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 <-- 1.006 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1vjpa1) 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 d1vjpa1 Hypothetical protein TM1419NAD(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 <-- 1.006 --> Hit
DALI alignment (Z-score: 5.4 Raw score:563.00) d1l7da1 1 agyravidgayefarafpmmmtaagtvPPARVLVFGVGVAGLQAIATAKR---------- 50 ::::::::::::::::::::::: d1vjpa1 1 ---------------------------HMVKVLILGQGYVASTFVAGLEKlrkgeiepyg 33 d1l7da1 51 -----------LGAVV-MATDVRAATK-EQVES-------------lGGKFIT------- 77 ::::: :::::::::: ::::: :::::: d1vjpa1 34 vplarelpigfEDIKIvGSYDVDRAKIgKKLSEvvkqywndvdsltsDPEIRKgvhlgsv 93 d1l7da1 78 ---------------vkKQAEAVLKELV--KTDIAITTALIPGKP--------------- 105 ::::::::::: ::::::::::::::: d1vjpa1 94 rnlpieaegledsmtlkEAVDTLVKEWTelDPDVIVNTCTTEAFVpfgnkedllkaienn 153 d1l7da1 106 ----APVL--ITEEMVTKM--KPGSVIIDLAvEAGGncplSEPG---kivVKHGVKIVG- 153 :::: ::::::::: :::::::::: :::: :::: ::::::::: d1vjpa1 154 dkerLTATqvYAYAAALYAnkRGGAAFVNVI-PTFI----ANDPafvelaKENNLVVFGd 208 d1l7da1 154 -----------------------------------HTNV--------------------- 157 :::: d1vjpa1 209 dgspalggllvdlvrlgkialdrkefgtvypvnafYMKNpgpaeeknipriiayekmriw 268 d1l7da1 158 ----psr 160 d1vjpa1 269 aglkpkw 275 FAST alignment (Normalized score: 4.09 Raw score:857.20) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAV------ 54 ::::::::::::::::::::::: d1vjpa1 1 ---------------------------HMVKVLILGQGYVASTFVAGLEK----LRKGEI 29 d1l7da1 55 --------------------VMATDVRAATK-EQVE-----------SLGGKFITVK--- 79 ::::::::::: :::: :::: d1vjpa1 30 EPYGVPLARELPIGFEDIKIVGSYDVDRAKIGKKLSEVVKQYWNDVDSLTS------DPE 83 d1l7da1 80 ---------------------------KQAEAVLKELV--KTDIAITTALIPGKPAPVLI 110 ::::::::::: ::::::::: d1vjpa1 84 IRKGVHLGSVRNLPIEAEGLEDSMTLKEAVDTLVKEWTELDPDVIVNTC----------- 132 d1l7da1 111 -----------------------------------TEEMVTKMKPGSVIIDLAVEAGGNC 135 ::::::: ::::::::: d1vjpa1 133 TTEAFVPFGNKEDLLKAIENNDKERLTATQVYAYAAALYANK-RGGAAFVNV-------- 183 d1l7da1 136 PLSEPGKIVVK-----------------HGVKIVGHTNVPSR------------------ 160 :::::: d1vjpa1 184 -----------IPTFIANDPAFVELAKENNLVVF--------GDDGSPALGGLLVDLVRL 224 d1l7da1 161 --------------------------------------------------- 161 d1vjpa1 225 GKIALDRKEFGTVYPVNAFYMKNPGPAEEKNIPRIIAYEKMRIWAGLKPKW 275 TMalign alignment (TM-score: 0.58 Raw score:92.91) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAK--R-------- 50 :: :::::::::::::::::::: : d1vjpa1 1 ---------------HM------------VKVLILGQGYVASTFVAGLEKLRKGEIEPYG 33 d1l7da1 51 -----------L-GAVVMATDVRAATK-EQVES-----------L--GGKFIT------- 77 : :::::::::::::: ::::: : :::::: d1vjpa1 34 VPLARELPIGFEDIKIVGSYDVDRAKIGKKLSEVVKQYWNDVDSLTSDPEIRKGVHLGSV 93 d1l7da1 78 ---------V--KK---QA-EAVLKELV--KTDIAITTALIPGKP--------------- 105 : :: :: :::::::: :::::::::::: :: d1vjpa1 94 RNLPIEAEGLEDSMTLKEAVDTLVKEWTELDPDVIVNTCTTE-AFVPFGNKEDLLKAIEN 152 d1l7da1 106 ------APV-LITEEMVTKM--KPGSVIIDLAVEAGGNCPLSEP---GKIV--VK-HGVK 150 ::: :::::::::: :::::::::: ::: : ::: : :: :::: d1vjpa1 153 NDKERLTATQVYAYAAALYANKRGGAAFVNVI--PTF--I-ANDPAF---VELAKENNLV 204 d1l7da1 151 IVGHTN--VP--S--------------------------R-------------------- 160 :::::: :: : : d1vjpa1 205 VFGDDGSPALGGLLVDLVRLGKIALDRKEFGTVYPVNAFYMKNPGPAEEKNIPRIIAYEK 264 d1l7da1 161 ----------- 161 d1vjpa1 265 MRIWAGLKPKW 275 HHsearch alignment (Probability: 0.12 E-value:0.01) d1l7da1 5 AVIDGAYEFARAF----PMMMTAAGTVPPARVLVFGV-----GVAGLQAIATAKRLGAVV 55 ::::::::::::: :::::::::::::::::::: :::::::::::::::::: d1vjpa1 16 TFVAGLEKLRKGEIEPYGVPLARELPIGFEDIKIVGSYDVDRAKIGKKLSEVVKQYWNDV 75 d1l7da1 56 M 56 : d1vjpa1 76 D 76