQALKEAKVDVLVSYLPV--GSEEADKFYAQ-CA 148 d1l7da1 116 TKMKPGSVIIDLAVEAGGNCPLSEP---GKIV--VK-HGVKIVG-HTNVPSR-------- 160 :::: ::::::: ::: : ::: : :: ::::::: ::::::: d1gr0a1 149 IDAG--VAFVNAL-PVF---I-ASDPVW---AKKFTDARVPIVGDDIKSPNSAGVIIDAV 198 d1l7da1 161 --------------------------------------------- 161 d1gr0a1 199 RAAKIAKDRGIGGPVIPASAYLMKSPPEQLPDDIARAQLEEFIIG 243 HHsearch alignment (Probability: 0.07 E-value:0.02) d1l7da1 5 AVIDGAYEFARA------FPMMMTAAGTVPPARVLVFGV 37 :::::::::::: ::::::::::::::::::::: d1gr0a1 16 SLVQGVEYYYNADDTSTVPGLMHVRFGPYHVRDVKFVAA 54