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 <-- 1.403 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1db3a_) 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 d1db3a_ GDP-​mannose 4,​6-​dehydrataseNAD(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 <-- 1.403 --> Hit
DALI alignment (Z-score: 7.1 Raw score:606.50) d1l7da1 1 agyravidgayefarafPmmmtaagtvppARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 : :::::::: :::::::::::::::::::::: d1db3a_ 1 -----------------S-----------KVALITGVtGQDGSYLAEFLLEKGYEVHGIK 32 d1l7da1 60 VraatkeqvesLGGKFIT-vkkQAEAVLKELV--KTDIAITTALIPGK------------ 104 : ::::::: :::::::::: :::::::::::::: d1db3a_ 33 R----------PKFHLHYgdlsDTSNLTRILRevQPDEVYNLGAMSHVavsfespeytad 82 d1l7da1 105 pAPVLIT--EEMVTK--MKPGSVIIDLA---------------------------vEAGG 133 :::::: :::::: ::::::::::: :::: d1db3a_ 83 vDAMGTLrlLEAIRFlgLEKKTRFYQAStselyglvqeipqkettpfyprspyavaKLYA 142 d1l7da1 134 ncPLSEpgkiVVKHGVKIVGHT-------------------------------------- 155 :::: :::::::::::: d1db3a_ 143 -yWITV--nyRESYGMYACNGIlfnhesprrgetfvtrkitraianiaqglesclylgnm 199 d1l7da1 156 ---------------------------NVPS----------------------------- 159 :::: d1db3a_ 200 dslrdwghakdyvkmqwmmlqqeqpedFVIAtgvqysvrqfvemaaaqlgiklrfegtgv 259 d1l7da1 160 ------------------------------------------------------------ 160 d1db3a_ 260 eekgivvsvtghdapgvkpgdviiavdpryfrpaeetllgdptkaheklgwkpeitlrem 319 d1l7da1 160 ---------------r 160 d1db3a_ 320 vsemvandleaakkhs 335 FAST alignment (Normalized score: 3.92 Raw score:907.60) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG-VGVAGLQAIATAKRLGAVVMATD 59 :::::::: :::::::::::::::::::::: d1db3a_ 1 ----------------------------SKVALITGVTGQDGSYLAEFLLEKGYEVHGI- 31 d1l7da1 60 VRAATKEQVES--LGGKFITVKK------QAEAVLKELV--KTDIAITTALIPGKPAPVL 109 ::::: :::::::::: :::::::: d1db3a_ 32 -----------KRPKFHL-----HYGDLSDTSNLTRILREVQPDEVYNL----------- 64 d1l7da1 110 I--------------------------TEEMVTKM---KPGSVIIDLAVEAGGNCPLSEP 140 ::::::: :::::::: d1db3a_ 65 -GAMSHVAVSFESPEYTADVDAMGTLRLLEAIRF-LGLEKKTRFYQ-------------- 108 d1l7da1 141 GKIV------------------------------------------VKHGVKIVGHTNVP 158 :::::::::: d1db3a_ 109 ----ASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYAYWITVNYRESYGMYACNG---- 160 d1l7da1 159 SR---------------------------------------------------------- 160 d1db3a_ 161 --ILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDSLRDWGHAKDYVKMQWMM 218 d1l7da1 161 ------------------------------------------------------------ 161 d1db3a_ 219 LQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEEKGIVVSVTGHDAPGVKP 278 d1l7da1 161 --------------------------------------------------------- 161 d1db3a_ 279 GDVIIAVDPRYFRPAEETLLGDPTKAHEKLGWKPEITLREMVSEMVANDLEAAKKHS 335 TMalign alignment (TM-score: 0.58 Raw score:93.31) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG-VGVAGLQAIATAKRLGAVVMATD 59 :::::::: ::::::::::::::::::::::: d1db3a_ 1 ----------------------------SKVALITGVTGQDGSYLAEFLLEKGYEVHGIK 32 d1l7da1 60 VRAATKEQVESLGGKFITVK-KQAEAVLKELV--KTDIAITTAL-IPG-K-------PA- 106 : : :::::::: ::::::::::: :::::::::: ::: : :: d1db3a_ 33 R--------P--KFHLHYGDLSDTSNLTRILREVQPDEVYNLGAMSHVAVSFESPEYTAD 82 d1l7da1 107 -PV-LIT--EEMVTKM-K-PGSVIIDLAV--E------------------------AGGN 134 :: ::: ::::::: : :::::::::: : :::: d1db3a_ 83 VDAMGTLRLLEAIRFLGLEKKTRFYQASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYA 142 d1l7da1 135 CPLSEPGKIVVKHGVKIVGHT--------------------------------------- 155 ::::: :::::::::::::: d1db3a_ 143 YWITV--NYRESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMD 200 d1l7da1 156 ---------------------------NVPS----------------------------- 159 :::: d1db3a_ 201 SLRDWGHAKDYVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVE 260 d1l7da1 160 -------------------------------------------------R---------- 160 : d1db3a_ 261 EKGIVVSVTGHDAPGVKPGDVIIAVDPRYFRPAEETLLGDPTKAHEKLGWKPEITLREMV 320 d1l7da1 161 --------------- 161 d1db3a_ 321 SEMVANDLEAAKKHS 335 HHsearch alignment (Probability: 0.93 E-value:0.00) d1l7da1 30 ARVLVFGV-GVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVKKQAEAVLKE 88 :::::::: :::::::::::::::::::::::::::: :::::::::::::: d1db3a_ 2 KVALITGVTGQDGSYLAEFLLEKGYEVHGIKRPKFHL---------HYGDLSDTSNLTRI 52 d1l7da1 89 LVKT--DIAITTALIPG---K-PAPV-------LITEEMVTKMK-----PGSVIIDLAVE 130 :::: ::::::::::: : :::: ::::::::::: ::::::::::: d1db3a_ 53 LREVQPDEVYNLGAMSHVAVSFESPEYTADVDAMGTLRLLEAIRFLGLEKKTRFYQASTS 112 d1l7da1 131 A-------GGNCPLSEPGKI 143 : :::::::::::: d1db3a_ 113 ELYGLVQEIPQKETTPFYPR 132