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 | d1psda2 | Phosphoglycerate dehydrogenase | Formate/glycerate dehydrogenase catalytic domain-like | Flavodoxin-like | 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 <-- 1.101 --> HitDALI alignment (Z-score: 6.5 Raw score:438.50) d1l7da1 1 agyravidgayefarAFPmmmtaagtvppARVLVFGVgvAGLQAIATAKRLGA-VVMATD 59 ::: :::::::: :::::::::::::: :::::: d1psda2 1 --------------eKDK-----------IKFLLVEG--VHQKALESLRAAGYtNIEFHK 33 d1l7da1 60 VraatkeqveslggkfitvkkQAEAVLKELVKTDIAITTAlipgkpaPVLITEEMVTKMK 119 : ::::::::::::::::::: ::::::::::::: d1psda2 34 G------------------alDDEQLKESIRDAHFIGLRS-------RTHLTEDVINAAE 68 d1l7da1 120 pgSVIIDLAvEAGGNCPLsepgkivVKHGVKIVGHTNVPS-------------------- 159 ::::::: :::::::: ::::::::::::::: d1psda2 69 klVAIGCFC-IGTNQVDL----daaAKRGIPVFNAPFSSTqeaqeniglevagklikysd 123 d1l7da1 160 --------r 160 d1psda2 124 ngstlsavn 132 FAST alignment (Normalized score: 5.45 Raw score:791.70) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP---PARVLVFGVGVA---GLQAIATAKRLG-A 53 ::::::: :::::::::::: : d1psda2 1 ----------------------------EKDKIKFLLV-----EGVHQKALESLRAAGYT 27 d1l7da1 54 VVMATDVRAATKEQVESLGGKFITVKK----QAEAVLKELVKTDIAITTALIPGKPAPV- 108 ::::: ::::::::::::::::: d1psda2 28 NIEFH----------------------KGALDDEQLKESIRDAHFIGL-----------R 54 d1l7da1 109 ---LITEEMVTKMKPG-SVIIDLAVEAGGNCPLSEPGKIV------------VKHGVKIV 152 ::::::::: ::: :::::: :::::::: d1psda2 55 SRTHLTEDVINA-AEKLVAIGCF-----------------CIGTNQVDLDAAAKRGIPVF 96 d1l7da1 153 GHTNVPSR-------------------------------- 160 :::: d1psda2 97 NAPF----SSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN 132 TMalign alignment (TM-score: 0.35 Raw score:56.03) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQ-AIATAKR---LGAVVM 56 : :: :::::: ::: ::: : ::::: :::::: d1psda2 1 ---------------E-KD---------KIKFLL-VEG--VHQKA-LESLRAAGYTNIEF 31 d1l7da1 57 ATDVRAATKEQVESLGGKFITV------------------KKQA-EAVLKELVKTDIAIT 97 : ::: :::: ::: :::::: :::::::: d1psda2 32 H-----KGA---------LDDEQLKESIRDAHFIGLRSRT-HLTEDVINAA-EKLVAIGC 75 d1l7da1 98 TALIPGKPAPV-LITEEMVTKMKPGSVIIDLAVEA-------------------GGNCPL 137 ::: ::: :::::::::: :::::: ::: d1psda2 76 FCI-----GTNQVDLDAAAKRG---IPVFNA-PFSSTQEAQENIGLEVAGKLIK------ 120 d1l7da1 138 SEPGKIVV---KHGVKIVGH--TNVPSR 160 : :::::: d1psda2 121 -------YSDN---GSTLSAVN------ 132 HHsearch alignment (Probability: 0.90 E-value:0.00) d1l7da1 53 AVVMATDV-RAATKEQVESLGGKFIT---VKKQAEAVLKELVKTDIAITTALIPGKPAPV 108 :::::::: ::::::::::::::::: :::::::::::::::::::::: :: d1psda2 5 IKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRS-------RT 57 d1l7da1 109 LITEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVPS 159 ::::::::::::::::::::::: ::::::::::::::::::::::: d1psda2 58 HLTEDVINAAEKLVAIGCFCIGT-----NQVDLDAAAKRGIPVFNAPFSST 103