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 <-- 1.674 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1q7ea_) 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 d1q7ea_ Hypothetical protein YfdWCoA-​transferase family III (CaiB/​BaiF)CoA-​transferase family III (CaiB/​BaiF)α/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 <-- 1.674 --> Hit
DALI alignment (Z-score: 6.1 Raw score:571.90) d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFGVGVAGLQAIATAKRLGAVVMATDV 60 :::: ::::::::::::::::::::::::::::::: d1q7ea_ 1 ------------lstPLQG----------IKVLDFTGVQSGPSCTQMLAWFGADVIKIER 38 d1l7da1 61 RAATK----------------eqvesLGGKFITV----KKQAEAVLKELVKTDIAITTAL 100 ::::: :::::::: :::::::::::::::::::::: d1q7ea_ 39 PGVGDvtrhqlrdipdidalyftmlnSNKRSIELntktAEGKEVMEKLIREADILVENFH 98 d1l7da1 101 IpgkpapvliTEEMVTKMkPGSVIIDLAVEAG---------------------------- 132 : :::::::: ::::::::::::: d1q7ea_ 99 P-------ftWEHIQEIN-PRLIFGSIKGFDEcspyvnvkayenvaqaaggaasttgfwd 150 d1l7da1 133 -------------------gncplsepgkivvkhGVKIVGHT--NVPSR----------- 160 :::::::: ::::: d1q7ea_ 151 gpplvsaaalgdsntgmhlligllaallhrektgRGQRVTMSmqDAVLNlcrvklrdqqr 210 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 211 ldklgyleeypqypngtfgdavprggnaggggqpgwilkckgwetdpnayiyftiqeqnw 270 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 271 entckaigkpewitdpaystaharqphifdifaeiekytvtidkheavayltqfdipcap 330 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 331 vlsmkeisldpslrqsgsvveveqplrgkyltvgcpmkfsaftpdikaapllgehtaavl 390 d1l7da1 161 -------------------- 161 d1q7ea_ 391 qelgysddeiaamkqnhaie 410 FAST alignment (Normalized score: 3.68 Raw score:943.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP------PARVLVFGVGVAGLQAIATAKRLGAV 54 :::::::::::::::::::::::::: d1q7ea_ 1 ----------------------------LSTPLQGIKVLDFTGVQSGPSCTQMLAWFGAD 32 d1l7da1 55 VMATDVRAATKEQVES---------------------------LGGKFITV-------KK 80 ::::: ::::: :: d1q7ea_ 33 VIKIE-----------RPGVGDVTRHQLRDIPDIDALYFTMLNSNKRS---IELNTKTAE 78 d1l7da1 81 QAEAVLKELVKTDIAITTALIPGKPAPVLI----TEEMVTKMKPGSVIIDLAVEAGGNCP 136 ::::::::::::::::::: ::::::: :::::::: d1q7ea_ 79 GKEVMEKLIREADILVENF-----------HPFTWEHIQEI-NPRLIFGS---------- 116 d1l7da1 137 LSEPGKIVVKH------------------------------------------------- 147 d1q7ea_ 117 -----------IKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNT 165 d1l7da1 148 -------------------GVKIVGHTNVPSR---------------------------- 160 ::::::: d1q7ea_ 166 GMHLLIGLLAALLHREKTGRGQRVTM------SMQDAVLNLCRVKLRDQQRLDKLGYLEE 219 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 220 YPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGK 279 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 280 PEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISL 339 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 340 DPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDE 399 d1l7da1 161 ----------- 161 d1q7ea_ 400 IAAMKQNHAIE 410 TMalign alignment (TM-score: 0.56 Raw score:89.17) d1l7da1 1 --AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMAT 58 :::: :::::::::::::::::::::::::::::: d1q7ea_ 1 LS---------------TPLQ---------GIKVLDFTGVQSGPSCTQMLAWFGADVIKI 36 d1l7da1 59 DVR-AAT--K---------E---QV-ESLGGKFITV--KK--QAEAVLKELVKTDIAITT 98 ::: ::: : : :: :::::::::: :: :::::::::::::::::: d1q7ea_ 37 ERPGVGDVTRHQLRDIPDIDALYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVEN 96 d1l7da1 99 ALIPGKPAPVLIT-EEMVTKMKPGSVIIDLA-VE-----AG------------------- 132 :: : :: ::::::::: ::::::: :: :: d1q7ea_ 97 FH-----P---FTWEHIQEINPR-LIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTG 147 d1l7da1 133 ----------------------------GNCPLSEPGKI---VV---KHGVKIVGHT--N 156 : : ::::::::: : d1q7ea_ 148 FWDGPPLVSAAALGDSNTGMHLLIGLLA----------ALLH-REKT-GRGQRVTMSMQD 195 d1l7da1 157 VP-SR------------------------------------------------------- 160 :: :: d1q7ea_ 196 AVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWET 255 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 256 DPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKH 315 d1l7da1 161 ------------------------------------------------------------ 161 d1q7ea_ 316 EAVAYLTQFDIPCAPVLSMKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPD 375 d1l7da1 161 ----------------------------------- 161 d1q7ea_ 376 IKAAPLLGEHTAAVLQELGYSDDEIAAMKQNHAIE 410 HHsearch alignment (Probability: 0.94 E-value:0.00) d1l7da1 28 PPARVLVFGVGVAGLQAIATAKRLGAVVMATDVR--AATKEQ--------------VESL 71 :::::::::::::::::::::::::::::::::: :::::: :::: d1q7ea_ 6 QGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTMLNS 65 d1l7da1 72 GGKFITVK----KQAEAVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDL 127 :::::::: :::::::::::::::::::: :: :::::::::::::::::: d1q7ea_ 66 NKRSIELNTKTAEGKEVMEKLIREADILVENF-HP-------FTWEHIQEINPRLIFGSI 117 d1l7da1 128 AV 129 :: d1q7ea_ 118 KG 119