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 | d1hwxa1 | Glutamate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 2.120 --> HitDALI alignment (Z-score: 8.8 Raw score:752.70) d1l7da1 1 ------AGYRAVIDGAYEFA-----------RAFPmmmtaagtvpPARVLVFGVGVAGLQ 43 :::::::::::::: :::: ::::::::::::::: d1hwxa1 1 hgrisaTGRGVFHGIENFIEnasymsilgmtPGFG----------DKTFAVQGFGNVGLH 50 d1l7da1 44 AIATAKRLGAVV-MATDVRA----atkeQVESL--------ggkfitvkkQAEAVlkeLV 90 :::::::::::: ::::::: ::::: ::::: :: d1hwxa1 51 SMRYLHRFGAKCvAVGESDGsiwnpdgiDPKELedfklqhgtilgfpkakIYEGS-ilEV 109 d1l7da1 91 KTDIAITTALipgkpaPVLITEEMVTKMKpgSVIIDLAVeagGNCPLsepgkivVKHGVK 150 :::::::::: ::::::::::::: :::::::: ::::: :::::: d1hwxa1 110 DCDILIPAAS------EKQLTKSNAPRVK-aKIIAEGAN---GPTTP-qadkifLERNIM 158 d1l7da1 151 IVGHT---NVPSR----------------------------------------------- 160 ::::: ::::: d1hwxa1 159 VIPDLylnAGGVTvsyfqilknlnhvsygrltfkyerdsnyhllmsvqeslerkfgkhgg 218 d1l7da1 161 ------------------------------------------------------------ 161 d1hwxa1 219 tipivptaefqdrisgasekdivhsglaytmersarqimrtamkynlgldlrtaayvnai 278 d1l7da1 161 --------------- 161 d1hwxa1 279 ekvfrvyneagvtft 293 FAST alignment (Normalized score: 4.88 Raw score:1057.00) d1l7da1 1 ------AGYRAVIDGAYEF------------ARAFPMMMTAAGTVP-PARVLVFGVGVAG 41 :::::::::::: :::: ::::::::::::: d1hwxa1 1 HGRISATGRGVFHGIENF-IENASYMSILGMTPGF-----------GDKTFAVQGFGNVG 48 d1l7da1 42 LQAIATAKRLGAV-VMATDVRAATKEQVESLGGKFITVKKQAEAVLKEL----------- 89 ::::::::::::: :::::: d1hwxa1 49 LHSMRYLHRFGAKCVAVGES-----------------------------DGSIWNPDGID 79 d1l7da1 90 -----------------------------VKTDIAITTALIPGKP-APVLITEEMVTKMK 119 ::::::::: :::::::::::: d1hwxa1 80 PKELEDFKLQHGTILGFPKAKIYEGSILEVDCDILIPA-------ASEKQLTKSNAPR-- 130 d1l7da1 120 PG---SVIIDLAVEAGGNCPLSEPGKIV-------------VKHGVKIVGHTNVPSR--- 160 :::::: ::::::::: d1hwxa1 131 --VKAKIIAEG-----------------ANGPTTPQADKIFLERNIMVIP-------DLY 164 d1l7da1 161 ------------------------------------------------------------ 161 d1hwxa1 165 LNAGGVTVSYFQILKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVP 224 d1l7da1 161 ------------------------------------------------------------ 161 d1hwxa1 225 TAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRV 284 d1l7da1 161 --------- 161 d1hwxa1 285 YNEAGVTFT 293 TMalign alignment (TM-score: 0.62 Raw score:99.88) d1l7da1 1 ------AGYRAVIDGAYEF-----A------RAFPMMMTAAGTVPPARVLVFGVGVAGLQ 43 ::::::::::::: : :::: ::::::::::::::: d1hwxa1 1 HGRISATGRGVFHGIENFIENASYMSILGMTPGFG----------DKTFAVQGFGNVGLH 50 d1l7da1 44 AIATAKRLGAVV-MATDVRA-ATK----EQVESLGG--------------KFITVKKQAE 83 :::::::::::: ::::::: :: :::::: ::::: : : d1hwxa1 51 SMRYLHRFGAKCVAVGESDGS-IWNPDG--IDPKELEDFKLQHGTILGFPKAKIY--E-G 104 d1l7da1 84 AVLKELVKTDIAITTALIPGKPAPVLITEEMVTK-MKPGSVIIDLAVEAGGNCPL-SE-- 139 :::: : :::::::::: : :::::::::: :: :::::::: ::::: :: d1hwxa1 105 SILE-V-DCDILIPAAS-----E-KQLTKSNAPRVKA--KIIAEGAN---GPTTPQADKI 151 d1l7da1 140 PGKIVVKHGVKIVGHT--NVP--S------------------------------------ 159 :::::::::::: ::: : d1hwxa1 152 ----FLERNIMVIPDLYLNAGGVTVSYFQILKNLNHVSYGRLTFKYERDSNYHLLMSVQE 207 d1l7da1 160 -----------------------------------------R------------------ 160 : d1hwxa1 208 SLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGL 267 d1l7da1 161 -------------------------- 161 d1hwxa1 268 DLRTAAYVNAIEKVFRVYNEAGVTFT 293 HHsearch alignment (Probability: 0.97 E-value:0.00) d1l7da1 22 TAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMA-TD----------VRAATKEQVES 70 :::::::::::::::::::::::::::::::::::: :: ::::::::::: d1hwxa1 29 GMTPGFGDKTFAVQGFGNVGLHSMRYLHRFGAKCVAVGESDGSIWNPDGIDPKELEDFKL 88 d1l7da1 71 LGGKFITVKKQAE-AVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAV 129 ::::::::::::: ::::::::::::::::: :::::::::::::::::: d1hwxa1 89 QHGTILGFPKAKIYEGSILEVDCDILIPAAS------EKQLTKSNAPRVKAKIIA----- 137 d1l7da1 130 EAGGNCPLSEP-GKIVVKHGVKI 151 :::::::::: ::::::::::: d1hwxa1 138 -EGANGPTTPQADKIFLERNIMV 159