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 <-- 1.680 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1h5qa_) 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 d1h5qa_ Mannitol 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 <-- 1.680 --> Hit
DALI alignment (Z-score: 8.6 Raw score:766.60) d1l7da1 1 agyravidgayefaRAFPmmmtaagtvpPARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 :::: ::::::::: :::::::::::::::::::::: d1h5qa_ 1 ----------pgftISFV----------NKTIIVTGGnRGIGLAFTRAVAAAGANVAVIY 40 d1l7da1 60 VRA-ATKEQVESLG------GKFIT----vKKQA-EAVLKEL---VKTDIAITTALI--- 101 ::: :::::::::: ::::: :::: ::::::: :::::::::::: d1h5qa_ 41 RSAaDAVEVTEKVGkefgvkTKAYQcdvsnTDIVtKTIQQIDadlGPISGLIANAGVsvv 100 d1l7da1 102 -----------PGKP---APVL--ITEEMVTKM---kPGSVIIDLA-------------- 128 :::: :::: ::::::::: ::::::::: d1h5qa_ 101 kpatelthedfAFVYdvnVFGVfnTCRAVAKLWlqkqQKGSIVVTSsmssqiinqsslng 160 d1l7da1 129 ---------vEAGGncPLSEpgkIVVK--HGVKIVG------------------------ 153 :::: :::: :::: ::::::: d1h5qa_ 161 sltqvfynssKAAC-sNLVK-glAAEWasAGIRVNAlspgyvntdqtahmdkkirdhqas 218 d1l7da1 154 ------------------------------HTNVPS-----r 160 :::::: d1h5qa_ 219 niplnrfaqpeemtgqailllsdhatymtgGEYFIDggqliw 260 FAST alignment (Normalized score: 5.52 Raw score:1126.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP--------PARVLVF-GVGVAGLQAIATAKRL 51 ::::::: :::::::::::::::: d1h5qa_ 1 ----------------------------PGFTISFVNKTIIVTGGNRGIGLAFTRAVAAA 32 d1l7da1 52 GAVVMATD-VRAATKEQVES------LGGKFITVKK------QAEAVLKELV-------K 91 :::::::: ::::::::::: ::::: :::::::::: : d1h5qa_ 33 GANVAVIYRSAADAVEVTEKVGKEFGVKTKA-----YQCDVSNTDIVTKTIQQIDADLGP 87 d1l7da1 92 TDIAITTALIPGKP--------------------APVLITEEMVTKMK---------PGS 122 :::::::::: :::: ::::::: ::: d1h5qa_ 88 ISGLIANAGV----SVVKPATELTHEDFAFVYDVNVFG-VFNTCRA--VAKLWLQKQQKG 140 d1l7da1 123 VIIDLAVEAGGNCPLSEPGKIVV------------------------------------- 145 :::: d1h5qa_ 141 SIVV-------------------TSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGL 181 d1l7da1 146 -----KHGVKIVGHTNVPSR---------------------------------------- 160 ::::::::: d1h5qa_ 182 AAEWASAGIRVNAL------SPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQA 235 d1l7da1 161 ------------------------- 161 d1h5qa_ 236 ILLLSDHATYMTGGEYFIDGGQLIW 260 TMalign alignment (TM-score: 0.66 Raw score:105.70) d1l7da1 1 ----AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-GVAGLQAIATAKRLGAVV 55 : ::: ::::::::: :::::::::::::::::: d1h5qa_ 1 PGFT---------I-----SFV----------NKTIIVTGGNRGIGLAFTRAVAAAGANV 36 d1l7da1 56 MATDVRAA-TKEQVESLG------GKFITV---K-KQA-EAVLKEL---VKTDIAITTAL 100 :::::::: ::::::::: :::::: : ::: ::::::: ::::::::::: d1h5qa_ 37 AVIYRSAADAVEVTEKVGKEFGVKTKAYQCDVSNTDIVTKTIQQIDADLGPISGLIANAG 96 d1l7da1 101 IPG--------------KP--AP-VL--ITEEMVTKM---KPGSVIIDLAV--E------ 130 ::: :: :: :: ::::::::: ::::::::::: : d1h5qa_ 97 VSVVKPATELTHEDFAFVYDVNVFGVFNTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQS 156 d1l7da1 131 --------------A-GGNCPLSEPGKIVV-K--HGVKIVG------------------- 153 : :: ::::: :::: : ::::::: d1h5qa_ 157 SLNGSLTQVFYNSSKAAC-SNLVK--GLAAEWASAGIRVNALSPGYVNTDQTAHMDKKIR 213 d1l7da1 154 ------------------------------------HTNVPSR---- 160 ::::::: d1h5qa_ 214 DHQASNIPLNRFAQPEEMTGQAILLLSDHATYMTGGEYFIDGGQLIW 260 HHsearch alignment (Probability: 0.96 E-value:0.00) d1l7da1 28 PPARVLVFGV-GVAGLQAIATAKRLGAVVMATDVRAATKEQV-----ESLGGKFITV--- 78 :::::::::: ::::::::::::::::::::::::::::::: :::::::::: d1h5qa_ 8 VNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAADAVEVTEKVGKEFGVKTKAYQCD 67 d1l7da1 79 KKQAEAVLKELV-------KTDIAITTALIPGK-------------------PAPVLITE 112 :::::::::::: :::::::::::::: :::::::: d1h5qa_ 68 VSNTDIVTKTIQQIDADLGPISGLIANAGVSVVKPATELTHEDFAFVYDVNVFGVFNTCR 127 d1l7da1 113 EMVTKM---KPGSVIIDLAVEAG 132 :::::: :::::::::::::: d1h5qa_ 128 AVAKLWLQKQQKGSIVVTSSMSS 150