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 | d1trba1 | Thioredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1j5va_ | 2-keto-3-deoxygluconate kinase | Ribokinase-like | Ribokinase-like | α/β |
Query <-- 1.208 --> IntermediateDALI alignment (Z-score: 4.0 Raw score:393.90) query 1 -gmenkKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCafwGLLLlrdpekasqedk 59 :::::: :::::::::::::::::::::: :::: d1trba1 1 gttkhsKLLILG------sGPAGYTAAVYAARANLQPVLIT---GMEK------------ 39 query 60 slyeqafssltpreaeELPLskmnlggigKKMLleMMKEE-----kapKLSDLLSGARKK 114 :::: :::: ::::: :::::::::::: d1trba1 40 -------------ggqLTTT---------TEVE--NWPGDpndltgplLMERMHEHATKF 75 query 115 EVKFY-AXQLsveimgfkkeelfpevqiMDVKEYlknalESDLQLFI------------- 160 ::::: :::: :::::: :::::::: d1trba1 76 ETEIIfDHIN------kvdlqnrpfrlnGDNGEY-----TCDALIIAtgasaryhspnta 124 query 161 ------------------------------------------------------------ 161 d1trba1 125 ifegqlelengyikvqsgihgnatqtsipgvfaagdvmdhiyrqaitsagtgcmaaldae 184 query 161 ----- 161 d1trba1 185 ryldg 189 FAST alignment (Normalized score: 3.91 Raw score:680.70) query 1 GMENK------KMNLLLFSGDYDK---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDP 51 :::: :::::::::::::::::::::::: d1trba1 1 -----GTTKHSKLLI---------LGSGPAGYTAAVYAARANLQPVLITGM--------- 37 query 52 EKASQEDKSLYEQAFSSLTPREAEE---LPLSKMNLGGIGKKM---LLEMMKEEKAP--- 102 :::: ::::: d1trba1 38 -------------------------EKGGQLT-----------TTTEVENW------PGD 55 query 103 --------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNA--- 151 ::::::::::::::::: ::::: d1trba1 56 PNDLTGPLLMERMHEHATKFETEII-------------------FDHIN--------KVD 88 query 152 --------------LESDLQLFI------------------------------------- 160 ::::::: d1trba1 89 LQNRPFRLNGDNGEYTCDALI--IATGASARYHSPNTAIFEGQLELENGYIKVQSGIHGN 146 query 161 ------------------------------------------- 161 d1trba1 147 ATQTSIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG 189 TMalign alignment (TM-score: 0.43 Raw score:69.20) query 1 -----GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKAS 55 ::::::: :::::::::::::::::::::::::: :: d1trba1 1 GTTKH----SKLLILG------SGPAGYTAAVYAARANLQPVLITGME--KG-------- 40 query 56 QEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKE------EKAPKLSDLLS 109 ::::: : :: : ::: :::: :::::::: d1trba1 41 ------------------GQLTT----T--TE-V-ENW-PGDPNDLTGP---LLMERMHE 70 query 110 GARKKEVKFYAXQLS------------VEIMGFKKEELFPEVQIMDVKEYLKNALESDLQ 157 ::::::::::::::: ::::: :: ::::: d1trba1 71 HATKFETEIIFDHINKVDLQNRPFRLN-----------------GDNGE--YT--CDALI 109 query 158 LFI--------------------------------------------------------- 160 ::: d1trba1 110 IATGASARYHSPNTAIFEGQLELENGYIKVQSGIHGNATQTSIPGVFAAGDVMDHIYRQA 169 query 161 -------------------- 161 d1trba1 170 ITSAGTGCMAALDAERYLDG 189 HHsearch alignment (Probability: 0.05 E-value:0.06) query 1 GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 :::::::::::::: :::::::::::::::::::: d1trba1 1 GTTKHSKLLILGSG-----PAGYTAAVYAARANLQPVLI 34
Intermediate <-- 1.367 --> HitDALI alignment (Z-score: 4.0 Raw score:527.30) d1trba1 1 gttkhSKLLILGSG-----------------------PAGYTAAVYAARANLQPVLITGm 37 ::::::::: :::::::::::::::::::::: d1j5va_ 1 --hhhMKVVTFGEImlrlsppdhkrifqtdsfdvtygGAEANVAAFLAQMGLDAYFVTK- 57 d1trba1 38 ekggqlttttevenwpgdpndltgPLLMERMHEHATKFETE-IIFD-------------- 82 ::::::::::::::::: :::: d1j5va_ 58 ---------------------lpnNPLGDAAAGHLRKFGVKtDYIArggnrigiyfleig 96 d1trba1 83 ---------hinkvdlqnrpfrlnGDNGEYT--CDALIIA-TGASaryHSPNTA------ 124 ::::::: ::::::: :::: :::::: d1j5va_ 97 asqrpskvvydrahsaiseakredFDWEKILdgARWFHFSgITPP--lGKELPLiledal 154 d1trba1 125 ----------------------------iFEGQLElengyikVQSGIH------------ 144 :::::: :::::: d1j5va_ 155 kvanekgvtvscdlnyrarlwtkeeaqkvMIPFME---yvdvLIANEEdiekvlgisnre 211 d1trba1 145 -----------------------------gnatqtsipgvfaagdvmdhiyrqaitsAGT 175 ::: d1j5va_ 212 ayakiaeevtrkynfktvgitlresisatvnywsvmvfengqphfsnryeihivdrvGAG 271 d1trba1 176 GCMAALDAERYLDG------------------------------------- 189 :::::::::::::: d1j5va_ 272 DSFAGALIYGSLMGfdsqkkaefaaaasclkhtipgdfvvlsieeieklas 322 FAST alignment (Normalized score: 3.81 Raw score:941.20) d1trba1 1 GTTKHS----KLLILGSG-------------------------PAGYTAAVYAARANLQP 31 :::::: ::::::::::::::::: d1j5va_ 1 ------HHHMKVVTFG--EIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDA 52 d1trba1 32 VLITGMEKGGQLTTTTEVENWPGDPNDLTG------PLLMERMHEHATKFETEIIFDHIN 85 :: :::::::::::::::::: d1j5va_ 53 YF----------------------------VTKLPNNPLGDAAAGHLRKFGVKT------ 78 d1trba1 86 -----------------------------------------KVDLQNRPFRLNGDNGE-- 102 :::: d1j5va_ 79 DYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDW-------------EK 125 d1trba1 103 --YTCDALIIATGASARYHSP---------NTAIFEGQLELENGYIKVQSGIHGNATQTS 151 ::::::::: ::::::: d1j5va_ 126 ILDGARWFHFS----------GITPPLGKELPLILED----------------------- 152 d1trba1 152 IP----------GVFAAGDVMDHIYRQAITS----------------------------- 172 :::: d1j5va_ 153 --ALKVANEKGVTVSC---------------DLNYRARLWTKEEAQKVMIPFMEYVDVLI 195 d1trba1 173 ------------------------------------------------------------ 173 d1j5va_ 196 ANEEDIEKVLGISNREAYAKIAEEVTRKYNFKTVGITLRESISATVNYWSVMVFENGQPH 255 d1trba1 173 -------------AGTGCMAALDAERYLDG------------------------------ 189 ::::::::::::::: d1j5va_ 256 FSNRYEIHIVDRVGAGDSFAGALIYGSL--MGFDSQKKAEFAAAASCLKHTIPGDFVVLS 313 d1trba1 190 --------- 190 d1j5va_ 314 IEEIEKLAS 322 TMalign alignment (TM-score: 0.48 Raw score:91.25) d1trba1 1 --GTTKHSKLLILGSG-----------------------PAGYTAAVYAARANLQPVLIT 35 :::::::::: ::::::::::::::::::::: d1j5va_ 1 HH----HMKVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVT 56 d1trba1 36 GMEKG--GQLTTTTEVENWPGDPNDLTGPLLMERMHEHATKFETEI-IFD---------- 82 ::: :: ::::::::::::::: ::: d1j5va_ 57 --KLPNN---------------------PL-GDAAAGHLRKFGVKTDYIARGGNRIGIYF 92 d1trba1 83 -----------------------HINK-VDLQNRPFRLNGDNGEYT-CDALIIA-TGASA 116 :::: :::::::: ::::::: ::::: d1j5va_ 93 LEIGASQRPSKVVYDRAHSAISEAKRED----------FDWEKILDGARWFHFSGITPPL 142 d1trba1 117 RYHSPN--TAI-FE--GQ-----L-E-------------LENGY--IK-----VQSG--- 142 : :::: ::: :: : : : ::::: :: :::: d1j5va_ 143 G-KELPLILEDALKVA-NEKGVTVSCDLNYRARLWTKEEAQKVMIPFMEYVDVLIANEED 200 d1trba1 143 ------------IH--GNA---TQ--TSIPGVF--------------------------- 156 :: : : ::::::: d1j5va_ 201 IEKVLGISNREAYAKI--AEEV-TRKYNFKTVGITLRESISATVNYWSVMVFENGQPHFS 257 d1trba1 157 --------AAGDVMDHIYRQAITSAGTGCMAALDAERYLDG------------------- 189 :::::::::::::::::::: d1j5va_ 258 NRYEIHIV-------------DRVGAGDSFAGALIYGSLMGFDSQKKAEFAAAASCLKHT 304 d1trba1 190 ------------------ 190 d1j5va_ 305 IPGDFVVLSIEEIEKLAS 322 HHsearch alignment (Probability: 0.46 E-value:0.01) d1trba1 14 GPAGYTAAVYAARANLQPVLIT 35 :::::::::::::::::::::: d1j5va_ 35 GGAEANVAAFLAQMGLDAYFVT 56