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 <-- 1.856 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1bdba_) 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 d1bdba_ Cis-​biphenyl-​2,​3-​dihydrodiol-​2,​3-​dehydrogenaseNAD(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 <-- 1.856 --> Hit
DALI alignment (Z-score: 8.4 Raw score:757.60) d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFG-VGVAGLQAIATAKRLGAVVMATD 59 :::: ::::::: ::::::::::::::::::::::: d1bdba_ 1 --------------mKLKG----------EAVLITGgASGLGRALVDRFVAEGAKVAVLD 36 d1l7da1 60 VRAATKEQVESLG---GKFIT----vkKQAEAVLKELV----KTDIAITTALIPG----- 103 ::::::::::::: ::::: ::::::::::: ::::::::::::: d1bdba_ 37 KSAERLAELETDHgdnVLGIVgdvrslEDQKQAASRCVarfgKIDTLIPNAGIWDystal 96 d1l7da1 104 ----------------kpAPVL---ITEEMVtKMKP--GSVIIDLA-------------- 128 :::: :::::: :::: :::::::: d1bdba_ 97 vdlpeesldaafdevfhiNVKGyihAVKACL-PALVasRGNVIFTIsnagfypngggply 155 d1l7da1 129 --vEAGGncPLSEpgkiVVKH--GVKIVGHT----------------------------- 155 :::: :::: :::: :::::::: d1bdba_ 156 taaKHAI-vGLVR--elAFELapYVRVNGVGsgginsdlrgpsslgpladmlksvlpigr 212 d1l7da1 156 ----------------------------NVPS----------------------r 160 :::: d1bdba_ 213 mpeveeytgayvffatrgdaapatgallNYDGglgvrgffsgaggndlleqlnih 267 FAST alignment (Normalized score: 5.29 Raw score:1093.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP----PARVLVF-GVGVAGLQAIATAKRLGAVV 55 ::::::: :::::::::::::::::::: d1bdba_ 1 ----------------------------MKLKGEAVLITGGASGLGRALVDRFVAEGAKV 32 d1l7da1 56 MATDVRAATKEQVESL----GGKFITVK------KQAEAVLKELV------KTDIAITTA 99 ::::::::::::::: :::::: ::::::::: ::::::::: d1bdba_ 33 AVLDKSAERLAELET-DHGDNVLGIV--GDVRSLEDQKQAASR--CVARFGKIDTLIPNA 87 d1l7da1 100 LIPGKPAPVLI------------------------------------TEEMVTKMKPGSV 123 :: ::::::: :::: d1bdba_ 88 GI---------WDYSTALVDLPEESLDAAFDEVFHINVKGYIHAVKACLPALVA--SRGN 136 d1l7da1 124 IIDLAVEAGGNCPLSEPGKIVVKH------------------------------------ 147 ::: d1bdba_ 137 VIF---------------------TISNAGFYPNGGGPLYTAAKHAIVGLVRELAFELAP 175 d1l7da1 148 GVKIVGHTNVPSR----------------------------------------------- 160 ::::::: d1bdba_ 176 YVRVNGV------GSGGINSDLRGPSSLGPLADMLKSVLPIGRMPEVEEYTGAYVFFATR 229 d1l7da1 161 -------------------------------------- 161 d1bdba_ 230 GDAAPATGALLNYDGGLGVRGFFSGAGGNDLLEQLNIH 267 TMalign alignment (TM-score: 0.67 Raw score:106.47) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG-VGVAGLQAIATAKRLGAVVMATD 59 : ::: :::::::: ::::::::::::::::::::::: d1bdba_ 1 ---------M-----KLK----------GEAVLITGGASGLGRALVDRFVAEGAKVAVLD 36 d1l7da1 60 VRAATKEQVESLG---GKFITV---K-KQAEAVLK-EL---VKTDIAITTALIPG----- 103 ::::::::::::: :::::: : :::::::: :: :::::::::::::: d1bdba_ 37 KSAERLAELETDHGDNVLGIVGDVRSLEDQKQAASRCVARFGKIDTLIPNAGIWDYSTAL 96 d1l7da1 104 --------------KP--APVLIT--EEMVTK-M-KPGSVIIDLAV--E----------- 130 :: :::::: :::::: : ::::::::::: : d1bdba_ 97 VDLPEESLDAAFDEVFHINVKGYIHAVKACLPALVASRGNVIFTISNAGFYPNGGGPLYT 156 d1l7da1 131 --A-GGNCPLSEPGKIVV-KH-GVKIVGHT------------------------------ 155 : :: ::::: :::: :: :::::::: d1bdba_ 157 AAKHAI-VGLVR--ELAFELAPYVRVNGVGSGGINSDLRGPSSLGPLADMLKSVLPIGRM 213 d1l7da1 156 ---------------------------NVPSR---------------------- 160 ::::: d1bdba_ 214 PEVEEYTGAYVFFATRGDAAPATGALLNYDGGLGVRGFFSGAGGNDLLEQLNIH 267 HHsearch alignment (Probability: 0.97 E-value:0.00) d1l7da1 28 PPARVLVFG-VGVAGLQAIATAKRLGAVVMATDVRAATKEQVES-LGGKFITVKK---QA 82 ::::::::: :::::::::::::::::::::::::::::::::: :::::::::: :: d1bdba_ 4 KGEAVLITGGASGLGRALVDRFVAEGAKVAVLDKSAERLAELETDHGDNVLGIVGDVRSL 63 d1l7da1 83 EAVLKEL-------VKTDIAITTALIPGK------------------------PAPVLIT 111 ::::::: ::::::::::::::: ::::::: d1bdba_ 64 EDQKQAASRCVARFGKIDTLIPNAGIWDYSTALVDLPEESLDAAFDEVFHINVKGYIHAV 123 d1l7da1 112 EEMVTKMK--PGSVIIDL 127 :::::::: :::::::: d1bdba_ 124 KACLPALVASRGNVIFTI 141