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 <-- 1.466 --> Intermediate <-- 1.350 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1ufka_) through the intermediate protein (d1q1ra2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1q1ra2 Putidaredoxin reductaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β
Hit d1ufka_ Hypothetical protein TT0836S-​adenosyl-​L-​methionine-​dependent methyltransferasesS-​adenosyl-​L-​methionine-​dependent methyltransferasesα/β

Supporting Alignments

Query <-- 1.466 --> Intermediate
DALI alignment (Z-score: 4.6 Raw score:383.50) query 1 -------------------------------gMENKKMNLLLfsgdydkALASLIIANAA 29 :::::::::: ::::::::::: d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG------gGYIGLEVAATA 54 query 30 REMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigk 89 :::::::::::: :::: ::::: d1q1ra2 55 IKANMHVTLLDT---AARV------------------------lERVTA----------- 76 query 90 kmllemmkeekapklSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKey 147 ::::::::::::::: :::: :::: d1q1ra2 77 -----------ppvsAFYEHLHREAGVDIRtgTQVC---gfemstdqqkvtavlCEDG-- 120 query 148 LKNAleSDLQLFI-- 160 :::: ::::::: d1q1ra2 121 TRLP--ADLVIAGig 133 FAST alignment (Normalized score: 4.48 Raw score:653.70) query 1 -------------------------------GMENKKMNLLLFSGDYDK---ALASLIIA 26 ::::::::: :::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV---------IGGGYIGLEVA 51 query 27 NAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGG 86 :::::::::::::: d1q1ra2 52 ATAIKANMHVTLLD---------------------------------------------- 65 query 87 IGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKE 133 ::::::::::::::::: d1q1ra2 66 ----------------TAARVLERVTAPPVSAFYEHLHREAGVDIR-------------- 95 query 134 ELFPEVQIMDVKEYLKNA----------------------LESDLQLFI---- 160 ::::: ::::::: d1q1ra2 96 ------TGTQV-------CGFEMSTDQQKVTAVLCEDGTRLPADLVI--AGIG 133 TMalign alignment (TM-score: 0.32 Raw score:51.98) query 1 --------------------------------GMENKKMNLLLFSGDYDKALASLIIANA 28 :::::::::::: :::::::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQL---IADNRLVVIGGG-YIGLEVAATAIK 56 query 29 AREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIG 88 :: ::::: ::: :: :::: : : d1q1ra2 57 AN-----MHVTL---LDT-----------------------AA----RVLE---R--V-- 74 query 89 KK--MLL--EMMKEEKAPKLSDLLSGARKKEV-KF--YA----------------XQLSV 125 :: : ::::::::::: : : : ::::: d1q1ra2 75 TAPP--VSA--------FYEHLHREAGV---DI-RTG-TQVCGFEMSTDQQKVTAVLCED 119 query 126 EIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI--- 160 : ::: :: : :::: d1q1ra2 120 G--------------TRL--PA---D-----LVIAGIG 133 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1q1ra2 45 YIGLEVAATAIKANMHVTLL 64
Intermediate <-- 1.350 --> Hit
DALI alignment (Z-score: 5.9 Raw score:414.90) d1q1ra2 1 ------------------------------------------------------------ 1 d1ufka_ 1 mwvyrlkgtlealdpilpglfdggarglweregevwaffpapvdlpyegvweevgdedwl 60 d1q1ra2 1 ----------------------rplpvasgavgkannfrYLRTleDAECIRRQLIADNRL 38 :::: ::::::::::::::: d1ufka_ 61 eawrrdlkpalappfvvlapwhtwegaeiplviepghheTTRL--ALKALARHLRPGDKV 118 d1q1ra2 39 VVIGGGYigLEVAATAIKANMHVTLLDTAARVlervtappvsAFYEHLHRE--AGVDIRT 96 ::::::: ::::::::::::::::::::::: ::::::::: ::::::: d1ufka_ 119 LDLGTGS--GVLAIAAEKLGGKALGVDIDPMV---------lPQAEANAKRngVRPRFLE 167 d1q1ra2 97 gTQVCgfemstdqqkvtavlcedgTRLP-ADLVIAGIG---------------------- 133 :::: :::: ::::::::: d1ufka_ 168 -GSLE-----------------aaLPFGpFDLLVANLYaelhaalapryrealvpggral 209 d1q1ra2 134 --------------------------------------- 134 d1ufka_ 210 ltgilkdraplvreamagagfrpleeaaegewvllaygr 248 FAST alignment (Normalized score: 4.04 Raw score:733.10) d1q1ra2 1 RPLPVASGAVGKANNFRYLR---------------------------------------- 20 d1ufka_ 1 --------------------MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFP 40 d1q1ra2 21 ------------------------------------------------------------ 21 d1ufka_ 41 APVDLPYEGVWEEVGDEDWLEAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGHHET 100 d1q1ra2 21 TLEDAECIRRQLIADNRLVVIGGGYIG-LEVAATAIKANMHVTLLDTAARVLERVTA--- 76 :::::::::::::::::::::::: :::::::::::::::::::: d1ufka_ 101 TRLALKALARHLRPGDKVLDLGTG---SGVLAIAAEKLGGKALGVDID---------PMV 148 d1q1ra2 77 PPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTR--------LPADLV 128 :::::::::: :::::::::: :::::: d1ufka_ 149 LPQAEANAKR-NGVRPRFLEG-------------------------SLEAALPFGPFDLL 182 d1q1ra2 129 IAGIG------------------------------------------------------- 133 ::: d1ufka_ 183 VAN--LYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGE 240 d1q1ra2 134 -------- 134 d1ufka_ 241 WVLLAYGR 248 TMalign alignment (TM-score: 0.51 Raw score:67.95) d1q1ra2 1 ------------------------------------------------------------ 1 d1ufka_ 1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVGDEDWL 60 d1q1ra2 1 --------------------------------------RPLPVASGAVGKANNFRYLRTL 22 :::: d1ufka_ 61 EAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGHH------------------ETTR 102 d1q1ra2 23 EDAECIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAF 82 ::::::::::::::::::::::: ::::::::::::::::::::::: ::: d1ufka_ 103 LALKALARHLRPGDKVLDLGTGS--GVLAIAAEKLGGKALGVDIDPMV---------LPQ 151 d1q1ra2 83 YEHLHR--EAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGI-------- 132 :::::: :::::::: ::: :::::::::::::::: d1ufka_ 152 AEANAKRNGVRPRFLE-GSL----------------EAALPFGPFDLLVANLYAELHAAL 194 d1q1ra2 133 -----------------G------------------------------------ 133 : d1ufka_ 195 APRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 248 HHsearch alignment (Probability: 0.09 E-value:0.03) d1q1ra2 23 EDAECIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAF 82 :::::::::::::::::::::::::: :::::::::::::::::::::: : d1ufka_ 103 LALKALARHLRPGDKVLDLGTGSGVL--AIAAEKLGGKALGVDIDPMVLP---------Q 151 d1q1ra2 83 YEHLHREAGVDI 94 :::::::::::: d1ufka_ 152 AEANAKRNGVRP 163