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 | d1fmta2 | Methionyl-tRNAfmet formyltransferase | Formyltransferase | Formyltransferase | 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 <-- 1.792 --> HitDALI alignment (Z-score: 5.6 Raw score:474.00) d1l7da1 1 agyravidgayefarafpmmmtaagtVPPARVLVFGVGVAGLQAIATAKRLGAVV-MATD 59 ::::::::::::::::::::::::::::: :::: d1fmta2 1 --------------------------SESLRIIFAGTPDFAARHLDALLSSGHNVvGVFT 34 d1l7da1 60 VRA------aTKEQVESLGGKFITV-----KKQAEAVLKElvKTDIAITTAlipgkpaPV 108 ::: ::::::::::::::: :::::::::: ::::::::: :: d1fmta2 35 QPDrplmpspVKVLAEEKGLPVFQPvslrpQENQQLVAEL--QADVMVVVA------yGL 86 d1l7da1 109 LITEEMVTKMKpgSVIIDLA------vEAGG------------------ncPLSEPGKIv 144 ::::::::::: ::::::: :::: :::::::: d1fmta2 87 ILPKAVLEMPR--LGCINVHgsllprwRGAApiqrslwagdaetgvtimqmDVGLDTGD- 143 d1l7da1 145 vkhgvkivghtnVPSR-------------------------------------------- 160 :::: d1fmta2 144 ----------mlYKLScpitaedtsgtlydklaelgpqglittlkqladgtakpevqdet 193 d1l7da1 161 ------- 161 d1fmta2 194 lvtyaek 200 FAST alignment (Normalized score: 4.74 Raw score:847.60) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAV-VMATD 59 :::::::::::::::::::::::::::: ::::: d1fmta2 1 --------------------------SESLRIIFAGTPDFAARHLDALLSSGHNVVGVFT 34 d1l7da1 60 VR--------AATKEQVESLGGKFITVKKQ----AEAVLKELV--KTDIAITTALIPGKP 105 ::::::::::::::::: ::::::::: ::::::: d1fmta2 35 --QPDRPLMPSPVKVLAEEKGLPVFQP---VSLRPQENQQLVAELQADVMVV-------- 81 d1l7da1 106 APV-----LITEEMVTKMKPG-SVIIDLAVEAGGNCPLSEP------------------- 140 :::::::::: ::::: d1fmta2 82 ---VAYGLILPKAVLEMP---RLGCIN--------------VHGSLLPRWRGAAPIQRSL 121 d1l7da1 141 --------GKIVVKHGVK-----------IVGHT------------NVPSR--------- 160 :::: :::: :::: d1fmta2 122 WAGDAETGVTIM------QMDVGLDTGDMLYKL-SCPITAEDTSGTLYDK-LAELGPQGL 173 d1l7da1 161 --------------------------- 161 d1fmta2 174 ITTLKQLADGTAKPEVQDETLVTYAEK 200 TMalign alignment (TM-score: 0.53 Raw score:84.03) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKR-LGAVVMATD 59 ::: ::::::::::::::::::::: ::::::::: d1fmta2 1 --------------SES------------LRIIFAGTPDFAARHLDALLSSGHNVVGVFT 34 d1l7da1 60 VRA----AT--KEQVESLGGKFITVKKQ-AEAVLKELV--KTDIAITTALIPGKPAPVLI 110 ::: :: ::::::::::::::::: ::::::::: :::::::::: :::: d1fmta2 35 QPDRPLMPSPVKVLAEEKGLPVFQPVSLRPQENQQLVAELQADVMVVVAY------GLIL 88 d1l7da1 111 TEEMVTKMKPGSVIIDLA---V---EAG------------------G-NCPL-SEPGKIV 144 ::::::::: ::::::: : ::: : :::: ::: :: d1fmta2 89 PKAVLEMPR--LGCINVHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDTG-DM- 144 d1l7da1 145 VKHGVKIVGHTNV--------------P--S---R------------------------- 160 :::::: : : : d1fmta2 145 -------LYKLSCPITAEDTSGTLYDKLAELGPQGLITTLKQLADGTAKPEVQDETLVTY 197 d1l7da1 161 --- 161 d1fmta2 198 AEK 200 HHsearch alignment (Probability: 0.90 E-value:0.00) d1l7da1 28 PPARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAA-------TKEQVESLGGKFITVK- 79 :::::::::::::::::::::::::::::::::::: :::::::::::::::: d1fmta2 2 ESLRIIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRPLMPSPVKVLAEEKGLPVFQPVS 61 d1l7da1 80 KQAEAVLKELV--KTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLA 128 ::::::::::: :::::::: :::::::::::::::::::::::: d1fmta2 62 LRPQENQQLVAELQADVMVVV------AYGLILPKAVLEMPRLGCINVHGS 106