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 | d1kyha_ | Hypothetical protein YxkO | Ribokinase-like | Ribokinase-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 <-- 1.200 --> HitDALI alignment (Z-score: 5.0 Raw score:517.70) d1l7da1 1 agyravidgayefarafpmmmTAAGTV--PPARVLVFGV----GVAGLQAIATAKRLGA- 53 :::::: :::::::::: :::::::::::::::: d1kyha_ 1 ------------nvpfwteehVRATLPerTYGTALLLAGsddmPGAALLAGLGAMRSGLg 48 d1l7da1 54 VVMATDvRAATKEQVE--SLGGKFITvkkqaeavlkelVKTDIAIT--TALIpgkPAPV- 108 :::::: ::::::::: :::::::: :::::::: :::: :::: d1kyha_ 49 KLVIGT-SENVIPLIVpvLPEATYWRdgwkkaadaqleETYRAIAIgpGLPQ--tESVQq 105 d1l7da1 109 LITEeMVTKMkpgSVIIDL--AVEAggncplsepgkiVVKHGVKIVGHTN---------- 156 :::: ::::: :::::: :::: ::::::::::::: d1kyha_ 106 AVDH-VLTAD---CPVILDagALAK----------rtYPKREGPVILTPHpgeffrmtgv 151 d1l7da1 157 ------------------------VPSR-------------------------------- 160 :::: d1kyha_ 152 pvnelqkkraeyakewaaqlqtviVLKGnqtviafpdgdcwlnptgngalakggtgdtlt 211 d1l7da1 161 --------------------------------------------------------- 161 d1kyha_ 212 gmilgmlcchedpkhavlnavylhgacaelwtdehsahtllahelsdilprvwkrfe 268 FAST alignment (Normalized score: 3.85 Raw score:797.20) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGT----------------VPPARVLVFGV-----GV 39 :::::::::: :: d1kyha_ 1 --------------------------NVPFWTEEHVRATLPERTYGTALLLA-GSDDMPG 33 d1l7da1 40 AGLQAIATAKRLG-AVVMATDVRAATKEQVES--LGGKFITVKKQAEAVLKEL------- 89 ::::::::::::: ::::::: :::::::::: ::::: d1kyha_ 34 AALLAGLGAMRSGLGKLVIGT-SENVIPLIVPVLPEATY--------------WRDGWKK 78 d1l7da1 90 -------VKTDIAITTAL----IPGKPAPVLI------TEEMVTKMK-PGSVIIDLAVEA 131 ::::::: :::: ::::: ::::::: d1kyha_ 79 AADAQLEETYRAIA----IGPGLPQT------ESVQQAVDHVL----TADCPVIL----- 119 d1l7da1 132 GGNCPLSEP-------GKIVVK-HGVKIVGHTNVPSR----------------------- 160 :::: :::::::: d1kyha_ 120 ---------DAGALAKRTYP--KREGPVILT------PHPGEFFRMTGVPVNELQKKRAE 162 d1l7da1 161 ------------------------------------------------------------ 161 d1kyha_ 163 YAKEWAAQLQTVIVLKGNQTVIAFPDGDCWLNPTGNGALAKGGTGDTLTGMILGMLCCHE 222 d1l7da1 161 ---------------------------------------------- 161 d1kyha_ 223 DPKHAVLNAVYLHGACAELWTDEHSAHTLLAHELSDILPRVWKRFE 268 TMalign alignment (TM-score: 0.57 Raw score:91.62) d1l7da1 1 ---------AGYRAVIDGAY--EFARAFPMMMTAAGTVPPARVLVFGV----GVAGLQAI 45 : ::: : : :::::::::: :::::::: d1kyha_ 1 NVPFWTEEH----------VRA--TLP-E-R-------TYGTALLLAGSDDMPGAALLAG 39 d1l7da1 46 ATAKRLGA-VVMATDVRAATKEQVES-L-GGKFITV--KKQA-EAVLKELVKTDIAITT- 98 :::::::: :::::: :::::::::: : ::::::: ::: :::::: :::::::: d1kyha_ 40 LGAMRSGLGKLVIGT-SENVIPLIVPVLPEATYWRDGW-KKAADAQLEE--TYRAIAIGP 95 d1l7da1 99 ALIPGKPA-PV-LITEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTN 156 ::: ::: :: ::: :::: :: :::::::::::: ::: :::::::::::: d1kyha_ 96 GLP--QTESVQQAVD-HVLT-AD--CPVILDAGALAK-RTY-------PKREGPVILTPH 141 d1l7da1 157 -----------------------------------VPS--R------------------- 160 ::: : d1kyha_ 142 PGEFFRMTGVPVNELQKKRAEYAKEWAAQLQTVIVLKGNQTVIAFPDGDCWLNPTGNGAL 201 d1l7da1 161 ------------------------------------------------------------ 161 d1kyha_ 202 AKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAELWTDEHSAHTLLAHELSDILP 261 d1l7da1 161 ------- 161 d1kyha_ 262 RVWKRFE 268 HHsearch alignment (Probability: 0.61 E-value:0.00) d1l7da1 25 GTVPPARVLVFGV----GVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVKK 80 ::::::::::::: ::::::::::::::::::::::::::::::::::::::::::: d1kyha_ 15 PERTYGTALLLAGSDDMPGAALLAGLGAMRSGLGKLVIGTSENVIPLIVPVLPEATYWRD 74 d1l7da1 81 --QAEAVLKELVKTDIA 95 ::::::::::::::: d1kyha_ 75 GWKKAADAQLEETYRAI 91