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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1l7da1 | Nicotinamide nucleotide transhydrogenase dI component | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1meoa_ | Glycinamide ribonucleotide transformylase, GART | Formyltransferase | Formyltransferase | α/β |
Query <-- 1.100 --> IntermediateDALI 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 <-- 1.863 --> HitDALI alignment (Z-score: 4.7 Raw score:435.30) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFG--vGVAGLQAiATAKR---LGAVV 55 ::::::: ::::::: ::::: ::::: d1meoa_ 1 -----------------------------ARVAVLIsgtGSNLQAL-IDSTRepnSSAQI 30 d1l7da1 56 -MATD-VRAA-TKEQVESLGGKFITV--------kKQAEAVLKELV--KTDIAITTAlip 102 :::: :::: ::::::::::::::: ::::::::::: ::::::::: d1meoa_ 31 dIVISnKAAVaGLDKAERAGIPTRVInhklyknrvEFDSAIDLVLEefSIDIVCLAG--- 87 d1l7da1 103 gkpAPVLiTEEMVTKMkpgSVIIDLA-------------------------veaggncPL 137 :::: :::::::: ::::::: :: d1meoa_ 88 --fMRIL-SGPFVQKW--nGKMLNIHpsllpsfkgsnaheqaletgvtvtgctvhfvaEA 142 d1l7da1 138 SEPgkivvkhgvkivGHTN----------------VPSR--------------------- 160 ::: :::: :::: d1meoa_ 143 GQI------------ILQEavpvkrgdtvatlserVKLAehkifpaalqlvasgtvqlge 190 d1l7da1 161 ------------ 161 d1meoa_ 191 ngkicwvkeehh 202 FAST alignment (Normalized score: 3.98 Raw score:715.20) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-----GVAGLQAIATAKR---LG 52 ::::: :::::::::::: :: d1meoa_ 1 -----------------------------ARVAV---LISGTGSNLQALIDSTR-EPNSS 27 d1l7da1 53 AV-VMATDVR--AATKEQVESLGGKFITVK----------KQAEAVLKELV--KTDIAIT 97 :: ::::::: :::::::::::::::: ::::::::::: ::::::: d1meoa_ 28 AQIDIVISNKAAVAGLDKAERAGIPTRV--INHKLYKNRVEFDSAIDLVLEEFSIDIVCL 85 d1l7da1 98 TALIPGKPAPV-----LITEEMVTKMKPGS---VIIDLAVEAGGNCPLSEPGKIVVKHGV 149 ::::::::: :::: d1meoa_ 86 -----------AGFMRILSGPFVQK-----WNGKMLN----------------------- 106 d1l7da1 150 KIVGHTNVPSR------------------------------------------------- 160 d1meoa_ 107 -----------IHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEAGQIILQEAVPVKR 155 d1l7da1 161 ----------------------------------------------- 161 d1meoa_ 156 GDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHH 202 TMalign alignment (TM-score: 0.51 Raw score:81.36) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG--VGVAGLQAIATAKR--L-GAVV 55 ::::::: :::::::::::::: : :::: d1meoa_ 1 -----------------------------ARVAVLISGTGSNLQALIDSTREPNSSAQID 31 d1l7da1 56 MATD-VRAAT-KEQVESLGGKFITV---KK-----QAEAVLKELV--KTDIAITTALIPG 103 :::: ::::: :::::::::::::: :: :::::::::: :::::::::: d1meoa_ 32 IVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGF--- 88 d1l7da1 104 KPAPVLITEEMVTKMKPGSVIIDLAV--E---AG-------------------GNCPLSE 139 :::::::::::: : :::::::: : :: ::::::: d1meoa_ 89 ---MRILSGPFVQKW-N-GKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEAG 143 d1l7da1 140 PGKIVVKHGVKIVGHTNV------------------PS--R------------------- 160 :: : :::: :: : d1meoa_ 144 --QI--------I-LQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENG 192 d1l7da1 161 ---------- 161 d1meoa_ 193 KICWVKEEHH 202 HHsearch alignment (Probability: 0.50 E-value:0.00) d1l7da1 30 ARVLVFGVGVAGLQAIATAK-----RLGAVVMA-TDVRA--ATKEQVESLGGKFITVKKQ 81 :::::::::: ::::::::: :::::::: ::::: ::::::::::::::::::: d1meoa_ 1 ARVAVLISGT-GSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHK 59 d1l7da1 82 --------AEAVLKELV--KTDIAITTALIPGKPAPVLITEEMVTKMKPGSVII 125 ::::::::: ::::::::: : ::::::::::::::::::: d1meoa_ 60 LYKNRVEFDSAIDLVLEEFSIDIVCLAG-F-----MRILSGPFVQKWNGKMLNI 107