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 | d1p91a_ | rRNA methyltransferase RlmA | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 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 <-- 1.004 --> HitDALI alignment (Z-score: 7.1 Raw score:583.10) d1l7da1 1 ------------------------------------------------------------ 1 d1p91a_ 1 sfscplchqplsreknsyicpqrhqfdmakegyvnllpvqhkrsrdpgdsaemmqarraf 60 d1l7da1 1 --------AGYRAVIDGAYEFARAFpmmmtaagtvppARVLVFGVGvagLQAIATAKRLG 52 ::::::::::::::::: ::::::::: ::::::::::: d1p91a_ 61 ldaghyqpLRDAIVAQLRERLDDKA------------TAVLDIGCG--eGYYTHAFADAL 106 d1l7da1 53 --AVVMATDVRAATK-EQVESL-GGKFITVkkqAEAVLKelVKTDIAITTAlipgkpapv 108 ::::::::::::: :::::: ::::::: :::::: :::::::::: d1p91a_ 107 peITTFGLDVSKVAIkAAAKRYpQVTFCVA-ssHRLPFS-dTSMDAIIRIY--------a 156 d1l7da1 109 LITEEMVTK-MKPGSVIIDLAVE----------aggncplsepgkiVVKHGvkivGHTNV 157 ::::::::: ::::::::::::: ::::: ::::: d1p91a_ 157 PCKAEELARvVKPGGWVITATPGprhlmelkgliynevhlhaphaeQLEGF-tlqQSAEL 215 d1l7da1 158 --------------------------------------------------psr 160 d1p91a_ 216 cypmrlrgdeavallqmtpfawrakpevwqtlaakevfdcqtdfnihlwqrsy 268 FAST alignment (Normalized score: 4.87 Raw score:1009.00) d1l7da1 1 ------------------------------------------------------------ 1 d1p91a_ 1 SFSCPLCHQPLSREKNSYICPQRHQFDMAKEGYVNLLPVQHKRSRDPGDSAEMMQARRAF 60 d1l7da1 1 --------AGYRAVIDGAYEFARAFPMMMTAAGTVPP----ARVLVFGVGVAG-LQAIAT 47 ::::::::::::: ::::::::: :::::: d1p91a_ 61 LDAGHYQPLRDAIVAQLRERL----------------DDKATAVLDIGCG---EGYYTHA 101 d1l7da1 48 AKR--LGAVVMATDVRAATKEQVES--LGGKFITVKKQAEAVLKEL----------VKTD 93 ::: :::::::::::::::::::: ::::::: :::: d1p91a_ 102 FADALPEITTFGLDVSKVAIKAAAKRYPQVTFCV------------ASSHRLPFSDTSMD 149 d1l7da1 94 IAITTALIPGKPAPV---LITEEMVT-KMKPGSVIIDLAVEAGGNCPLSEPGK------- 142 :::: :::::::: :::::::::: d1p91a_ 150 AIIR-----------IYAPCKAEELARVVKPGGWVIT----------------ATPGPRH 182 d1l7da1 143 ------------------IVVKHGVK-IVGHTNVPSR----------------------- 160 :::::::: :::: d1p91a_ 183 LMELKGLIYNEVHLHAPHAEQLEGFTLQQSA------ELCYPMRLRGDEAVALLQMTPFA 236 d1l7da1 161 -------------------------------- 161 d1p91a_ 237 WRAKPEVWQTLAAKEVFDCQTDFNIHLWQRSY 268 TMalign alignment (TM-score: 0.60 Raw score:96.61) d1l7da1 1 ------------------------------------------------------------ 1 d1p91a_ 1 SFSCPLCHQPLSREKNSYICPQRHQFDMAKEGYVNLLPVQHKRSRDPGDSAEMMQARRAF 60 d1l7da1 1 --------AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKR-L 51 ::::::::::::: :: : ::::::::::: ::: :::::: : d1p91a_ 61 LDAGHYQPLRDAIVAQLRERL-DD----------K-ATAVLDIGCGE-GYY-THAFADAL 106 d1l7da1 52 G-AVVMATDVRAATKEQVE-SL-GGKFITVKKQAEAVLKELVKTDIAITTALIPGKPAPV 108 : ::::::::::::::::: :: ::::::: :::: ::::::::::::::: :: d1p91a_ 107 PEITTFGLDVSKVAIKAAAKRYPQVTFCVA-SSHR-LPFSDTSMDAIIRIY-------AP 157 d1l7da1 109 LITEEMVTK-MKPGSVIIDLAVEA------------------GG-NCPLSEPGKIVVKHG 148 : ::::::: :::::::::::::: :: ::: ::: d1p91a_ 158 C-KAEELARVVKPGGWVITATPGPRHLMELKGLIYNEVHLHAPHA--EQL-------EGF 207 d1l7da1 149 VKIVGHTNVP----------------------------------------S--R------ 160 :::::::::: : : d1p91a_ 208 TLQQSAELCYPMRLRGDEAVALLQMTPFAWRAKPEVWQTLAAKEVFDCQTDFNIHLWQRS 267 d1l7da1 161 - 161 d1p91a_ 268 Y 268 HHsearch alignment (Probability: 0.94 E-value:0.00) d1l7da1 26 TVPPARVLVFGVGVAGLQAIATAKR-LGAVVMATDVRAATKEQVESLGGKFITVKKQAEA 84 :::::::::::::: :::::::::: :::::::::::::::::::::::::::::::::: d1p91a_ 82 DDKATAVLDIGCGE-GYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHR 140 d1l7da1 85 VLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAG 132 :::::::::::: :::::: ::::::::::::::::::::::: d1p91a_ 141 LPFSDTSMDAII-RIYAPC------KAEELARVVKPGGWVITATPGPR 181