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 <-- 0.984 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1efpa1) 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 d1efpa1 Large,​ alpha subunit of electron transfer flavoprotein ETFP,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/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 <-- 0.984 --> Hit
DALI alignment (Z-score: 4.4 Raw score:410.60) d1l7da1 1 agyravidgayefarafpmmmtaagtvppaRVLVFGV-------GVAGLQAIATAKrLGA 53 ::::::: :::::::::::: ::: d1efpa1 1 ------------------------------AVLLLGEvtngalnRDATAKAVAAVK-ALG 29 d1l7da1 54 VVMATDV---RAATKEQVE-SLGG-KFITV----------kKQAEAVLKELVKTDIAITT 98 ::::::: ::::::::: :::: ::::: ::::::::::::::::::: d1efpa1 30 DVTVLCAgasAKAAAEEAAkIAGVaKVLVAedalyghrlaePTAALIVGLAGDYSHIAAP 89 d1l7da1 99 ALIpgkpaPVLITE--EMVTK-----------------------------mkPGSVIIDL 127 ::: :::::: ::::: :::::::: d1efpa1 90 ATT---daKNVMPRvaALLDVmvlsdvsaildadtferpiyagnaiqvvkskDAKKVFTI 146 d1l7da1 128 A----veaggncplsepgkivvkhgvkivghtnvpsr 160 : d1efpa1 147 Rtasfdaageggtapvtetaaaadpglsswvadevae 183 FAST alignment (Normalized score: 2.49 Raw score:425.40) d1l7da1 1 A-------------GYRAVIDGAY-EFARAFPMMMTAAGTVPPARVLVFGVGV--AGLQA 44 :::::::::: :::: :::::::: ::::: d1efpa1 1 -AVLLLGEVTNGALNRDATAKAVAAVKAL------------GDVTVLCA----GASAKAA 43 d1l7da1 45 IATAKRLG---AVVMATDVRAATKEQVESLGGKFITVKK-------QAEAVLKELVKTDI 94 ::::::: ::::::: :::::::::: d1efpa1 44 AEEAAKI-AGVAKVLVAE---------------------DALYGHRLAEPTAALIV---- 77 d1l7da1 95 AITTALIPGKPAPVLITEEMVTKM-----KPGSVIIDLAVEAGGNCPLSEPGKIVVK--- 146 :::::::: d1efpa1 78 ------------------------GLAGDYSHIAAPA--------------------TTD 93 d1l7da1 147 -----------------------------------------------HGVKIVGHTNVPS 159 ::::::: d1efpa1 94 AKNVMPRVAALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIR------ 147 d1l7da1 160 R------------------------------------ 160 d1efpa1 148 -TASFDAAGEGGTAPVTETAAAADPGLSSWVADEVAE 183 TMalign alignment (TM-score: 0.46 Raw score:74.31) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV------G-VAGLQAIATAKRLGA 53 ::::::: : ::::::::::::::: d1efpa1 1 ------------------------------AVLLLGEVTNGALNRDATAKAVAAVKALGD 30 d1l7da1 54 VVMATDV-RA-ATKEQVESL---GGKFIT-V-K-------KQAEAVLKELVKTDIAITTA 99 ::::::: :: ::::::::: :::::: : : :::::::::::::::::::: d1efpa1 31 VTVLCAGASAKAAAEEAAKIAGVAKVLVAEDALYGHRLAEPTAALIVGLAGDYSHIAAPA 90 d1l7da1 100 LIPGKPAPVLI-T-EEMVTKMKPGSVIIDLAV---------EAGGNCPLSEP-----GK- 142 :: :::::: : ::::: : ::::::: ::: :: d1efpa1 91 TT---DAKNVMPRVAALLD-V----MVLSDVSAILDADTFE--------RPIYAGNAIQV 134 d1l7da1 143 IVVKHGVKIVGHTNVPSR------------------------------- 160 :::::::::::::::::: d1efpa1 135 VKSKDAKKVFTIRTASFDAAGEGGTAPVTETAAAADPGLSSWVADEVAE 183 HHsearch alignment (Probability: 0.05 E-value:0.09) d1l7da1 83 EAVLKELVKTDIAITT 98 :::::::::::::::: d1efpa1 74 ALIVGLAGDYSHIAAP 89