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 <-- 0.975 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1d4aa_) 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 d1d4aa_ NAD(P)H:quinone reductaseFlavoproteinsFlavodoxin-​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 <-- 0.975 --> Hit
DALI alignment (Z-score: 5.5 Raw score:514.30) d1l7da1 1 agyravidgayefarafpmmmtaagtvPPARVLVFG--------vGVAGLQAIATAKRLG 52 ::::::::: ::::::::::::::: d1d4aa_ 1 ---------------------------VGRRALIVLahsertsfnYAMKEAAAAALKKKG 33 d1l7da1 53 AVVMATD-VRAA--------------------tkeqveslggkfitvKKQAEAVLKELVK 91 ::::::: :::: ::::::::::::: d1d4aa_ 34 WEVVESDlYAMNfnpiisrkditgklkdpanfqypaesvlaykeghlSPDIVAEQKKLEA 93 d1l7da1 92 TDIAITTALIPGKPAP---vliTEEM-------------vtkmKPGSVIIDLA------- 128 :::::::::::::::: :::: :::::::::: d1d4aa_ 94 ADLVIFQFPLQWFGVPailkgwFERVfigefaytyaamydkgpFRSKKAVLSIttggsgs 153 d1l7da1 129 ---------veaggncPLSEpgkivVKHGVKIVGHtnVPSR------------------- 160 :::: :::::::::: :::: d1d4aa_ 154 myslqgihgdmnvilwPIQS--gilHFCGFQVLEP-qLTYSightpadariqilegwkkr 210 d1l7da1 161 ------------------------------------------------------------ 161 d1d4aa_ 211 leniwdetplyfapsslfdlnfqagflmkkevqdeeknkkfglsvghhlgksiptdnqik 270 d1l7da1 161 --- 161 d1d4aa_ 271 ark 273 FAST alignment (Normalized score: 3.83 Raw score:801.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPP--ARVLVFGV-----------GVAGLQAIAT 47 ::::: :::::::::: d1d4aa_ 1 -----------------------------VGRRALI---VLAHSERTSFNYAMKEAAAAA 28 d1l7da1 48 AKRLGAVVMATDVRAATKEQVESLGGKFITV----------------------------- 78 ::::::::::::: d1d4aa_ 29 LKKKGWEVVESDL------------------YAMNFNPIISRKDITGKLKDPANFQYPAE 70 d1l7da1 79 ----------KKQAEAVLKELVKTDIAITTAL-IPGKPAPVLITEEMVTKM--------- 118 ::::::::::::::::::::: ::::: d1d4aa_ 71 SVLAYKEGHLSPDIVAEQKKLEAADLVIFQF-PLQWFG-------------VPAILKGWF 116 d1l7da1 119 --------------------KPGSVIIDLAVEAGGNCPLSEPGKI--------------- 143 :::::::: d1d4aa_ 117 ERVFIGEFAYTYAAMYDKGPFRSKKAVL-----------------SITTGGSGSMYSLQG 159 d1l7da1 144 ----------------VVKHGVKIVGH------TNVPSR--------------------- 160 :::::::: :::: d1d4aa_ 160 IHGDMNVILWPIQSGILHFCGFQV---LEPQLTYSIG--HTPADARIQILEGWKKRLENI 214 d1l7da1 161 ----------------------------------------------------------- 161 d1d4aa_ 215 WDETPLYFAPSSLFDLNFQAGFLMKKEVQDEEKNKKFGLSVGHHLGKSIPTDNQIKARK 273 TMalign alignment (TM-score: 0.41 Raw score:65.10) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG-------VGVAGLQAIATAKR-LG 52 ::: : :::::: :::::::::::::: :: d1d4aa_ 1 ---------------VGR----------R-ALIVLAHSERTSFNYAMKEAAAAALKKKGW 34 d1l7da1 53 AVVMATDVRAATKEQVESLGGKFITVKK-------------------------------- 80 ::::::: : : :::::: d1d4aa_ 35 EVVESDL--Y--A---------MNFNPIISRKDITGKLKDPANFQYPAESVLAYKEGHLS 81 d1l7da1 81 -----------------------------Q-AEAVL-KEL---V-----------K--TD 93 : ::::: ::: : : :: d1d4aa_ 82 PDIVAEQKKLEAADLVIFQFPLQWFGVPAILKGWFERVFIGEFAYTYAAMYDKGPFRSKK 141 d1l7da1 94 IAITTALIPG--KP--------A--PV-LITEEMVTKMKPGSVIIDLAVEA--------- 131 :::::::::: :: : :: :::::::::::: :::::::::: d1d4aa_ 142 AVLSITTGGSGSMYSLQGIHGDMNVILWPIQSGILHFCGF-QVLEPQLTYSIGHTPADAR 200 d1l7da1 132 -----------------GGNCPLSEPGKIVVKHG-------------------------- 148 ::::::: d1d4aa_ 201 IQILEGWKKRLENIWDE----------TPLYFAPSSLFDLNFQAGFLMKKEVQDEEKNKK 250 d1l7da1 149 ----------------VKIVGH--TNVPSR 160 ::::: d1d4aa_ 251 FGLSVGHHLGKSIPTD-NQIKARK------ 273 HHsearch alignment (Probability: 0.27 E-value:0.01) d1l7da1 30 ARVLVFGV--------GVAGLQAIATAKRLGAVVMATDVRAATKE---QVESL------G 72 :::::::: ::::::::::::::::::::::::::::: ::::: : d1d4aa_ 3 RRALIVLAHSERTSFNYAMKEAAAAALKKKGWEVVESDLYAMNFNPIISRKDITGKLKDP 62 d1l7da1 73 GKFI------------TVKKQAEAVLKELVKTDIAITT 98 :::: :::::::::::::::::::::: d1d4aa_ 63 ANFQYPAESVLAYKEGHLSPDIVAEQKKLEAADLVIFQ 100