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 <-- 1.811 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1i24a_) 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 d1i24a_ Sulfolipid biosynthesis protein SQD1NAD(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 <-- 1.811 --> Hit
DALI alignment (Z-score: 5.7 Raw score:638.50) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFG-VGVAGLQAIATAKRLGAVVMATD 59 ::::::: ::::::::::::::::::::::: d1i24a_ 1 -----------------------------SRVMVIGgDGYCGWATALHLSKKNYEVCIVD 31 d1l7da1 60 VR-----------------aATKEQVES------lGGKFIT-vkkQAEAVLKELV--KTD 93 :: :::::::: :::::: :::::::::: ::: d1i24a_ 32 NLvrrlfdhqlglesltpiaSIHDRISRwkaltgkSIELYVgdicDFEFLAESFKsfEPD 91 d1l7da1 94 IAITT-ALIPG-------------KPAP--VLIT-EEMVTKMKPGSVIIDLA-------- 128 ::::: ::::: :::: :::: ::::::::::::::::: d1i24a_ 92 SVVHFgEQRSApysmidrsravytQHNNviGTLNvLFAIKEFGEECHLVKLGtmgeygtp 151 d1l7da1 129 --------------------------------vEAGGncPLSEpgkiVVKHGVKIVGHTn 156 :::: :::: :::::::::::: d1i24a_ 152 nidieegyitithngrtdtlpypkqassfyhlsKVHD-sHNIA--ftCKAWGIRATDLN- 207 d1l7da1 157 VPSR-------------------------------------------------------- 160 :::: d1i24a_ 208 QGVVygvktdetemheelrnrldydavfgtalnrfcvqaavghpltvygkggqtrgyldi 267 d1l7da1 161 ------------------------------------------------------------ 161 d1i24a_ 268 rdtvqcveiaianpakagefrvfnqfteqfsvnelaslvtkagsklgldvkkmtvpnprv 327 d1l7da1 161 ------------------------------------------------------------ 161 d1i24a_ 328 eaeehyynakhtklmelglephylsdslldsllnfavqfkdrvdtkqimpsvswkkigvk 387 d1l7da1 161 ---- 161 d1i24a_ 388 tksm 391 FAST alignment (Normalized score: 4.33 Raw score:1082.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVF-GVGVAGLQAIATAKRLGAVVMATD 59 :::::: :::::::::::::::::::::::: d1i24a_ 1 -----------------------------SRVMVIGGDGYCGWATALHLSKKNYEVCIVD 31 d1l7da1 60 VRA--------------------ATKEQVES------LGGKFITVKK----QAEAVLKEL 89 :::::::: ::::::: ::::::::: d1i24a_ 32 ---NLVRRLFDHQLGLESLTPIASIHDRISRWKALTGKSIELYV---GDICDFEFLAESF 85 d1l7da1 90 V--KTDIAITTALIPGKPAPVLI---------------------------TEEMVTKMKP 120 : :::::::::: :::::::::: d1i24a_ 86 KSFEPDSVVHFGE----------QRSAPYSMIDRSRAVYTQHNNVIGTLNVLFAIKEFGE 135 d1l7da1 121 GSVIIDLAVEAGGNCPLSEPGKIV------------------------------------ 144 :::::: d1i24a_ 136 ECHLVK------------------LGTMGEYGTPNIDIEEGYITITHNGRTDTLPYPKQA 177 d1l7da1 145 -------------------VKHGVKIVGHTNVPSR------------------------- 160 :::::::::: d1i24a_ 178 SSFYHLSKVHDSHNIAFTCKAWGIRATDL------NQGVVYGVKTDETEMHEELRNRLDY 231 d1l7da1 161 ------------------------------------------------------------ 161 d1i24a_ 232 DAVFGTALNRFCVQAAVGHPLTVYGKGGQTRGYLDIRDTVQCVEIAIANPAKAGEFRVFN 291 d1l7da1 161 ------------------------------------------------------------ 161 d1i24a_ 292 QFTEQFSVNELASLVTKAGSKLGLDVKKMTVPNPRVEAEEHYYNAKHTKLMELGLEPHYL 351 d1l7da1 161 ---------------------------------------- 161 d1i24a_ 352 SDSLLDSLLNFAVQFKDRVDTKQIMPSVSWKKIGVKTKSM 391 TMalign alignment (TM-score: 0.62 Raw score:98.51) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG-VGVAGLQAIATAKRLGAVVMATD 59 ::::::: ::::::::::::::::::::::: d1i24a_ 1 -----------------------------SRVMVIGGDGYCGWATALHLSKKNYEVCIVD 31 d1l7da1 60 VR--A---------------ATKEQVESL------GGKFITVK-KQAEAVLKELV--KTD 93 :: : ::::::::: :::::::: ::::::::::: ::: d1i24a_ 32 NLVRRLFDHQLGLESLTPIASIHDRISRWKALTGKSIELYVGDICDFEFLAESFKSFEPD 91 d1l7da1 94 IAITT-ALIPG--K---------PA--PV-LIT--EEMVTKMKPGSVIIDLAVE------ 130 ::::: ::::: : :: :: ::: :::::::::::::::: :: d1i24a_ 92 SVVHFGEQRSAPYSMIDRSRAVYTQHNNVIGTLNVLFAIKEFGEECHLVKL-GTMGEYGT 150 d1l7da1 131 -------------------------------A-GGNCP--LSE--PGKIVVKHGVKIVGH 154 : ::::: ::: ::::::::::: d1i24a_ 151 PNIDIEEGYITITHNGRTDTLPYPKQASSFYHLSKVHDSHNIAFT----CKAWGIRATDL 206 d1l7da1 155 TN---------------------------------------------------------- 156 :: d1i24a_ 207 NQGVVYGVKTDETEMHEELRNRLDYDAVFGTALNRFCVQAAVGHPLTVYGKGGQTRGYLD 266 d1l7da1 157 -------------------------VPS-------------------------------- 159 ::: d1i24a_ 267 IRDTVQCVEIAIANPAKAGEFRVFNQFTEQFSVNELASLVTKAGSKLGLDVKKMTVPNPR 326 d1l7da1 160 --------------R--------------------------------------------- 160 : d1i24a_ 327 VEAEEHYYNAKHTKLMELGLEPHYLSDSLLDSLLNFAVQFKDRVDTKQIMPSVSWKKIGV 386 d1l7da1 161 ----- 161 d1i24a_ 387 KTKSM 391 HHsearch alignment (Probability: 0.94 E-value:0.00) d1l7da1 30 ARVLVFG-VGVAGLQAIATAKRLGAVVMATDVRAAT--------------------KEQV 68 ::::::: :::::::::::::::::::::::::::: :::: d1i24a_ 1 SRVMVIGGDGYCGWATALHLSKKNYEVCIVDNLVRRLFDHQLGLESLTPIASIHDRISRW 60 d1l7da1 69 ESLGG---KFI-TVKKQAEAVLKELVK--TDIAITTALIPGKP 105 ::::: ::: ::::::::::::::: :::::::::::::: d1i24a_ 61 KALTGKSIELYVGDICDFEFLAESFKSFEPDSVVHFGEQRSAP 103