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 <-- 1.440 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1m2ka_) 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 d1m2ka_ AF1676,​ Sir2 homolog (Sir2-​AF1?)DHS-​like NAD/​FAD-​binding domainDHS-​like NAD/​FAD-​binding domainα/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 <-- 1.440 --> Hit
DALI alignment (Z-score: 6.3 Raw score:488.30) d1l7da1 1 agyravidGAYEFARafpmmmtaagtvppARVLVFG------------------------ 36 ::::::: ::::::: d1m2ka_ 1 ----mdekLLKTIAE-------------sKYLVALTgagvsaesgiptfrgkdglwnryr 43 d1l7da1 37 -------------------------------vgVAGLQAIATAKRLGAVVMATDVRAAtk 65 ::::::::::::::::::::::::: d1m2ka_ 44 peelanpqafakdpekvwkwyawrmekvfnaqpNKAHQAFAELERLGVLKCLITQNVD-- 101 d1l7da1 66 EQVES-LGGKFIT----------------------------------------------- 77 ::::: ::::::: d1m2ka_ 102 DLHERaGSRNVIHlhgslrvvrctscnnsfevesapkipplpkcdkcgsllrpgvvwage 161 d1l7da1 78 --vKKQAEAVLKELVKTDIAITTALipgkpAPVL-iteEMVTKM-KPGSVIIDLAvEAGG 133 :::::::::::::::::::::: :::: :::::: :::::::::: :::: d1m2ka_ 162 mlpPDVLDRAMREVERADVIIVAGT-----SAVVqpaaSLPLIVkQRGGAIIEIN-PDET 215 d1l7da1 134 ncPLSEpgkivvkhgvkIVGHTNV------------------psr 160 :::: ::::::: d1m2ka_ 216 --PLTP---------iaDYSLRGKagevmdelvrhvrkalslkln 249 FAST alignment (Normalized score: 2.67 Raw score:533.50) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTV------------PPARVLVFGVGVAG------- 41 ::::::: d1m2ka_ 1 ---------------------------MDEKLLKTIAESKYLVALT-------GAGVSAE 26 d1l7da1 42 --------------------------------------------------LQAIATAKRL 51 ::::::::: d1m2ka_ 27 SGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAE- 85 d1l7da1 52 G-------AVVMATDVRAATKEQVESLGGKFITV-------------------------- 78 ::::::::: ::::::: d1m2ka_ 86 -LERLGVLKCLITQNVD----DLHERAG------SRNVIHLHGSLRVVRCTSCNNSFEVE 134 d1l7da1 79 ------------------------------KKQAEAVLKELVKTDIAITTALIPGKPAPV 108 ::::::::::::::::::: d1m2ka_ 135 SAPKIPPLPKCDKCGSLLRPGVVWAGEMLPPDVLDRAMREVERADVIIV----------- 183 d1l7da1 109 LI---------TEEMVTKMK---PGSVIIDLAVEAGGNCPLSEPGKIVVKHGVK------ 150 ::::::: ::::::: d1m2ka_ 184 --AGTSAVVQPAASLPLI--VKQRGGAIIE------------------------INPDET 215 d1l7da1 151 ------IVGHTNVPSR----------------------- 160 ::::: d1m2ka_ 216 PLTPIADYSLR-----GKAGEVMDELVRHVRKALSLKLN 249 TMalign alignment (TM-score: 0.43 Raw score:68.88) d1l7da1 1 -------------------------A---------------------------------- 1 : d1m2ka_ 1 MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKV 60 d1l7da1 2 ----------------GYRAVIDGAYEF-ARAFPMMMTAAGTVPPARVLVFGVGVAGLQA 44 :::::::::: : ::: :::::::::: ::: d1m2ka_ 61 WKWYAWRMEKVFNAQPNKAHQAFAEL-ER-LGV-----------LKCLITQNVD---DLH 104 d1l7da1 45 IATAKRLGAVVMATDVRAATK----------EQV--------------------ESLGGK 74 ::::: :::::::: :::: ::: d1m2ka_ 105 ERAGS---RNVIHLHG-SLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRP------ 154 d1l7da1 75 FIT---VKKQAEAVLKELVKT---D--IAITTALIPGKPAPVL--ITEEMVTKM--KPGS 122 ::: :::::::::::::: : :::::: :::: :: :::::: :::: d1m2ka_ 155 GVVWAG-EMLPPDVLDRAMREVERADVIIVAGT------SAVVQPAA-SLPLIVKQRGGA 206 d1l7da1 123 VIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVPSR----------------- 160 :::: ::::: :::: ::: :::::::::: d1m2ka_ 207 IIEI--NPDET--PLTP---IAD-----YSLRGKAGEVMDELVRHVRKALSLKLN 249 HHsearch alignment (Probability: 0.03 E-value:0.13) d1l7da1 40 AGLQAIATAKRLGAVVMATDVRAATKEQ 67 :::::::::::::::::::::::::::: d1m2ka_ 78 KAHQAFAELERLGVLKCLITQNVDDLHE 105