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 <-- 1.127 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1rtta_) 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 d1rtta_ Hypothetical protein PA1204FlavoproteinsFlavodoxin-​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 <-- 1.127 --> Hit
DALI alignment (Z-score: 5.3 Raw score:434.70) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFG--------vGVAGLQAIATaKRLG 52 ::::::: :::::::::: :::: d1rtta_ 1 -----------------------------IKVLGISgslrsgsynSAALQEAIGL-VPPG 30 d1l7da1 53 AVVMATDVRaatkeqveslggkfitvKKQAEAVLKELVKTDIAITTALIPGKPAP---vl 109 ::::::::: ::::::::::::::::::::::::::::: d1rtta_ 31 MSIELADIS---giplynedvyalgfPPAVERFREQIRAADALLFATPEYNYSMAgvlkn 87 d1l7da1 110 iTEEM----vTKMKpGSVIIDLA-------vEAGGncPLSEpgkivVKHGVKIV--gHTN 156 :::: :::: :::::::: :::: :::: :::::::: ::: d1rtta_ 88 aIDWAsrppeQPFS-GKPAAILGasagrfgtARAQ-yHLRQ---tlVFLDVHPLnkpEVM 142 d1l7da1 157 VPS----------------------------r 160 ::: d1rtta_ 143 ISSaqnafdaqgrllddkareliqqqlqalql 174 FAST alignment (Normalized score: 3.20 Raw score:534.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVG--VAGLQAIATAKRL------G 52 ::::::::::: :::::::::::: : d1rtta_ 1 ---------------------------IKVLGISGSLRSGSYNSAALQEAIG-LVPPGMS 32 d1l7da1 53 AVVMATDVRAATKEQVESLGGKFITV---------------KKQAEAVLKELVKT--DIA 95 :::::: :::::::::::::: ::: d1rtta_ 33 IELADI--------------------SGIPLYNEDVYALGFPPAVERFREQIRAADALLF 72 d1l7da1 96 ITTALIPGKPAPVLI--------TEEMV-----TKMK-PGSVIIDLAVEAGGNCPLSEPG 141 ::: ::::: :::: :::: ::::::: d1rtta_ 73 ATP--EYNYS-----MAGVLKNAIDWA-SRPPEQPFSGKPAAILG--------------- 109 d1l7da1 142 KIV-------------------VKHGVK-----IVGHTNVPSR----------------- 160 :::::: ::::::::: d1rtta_ 110 ---ASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISSAQN-AFDAQGRLLDDKARELI 165 d1l7da1 161 --------- 161 d1rtta_ 166 QQQLQALQL 174 TMalign alignment (TM-score: 0.47 Raw score:74.52) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVF-GV---GVAGLQAIATAKRL---GA 53 ::::::: :: :::::::::::::: :: d1rtta_ 1 ----------------------------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMS 32 d1l7da1 54 VVMATDVR-------------AATKEQVESLGGKFITVKKQAEAVLKELVKT-DIAITTA 99 :::::::: :::::::::::::: ::::::: d1rtta_ 33 IELADISGIPLYNEDVYALGF-----------------PPAVERFREQIRAADALLFATP 75 d1l7da1 100 LIPGKP-AP--V-LIT-EEM--VTKMKPGSVIIDL-------AVEAGGNCPLSEPGKIVV 145 :: ::: :: : ::: ::: ::::::::::::: :::: : ::::: ::: d1rtta_ 76 EY-NYSMAGVLKNAIDWASRPPEQPFSGKPAAILGASAGRFGTARA-Q-YHLRQ---TLV 129 d1l7da1 146 KHGVKIVGH-TNVPS-------------------R---------- 160 ::::::::: ::::: : d1rtta_ 130 FLDVHPLNKPEVMISSAQNAFDAQGRLLDDKARELIQQQLQALQL 174 HHsearch alignment (Probability: 0.25 E-value:0.00) d1l7da1 42 LQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVKKQAEAVLKELVKTDIAITTALI 101 ::::::::::::::::::::::::::::: :::::::::::::::::::::::::::: d1rtta_ 20 LQEAIGLVPPGMSIELADISGIPLYNEDV---YALGFPPAVERFREQIRAADALLFATPE 76 d1l7da1 102 PGKPAPVL 109 :::::::: d1rtta_ 77 YNYSMAGV 84