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 <-- 1.538 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1orra_) 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 d1orra_ CDP-​tyvelose-​2-​epimeraseNAD(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 <-- 1.538 --> Hit
DALI alignment (Z-score: 6.0 Raw score:636.20) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 :::::::: :::::::::::::::::::::: d1orra_ 1 -----------------------------AKLLITGGcGFLGSNLASFALSQGIDLIVFD 31 d1l7da1 60 VRA--ATKEQVESL----GGKFIT----vkKQAEAV-LKELvkTDIAITT-ALIPG---- 103 ::: ::::::::: :::::: :::::: :::: ::::::: ::::: d1orra_ 32 NLSrkGATDNLHWLsslgNFEFVHgdirnkNDVTRLiTKYM--PDSCFHLaGQVAMttsi 89 d1l7da1 104 ------KPAP--VLIT-EEMVT-KMKPgSVIIDLA------------------------- 128 :::: :::: ::::: :::: ::::::: d1orra_ 90 dnpcmdFEINvgGTLNlLEAVRqYNSN-CNIIYSStnkvygdleqykynetetrytcvdk 148 d1l7da1 129 ------------------vEAGGncPLSEpgkiVVKHGVKIVGHTN-------------- 156 :::: :::: ::::::::::::: d1orra_ 149 pngydestqldfhspygcsKGAA-dQYML--dyARIFGLNTVVFRHssmyggrqfatydq 205 d1l7da1 157 ----------------------------------------------------------VP 158 :: d1orra_ 206 gwvgwfcqkaveiknginkpftisgngkqvrdvlhaedmislyftalanvskirgnafNI 265 d1l7da1 159 SR---------------------------------------------------------- 160 :: d1orra_ 266 GGtivnslsllelfklledycnidmrftnlpvresdqrvfvadikkitnaidwspkvsak 325 d1l7da1 161 ------------- 161 d1orra_ 326 dgvqkmydwtssi 338 FAST alignment (Normalized score: 4.70 Raw score:1093.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVF-GVGVAGLQAIATAKRLGAVVMATD 59 :::::: :::::::::::::::::::::::: d1orra_ 1 -----------------------------AKLLITGGCGFLGSNLASFALSQGIDLIVFD 31 d1l7da1 60 V------RAATKEQVES-LGGKFITVKK-----QAEAVLKELV--KTDIAITTALIPGKP 105 :::::::::: :::::: :::::::::: ::::::::::: d1orra_ 32 -NLSRKGATDNLHWLSSLGNFEFV----HGDIRNKNDVTRLITKYMPDSCFHLAGQ---- 82 d1l7da1 106 APVLI-----------------------TEEMVTKM---KPGSVIIDLAVEAGGNCPLSE 139 ::::: :::::::: d1orra_ 83 -----VAMTTSIDNPCMDFEINVGGTLNLLEAV---RQYNSNCNIIY------------- 121 d1l7da1 140 PGKIV------------------------------------------------------- 144 d1orra_ 122 -----SSTNKVYGDLEQYKYNETETRYTCVDKPNGYDESTQLDFHSPYGCSKGAADQYML 176 d1l7da1 145 ---VKHGVKIVGHTNVPSR----------------------------------------- 160 :::::::::: d1orra_ 177 DYARIFGLNTVVF------RHSSMYGGRQFATYDQGWVGWFCQKAVEIKNGINKPFTISG 230 d1l7da1 161 ------------------------------------------------------------ 161 d1orra_ 231 NGKQVRDVLHAEDMISLYFTALANVSKIRGNAFNIGGTIVNSLSLLELFKLLEDYCNIDM 290 d1l7da1 161 ------------------------------------------------ 161 d1orra_ 291 RFTNLPVRESDQRVFVADIKKITNAIDWSPKVSAKDGVQKMYDWTSSI 338 TMalign alignment (TM-score: 0.61 Raw score:98.26) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG-VGVAGLQAIATAKRLGAVVMATD 59 ::::::: ::::::::::::::::::::::: d1orra_ 1 -----------------------------AKLLITGGCGFLGSNLASFALSQGIDLIVFD 31 d1l7da1 60 VR----AA-TKEQVESLG-GKFITV---K-KQAEAVLKELVKTDIAITT-ALIPG--K-- 104 :: :: ::::::::: :::::: : :::::::::: :::::::: ::::: : d1orra_ 32 NLSRKGATDNLHWLSSLGNFEFVHGDIRNKNDVTRLITKY-MPDSCFHLAGQVAMTTSID 90 d1l7da1 105 ----P--APV-LIT--EEMVT-KMKPGSVIIDLAVE------------------------ 130 : ::: ::: ::::: :::: :::::: :: d1orra_ 91 NPCMDFEINVGGTLNLLEAVRQYNSN-CNIIYS-STNKVYGDLEQYKYNETETRYTCVDK 148 d1l7da1 131 ----------------A--GG-NCPLSEPGKIVVKHGVKIVGHTN--------------- 156 : :: :::::: ::::::::::::::: d1orra_ 149 PNGYDESTQLDFHSPYGCSKGAADQYML--DYARIFGLNTVVFRHSSMYGGRQFATYDQG 206 d1l7da1 157 ----------------------------------------------------------VP 158 :: d1orra_ 207 WVGWFCQKAVEIKNGINKPFTISGNGKQVRDVLHAEDMISLYFTALANVSKIRGNAFNIG 266 d1l7da1 159 S---------------------------------------------------R------- 160 : : d1orra_ 267 GTIVNSLSLLELFKLLEDYCNIDMRFTNLPVRESDQRVFVADIKKITNAIDWSPKVSAKD 326 d1l7da1 161 ------------ 161 d1orra_ 327 GVQKMYDWTSSI 338 HHsearch alignment (Probability: 0.95 E-value:0.00) d1l7da1 30 ARVLVFGV-GVAGLQAIATAKRLGAVVMATDVR-----AATKEQVESLGG-KFI-TVKKQ 81 :::::::: :::::::::::::::::::::::: :::::::::::: ::: ::::: d1orra_ 1 AKLLITGGCGFLGSNLASFALSQGIDLIVFDNLSRKGATDNLHWLSSLGNFEFVHGDIRN 60 d1l7da1 82 AEAVLKELVKT--DIAITTALIPGK----PAPV-------LITEEMVTKMKP-G--SVII 125 ::::::::::: :::::::::::: :::: :::::::::::: : :::: d1orra_ 61 KNDVTRLITKYMPDSCFHLAGQVAMTTSIDNPCMDFEINVGGTLNLLEAVRQYNSNCNII 120 d1l7da1 126 DLAVE 130 ::::: d1orra_ 121 YSSTN 125