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 | d1lhpa_ | Pyridoxal kinase | 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 <-- 0.976 --> HitDALI alignment (Z-score: 5.1 Raw score:443.90) d1l7da1 1 agyravidgayefarafpmmmtaagtvpPARVLVFGVG-----VAGLQAIATAKRLGAVV 55 :::::::::: ::::::::::::::::: d1lhpa_ 1 ----------------------------ECRVLSIQSHvvrgyVGNRAATFPLQVLGFEV 32 d1l7da1 56 MATD-VRAAtkeqveslggkfitvkKQAEAVLK-----elVKTDIAITTALIpgkpaPVL 109 :::: :::: :::::::: :::::::::::: ::: d1lhpa_ 33 DAVNsVQFS-nhtgyshwkgqvlnsDELQELYDglklnhvNQYDYVLTGYTR-dksfLAM 90 d1l7da1 110 ITeEMVTKM---KPGSVIIDLAVE-----------------aggncPLSEpgkivvkhgv 149 :: :::::: :::::::::::: :::: d1lhpa_ 91 VV-DIVQELkqqNPRLVYVCDPVMgdqrngegamyvpddllpvyreKVVP---------v 140 d1l7da1 150 KIVGHTN----------------------------------VPSR--------------- 160 ::::::: :::: d1lhpa_ 141 ADIITPNqfeaelltgrkihsqeealevmdmlhsmgpdtvvITSSnllsprgsdylmalg 200 d1l7da1 161 ------------------------------------------------------------ 161 d1lhpa_ 201 sqrtrgsvvtqrirmemhkvdavfvgtgdlfaamllawthkhpnnlkvacektvsamhhv 260 d1l7da1 161 ---------------------------------------------- 161 d1lhpa_ 261 lqrtikcakaksgegvkpspaqlelrmvqskkdiespeivvqatvl 306 FAST alignment (Normalized score: 1.96 Raw score:432.60) d1l7da1 1 A----------------------------------------------------------G 2 : d1lhpa_ 1 -ECRVLSIQSHVVRGYVGNRAATFPLQVLGFEVDAVNSVQFSNHTGYSHWKGQVLNSDEL 59 d1l7da1 3 YRAVIDGAYEFARAFPMMMTAAGTVPP------ARVLVFGV------GVAGLQAIATAKR 50 ::::::::: ::::::: ::::::::::::: d1lhpa_ 60 QELYDGLKL------------------NHVNQYDYVLTGY-TRDKSFLAMVVDIVQELKQ 100 d1l7da1 51 --LGAVVMATDV-----------------RAATK-EQVESLG--GKFITVKK-------- 80 ::::::::: ::::: ::::: ::::: d1lhpa_ 101 QNPRLVYVCDP-VMGDQRNGEGAMYVPDDLLPVYREKVVP--VADIITP---NQFEAELL 154 d1l7da1 81 ------------------------------------------------------------ 81 d1lhpa_ 155 TGRKIHSQEEALEVMDMLHSMGPDTVVITSSNLLSPRGSDYLMALGSQRTRGSVVTQRIR 214 d1l7da1 81 ----------QAEAVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVE 130 :::::::::: d1lhpa_ 215 MEMHKVDAVFVGTGDLFAAM---------------------------------------- 234 d1l7da1 131 AGGNCPLSEPGKIVVKHGVKIVGHTNVPSR------------------------------ 160 d1lhpa_ 235 ------------------------------LLAWTHKHPNNLKVACEKTVSAMHHVLQRT 264 d1l7da1 161 ------------------------------------------ 161 d1lhpa_ 265 IKCAKAKSGEGVKPSPAQLELRMVQSKKDIESPEIVVQATVL 306 TMalign alignment (TM-score: 0.50 Raw score:80.54) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVG-----VAGLQAIATAKRLGAVV 55 :::::::::: ::::::::::::::::: d1lhpa_ 1 ----------------------------ECRVLSIQSHVVRGYVGNRAATFPLQVLGFEV 32 d1l7da1 56 MATDVRAAT----------------KEQVESLGGKFITVK--KQAEAVLK-ELVKTDIAI 96 ::::::::: : :::::::: ::::::::: d1lhpa_ 33 DAVNSVQFSNHTGYSHWKGQVLNSD--------------ELQELYDGLKLNHVNQYDYVL 78 d1l7da1 97 TTALIPGKPAPV-LITEEMVTKM--KPGSVIIDLAVE---------------AG--GNCP 136 ::::: ::::: :::::::::: :::::::::::: :: :::: d1lhpa_ 79 TGYTR--DKSFLAMVVDIVQELKQQNPRLVYVCDPVMGDQRNGEGAMYVPDDLLPVYREK 136 d1l7da1 137 LSEPGKIVVKHGVKIVGHTN----------------------------------VPS--- 159 ::: : ::::::: ::: d1lhpa_ 137 VVP------V---ADIITPNQFEAELLTGRKIHSQEEALEVMDMLHSMGPDTVVITSSNL 187 d1l7da1 160 ----------R------------------------------------------------- 160 : d1lhpa_ 188 LSPRGSDYLMALGSQRTRGSVVTQRIRMEMHKVDAVFVGTGDLFAAMLLAWTHKHPNNLK 247 d1l7da1 161 ----------------------------------------------------------- 161 d1lhpa_ 248 VACEKTVSAMHHVLQRTIKCAKAKSGEGVKPSPAQLELRMVQSKKDIESPEIVVQATVL 306 HHsearch alignment (Probability: 0.01 E-value:0.40) d1l7da1 87 KELVKTDIA 95 ::::::::: d1lhpa_ 136 KVVPVADII 144