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 <-- 1.961 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1k2wa_) 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 d1k2wa_ Sorbitol 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 <-- 1.961 --> Hit
DALI alignment (Z-score: 9.8 Raw score:779.40) d1l7da1 1 agyravidgayefaRAFPmmmtaagtvppARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 :::: :::::::: :::::::::::::::::::::: d1k2wa_ 1 --------------MRLD----------gKTALITGSaRGIGRAFAEAYVREGARVAIAD 36 d1l7da1 60 VRAAT-KEQVESLG--GKFIT----vkKQAEAVLKELV----KTDIAITTALI------- 101 ::::: :::::::: ::::: ::::::::::: ::::::::::: d1k2wa_ 37 INLEAaRATAAEIGpaACAIAldvtdqASIDRCVAELLdrwgSIDILVNNAALfdlapiv 96 d1l7da1 102 -------PGKP---APVL--ITEEMVTKMK---PGSVIIDLA----------------vE 130 :::: :::: :::::::::: ::::::::: : d1k2wa_ 97 eitresyDRLFainVSGTlfMMQAVARAMIaggRGGKIINMAsqagrrgealvgvycatK 156 d1l7da1 131 AGGncPLSEpgkIVVK--HGVKIVGHTN-------------------------------- 156 ::: :::: :::: :::::::::: d1k2wa_ 157 AAV-iSLTQ-saGLNLirHGINVNAIAPgvvdgehwdgvdakfadyenlprgekkrqvga 214 d1l7da1 157 ---------------------------------VPSR----- 160 :::: d1k2wa_ 215 avpfgrmgraedltgmaiflatpeadyivaqtyNVDGgnwms 256 FAST alignment (Normalized score: 5.20 Raw score:1053.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP----PARVLVF-GVGVAGLQAIATAKRLGAVV 55 ::::::: :::::::::::::::::::: d1k2wa_ 1 ----------------------------MRLDGKTALITGSARGIGRAFAEAYVREGARV 32 d1l7da1 56 MATDVRA-ATKEQVESL--GGKFITVK--------KQAEAVLKELV------KTDIAITT 98 ::::::: ::::::::: :::: ::::::::: :::::::: d1k2wa_ 33 AIADINLEAARATAAEIGPAACA----IALDVTDQASIDRCVAE--LLDRWGSIDILVNN 86 d1l7da1 99 ALIPGKPAPVLI------------------------TEEMVTKMK---------PGSVII 125 ::: ::::::: :::::: d1k2wa_ 87 AAL---------FDLAPIVEITRESYDRLFAINVSGTLFMMQA--VARAMIAGGRGGKII 135 d1l7da1 126 DLAVEAGGNCPLSEPGKIVV-----------------------------------KHGVK 150 : ::::: d1k2wa_ 136 N-------------------MASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGIN 176 d1l7da1 151 IVGHTNVPSR-------------------------------------------------- 160 :::: d1k2wa_ 177 VNAI------APGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGM 230 d1l7da1 161 -------------------------- 161 d1k2wa_ 231 AIFLATPEADYIVAQTYNVDGGNWMS 256 TMalign alignment (TM-score: 0.67 Raw score:107.36) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 : ::: ::::::::: :::::::::::::::::::::: d1k2wa_ 1 ---------M-----RLD----------GKTALITGSARGIGRAFAEAYVREGARVAIAD 36 d1l7da1 60 VRAATK-EQVESLG--GKFITV---K-KQAEAVLK-EL---VKTDIAITTALIPG----- 103 :::::: ::::::: :::::: : :::::::: :: :::::::::::::: d1k2wa_ 37 INLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIV 96 d1l7da1 104 ---------KP--AP-VL--ITEEMVTKM--K-PGSVIIDLAV--E-------------A 131 :: :: :: ::::::::: : :::::::::: : : d1k2wa_ 97 EITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATK 156 d1l7da1 132 -GGNCPLSEPGKIVV-K--HGVKIVG---------------------------------- 153 :: ::::: :::: : ::::::: d1k2wa_ 157 AAV-ISLTQ--SAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVG 213 d1l7da1 154 --------------------------------HTNVPSR---- 160 ::::::: d1k2wa_ 214 AAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS 256 HHsearch alignment (Probability: 0.97 E-value:0.00) d1l7da1 27 VPPARVLVFGV-GVAGLQAIATAKRLGAVVMATDVRAATKEQVESL-GGKFITV---KKQ 81 ::::::::::: :::::::::::::::::::::::::::::::::: ::::::: ::: d1k2wa_ 3 LDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTD 62 d1l7da1 82 AEAVLKEL-------VKTDIAITTALIPGK-------------------PAPVLITEEMV 115 :::::::: ::::::::::::::: ::::::::::: d1k2wa_ 63 QASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVA 122 d1l7da1 116 TKMKP---GSVIIDLAVEA 131 ::::: ::::::::::: d1k2wa_ 123 RAMIAGGRGGKIINMASQA 141