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 <-- 1.477 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1duvg2) 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 d1duvg2 Ornithine transcarbamoylaseAspartate/​ornithine carbamoyltransferaseATC-​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 <-- 1.477 --> Hit
DALI alignment (Z-score: 8.0 Raw score:638.00) d1l7da1 1 agyravidgayefaRAFPmmmtaagtvpPARVLVF-GVGV-AGLQAIATAKRLGAVVMAT 58 :::: ::::::: :::: ::::::::::::::::::: d1duvg2 1 --------------KAFN----------EMTLVYAgDARNnMGNSMLEAAALTGLDLRLV 36 d1l7da1 59 DVRAaTKEQ--VESLG---------GKFITvkkqaeAVLKELVKTDIAITTAL-IPGK-- 104 :::: :::: ::::: ::::: ::::::::::::::::: :::: d1duvg2 37 APQAcWPEAalVTECRalaqqnggnITLTE------DVAKGVEGADFIYTDVWvSMGEak 90 d1l7da1 105 ---------papvLITEEMVTKM-KPGSVIIDLaVEAG--------------------GN 134 :::::::::: ::::::::: :::: :: d1duvg2 91 ekwaeriallreyQVNSKMMQLTgNPEVKFLHC-LPAFhddqttlgkkmaeefglhggME 149 d1l7da1 135 CPLsepgkIVVKhgvKIVGH--TNVPSR------------ 160 ::: :::: ::::: :::::: d1duvg2 150 VTD---evFESA---ASIVFdqAENRMHtikavmvatlsk 183 FAST alignment (Normalized score: 4.83 Raw score:826.10) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP----PARVLVF--GVGVAGLQAIATAKRLGAV 54 ::::::: ::::::::::::::::::: d1duvg2 1 ----------------------------KAFNEMTLVYAGDARNNMGNSMLEAAALTGLD 32 d1l7da1 55 VMATDVRAA-----TKEQVESL----------GGKFITVKKQAE--AVLKELVKTDIAIT 97 :::::: ::::::: :::: :::::::::::::: d1duvg2 33 LRLVAP---QACWPEAALVTE-CRALAQQNGGNITL--------TEDVAKGVEGADFIYT 80 d1l7da1 98 TALIPGKPAPV-----------------------LITEEMVTK-MKPGSVIIDLAVEAGG 133 ::::::::: ::::::::: d1duvg2 81 -----------DVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLH------- 122 d1l7da1 134 NCPLSEPGKIVVKHGVKIVG---------------------------------------- 153 d1duvg2 123 --------------------CLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIV 162 d1l7da1 154 --HTNVPSR------------- 160 :::::: d1duvg2 163 FDQAENRM-HTIKAVMVATLSK 183 TMalign alignment (TM-score: 0.59 Raw score:94.85) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVF-GV-GVAGLQAIATAKRLGAVVMAT 58 :::: ::::::: :: ::::::::::::::::::::: d1duvg2 1 --------------KAFN----------EMTLVYAGDARNNMGNSMLEAAALTGLDLRLV 36 d1l7da1 59 DV-RAATKE-QVESLG---------GKFITVKKQAEAVLKELVKTDIAITTALIP----G 103 :: :::::: :::::: ::::: ::::::::::::::::::: : d1duvg2 37 APQACWPEAALVTECRALAQQNGGNITLTE------DVAKGVEGADFIYTDVWVSMGEAK 90 d1l7da1 104 --K---P--AP-VLITEEMVTKM-KPGSVIIDLAVEAG-------------------GNC 135 : : :: ::::::::::: :::::::::::::: ::: d1duvg2 91 EKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEV 150 d1l7da1 136 P--LSEPGKIVVKHGVKIVGHTNV-PSR------------- 160 : ::: :: :::::::: ::: d1duvg2 151 TDEVFE----SA----ASIVFDQAENRMHTIKAVMVATLSK 183 HHsearch alignment (Probability: 0.96 E-value:0.00) d1l7da1 27 VPPARVLVFGV--GVAGLQAIATAKRLGAVVMATDV-----RAATKEQVESLGGKFITVK 79 ::::::::::: ::::::::::::::::::::::: ::::::::::::::::::: d1duvg2 3 FNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNI 62 d1l7da1 80 KQAEAVLKELVKTDIAITTALIP----GK--------PAPVLITEEMVTK-MKPGSVIID 126 ::::::::::::::::::::::: :: ::::::::::::: ::::::::: d1duvg2 63 TLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLH 122