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 | d1l7da2 | Nicotinamide nucleotide transhydrogenase dI component | 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 <-- 2.065 --> HitDALI alignment (Z-score: 6.1 Raw score:515.00) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFG-------vgvaGLQAIATAKRLGA 53 ::::::: ::::::::::::: d1l7da2 1 -----------------------------MKIAIPKerrpgedrvaiSPEVVKKLVGLGF 31 d1l7da1 54 VVMAT--DVRA--ATKEQVESLGGKFITvkkqaeAVLKELVKTDIAITTalipgkpapvl 109 ::::: :::: ::::::::::::::: ::::::::::::::: d1l7da2 32 EVIVEqgAGVGasITDDALTAAGATIAS------TAAQALSQADVVWKV---------qr 76 d1l7da1 110 ITEE-----MVTKMKPGSVIIDLaveaggncplSEPG------kivVKHGVKIVGHT--- 155 :::: :::::::::::::: :::: ::::::::::: d1l7da2 77 PMTAeegtdEVALIKEGAVLMCH----------LGALtnrpvvealTKRKITAYAMElmp 126 d1l7da1 156 --------NVPSR----------------------------------------------- 160 ::::: d1l7da2 127 risraqsmDILSSqsnlvaadasplfaknllnfltphvdkdtktlvmkledetvsgtcvt 186 d1l7da1 161 -------- 161 d1l7da2 187 rdgaivhp 194 FAST alignment (Normalized score: 4.72 Raw score:832.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVA-------------GLQAIAT 47 ::::: ::::::: d1l7da2 1 -----------------------------MKIAI------PKERRPGEDRVAISPEVVKK 25 d1l7da1 48 AKRLGAVVMATDVRAA---------TKEQVESLGGKFITVKKQAE--AVLKELVKTDIAI 96 ::::::::::: :::::::::::: ::::::::::::: d1l7da2 26 LVGLGFEVIVE-----QGAGVGASITDDALTAAGATI--------ASTAAQALSQADVVW 72 d1l7da1 97 TTALIPGKPAPVLITE-----------EMVTKMKPGSVIID-LAVEAGGNCPLSEPGKIV 144 : :::::::::::::: :::: d1l7da2 73 K---------------VQRPMTAEEGTDEVALIKEGAVLMCHLGAL-------------- 103 d1l7da1 145 ---------VKHGVKIVGHTNVPSR----------------------------------- 160 :::::::::: d1l7da2 104 TNRPVVEALTKRKITAYAM------ELMPRISRAQSMDILSSQSNLVAADASPLFAKNLL 157 d1l7da1 161 ------------------------------------- 161 d1l7da2 158 NFLTPHVDKDTKTLVMKLEDETVSGTCVTRDGAIVHP 194 TMalign alignment (TM-score: 0.52 Raw score:83.42) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG------VGVAGL-QAIATAKRLGA 53 ::::::: :::::: ::::::::::: d1l7da2 1 -----------------------------MKIAIPKERRPGEDRVAISPEVVKKLVGLGF 31 d1l7da1 54 VVMAT--DVR--AATKEQVESLGGKFITVKKQAEAVLKELVKTDIAITTALIPGKPAPVL 109 ::::: ::: :::::::::::::::: ::::::::::::::: : : d1l7da2 32 EVIVEQGAGVGASITDDALTAAGATIAS------TAAQALSQADVVWKV-------Q-R- 76 d1l7da1 110 ITE-----EMVTKMKPGSVIIDLAVEAGG--NCPLSE-PGKIVVKHGVKIVGHTNV---- 157 ::: :::::::::::::: :::::: :::: :::::::::::::: d1l7da2 77 PMTAEEGTDEVALIKEGAVLMC-HLGALTNR--PVVEA----LTKRKITAYAMELMPRIS 129 d1l7da1 158 -PS-R------------------------------------------------------- 160 :: : d1l7da2 130 RAQSMDILSSQSNLVAADASPLFAKNLLNFLTPHVDKDTKTLVMKLEDETVSGTCVTRDG 189 d1l7da1 161 ----- 161 d1l7da2 190 AIVHP 194 HHsearch alignment (Probability: 0.97 E-value:0.00) d1l7da1 44 AIATAKRLGAVVMATDVRAATK----EQVESLGGKFITVKKQAEAVLKELVKTDIAITTA 99 :::::::::::::::::::::: :::::::::: ::::::::::::::: d1l7da2 22 VVKKLVGLGFEVIVEQGAGVGASITDDALTAAGATI------ASTAAQALSQADVVW--- 72 d1l7da1 100 LIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVP 158 :::::::::::::::::::::::::::::::::::::: :::::::::::::::: d1l7da2 73 -KVQRPMTAEEGTDEVALIKEGAVLMCHLGALTNRPVVE----ALTKRKITAYAMELMP 126