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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1xi3a_ | Thiamin phosphate synthase | Thiamin phosphate synthase | TIM beta/alpha-barrel | α/β |
| Hit | d1o14a_ | Putative sugar kinase TM0828 | Ribokinase-like | Ribokinase-like | α/β |
Query <-- 0.898 --> IntermediateDALI alignment (Z-score: 9.4 Raw score:847.60) query 1 --mietpyylidkakltRNMERIAHVREKSGAKALLAlKCFATWSV-FDLM---RDYM-- 52 :::::::::::::::::::: :::::::: :::: :::: d1xi3a_ 1 nlrnklklyvitdrrlkPEVESVREALEGGATAIQMR-IKNAPTREmYEIGktlRQLTre 59 query 53 ----DGTTSsslfEVRLGrERFGK-ETHAYSvaygdnEIDEVVS----HADKIIFNSISQ 103 ::::: ::::: ::::: :::::: ::::::: :::::::::::: d1xi3a_ 60 ydalFFVDD----RVDVA-LAVDAdGVQLGP---edmPIEVAKEiapnLIIGASVYSLEE 111 query 104 LERFADKAagIARGLRLNPQ--RLGEWDVP--KVERVMDRINGFMIHnncenkdfglfdr 159 :::::::: :::::::::: :::::::: ::::::::::::::: d1xi3a_ 112 ALEAEKKG-aDYLGAGSVFPtdARVIGLEGlrKIVESVKIPVVAIGG------------i 158 query 160 MLGEIEErFGALiaRVDWVSLGG-GIHFtgddYPVDAFSARLRAFSDRYGvqiylepgea 218 ::::::: :::: ::::::::: :::: :::::::::::::::::: d1xi3a_ 159 NKDNARE-VLKT--GVDGIAVISaVMGA----EDVRKATEELRKIVEEVL---------- 201 query 219 sitksttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgksc 278 d1xi3a_ 202 ------------------------------------------------------------ 202 query 279 lagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvref 338 d1xi3a_ 202 ------------------------------------------------------------ 202 query 339 tyadyeqsls 348 d1xi3a_ 202 ---------g 202 FAST alignment (Normalized score: 3.44 Raw score:911.10) query 1 MIETPYY---------------------------------------LIDKAKLTRNMERI 21 :::::::::::::: d1xi3a_ 1 -------NLRNKLKLYVITDRRLKPEVESVREALEGGATAIQMRIKNAPTREMYEIGKTL 53 query 22 AHVREKSGAKALLALKCFATWSVFDLMRD-YMDGTTSSSLF--EVRLGRERFGKETHAYS 78 ::::::::::::: ::::::::: ::::::: ::: :::::::::: d1xi3a_ 54 RQLTREYDALFFV----DDRVDVALA---VDADGVQL-GPEDMPIEVAKEIAP------- 98 query 79 VAYGDNEIDEVVSHA---DKIIFNSISQLERFADKAAG---IARGLRLNPQRLGEW---- 128 :::::::::::::::: ::::: d1xi3a_ 99 ---------------NLIIGASVYSLEEALEAEK----KGADYLGA----------GSVF 129 query 129 -------DVPKVERVMDRINGFMIHNNCENKDFGL----------FDRMLGEIEERFGAL 171 :::::::::::: :::: :::::: d1xi3a_ 130 PTDARVIGLEGLRKIVESV----------------KIPVVAIGGINKDN----AREVLK- 168 query 172 IARVDWVSLGGGIHFTGDD--------YPVDAFSARLRAFSDRYGVQIYLEPGEASITKS 223 ::::::: :::::::::::::::: d1xi3a_ 169 -TGVDGIA-----------VISAVMGAEDVRKATEELRKIVEE----------------- 199 query 224 TTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDV 283 d1xi3a_ 200 ------------------------------------------------------------ 200 query 284 FGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADY 343 d1xi3a_ 200 ------------------------------------------------------------ 200 query 344 EQSLS--- 348 d1xi3a_ 200 -----VLG 202 TMalign alignment (TM-score: 0.41 Raw score:141.96) query 1 -----------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF-A-T 41 :::::::::::::::::::::::: : : d1xi3a_ 1 NLRNKLKLYVITDRRLK---------------PEVESVREALEGGATAIQMRIKNAPTRE 45 query 42 WSV-FDLMRDYM-----DGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVS-H-- 92 ::: :::::::: :::::: : ::::::::::::::: ::: :::::::: : d1xi3a_ 46 MYEIGKTLRQLTREYDALFFVDD---R-VDVALAVDADGVQLG-PED-MPIEVAKEIAPN 99 query 93 AD-KIIFNSISQLERFADKAAGIARGLRLNPQ--RLGEWDVPKVERVMDR-INGFMIHNN 148 :: :::::::::::::::::: :::::::::: :::::::::::::::: ::::::::: d1xi3a_ 100 LIIGASVYSLEEALEAEKKGA-DYLGAGSVFPTDARVIGLEGLRKIVESVKIPVVAIGGI 158 query 149 CENKDFGLFDRMLGEIEERFGALIARVDWVSLGGG-IHFTGDDYPVDAFSARLRAFSDRY 207 ::::::: :::: :::::::::: ::: ::::::::::::::::: d1xi3a_ 159 -----------NKDNARE-VLKT--GVDGIAVISAVMGA----EDVRKATEELRKIVEEV 200 query 208 GVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEG 267 :: d1xi3a_ 201 LG---------------------------------------------------------- 202 query 268 SHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRE 327 d1xi3a_ 203 ------------------------------------------------------------ 203 query 328 LDGSVRTVREFTYADYEQSLS 348 d1xi3a_ 203 --------------------- 203 HHsearch alignment (Probability: 0.58 E-value:0.01) query 6 YYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATW-------SVFDLMRDYMDGTTSS 58 ::::::::::::::::::::::::::::::::::::: :::::::::::::::: d1xi3a_ 8 LYVITDRRLKPEVESVREALEGGATAIQMRIKNAPTREMYEIGKTLRQLTREYDALFFVD 67 query 59 SLFEVRLGRERF-----------------GKETHAYSVAYGDNEIDEVVSHA-DKIIFNS 100 :::::::::::: ::::::::::::::::::::::: ::::::: d1xi3a_ 68 DRVDVALAVDADGVQLGPEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKKGADYLGAGS 127 query 101 I-------SQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKD 153 : ::::::::::::::::::: ::::::::::::::::::::: ::::::: d1xi3a_ 128 VFPTDARVIGLEGLRKIVESVKIPVVA---IGGINKDNAREVLKTGVDGIA--VISAVMG 182 query 154 FGLFDRMLGEIEERFGA 170 ::::::::::::::::: d1xi3a_ 183 AEDVRKATEELRKIVEE 199
Intermediate <-- 0.697 --> HitDALI alignment (Z-score: 3.4 Raw score:492.90) d1xi3a_ 1 nlrnklkLYVITDRRL-------------------------------------------- 16 ::::::::: d1o14a_ 1 -------MVLTVTLNPaldreifiedfqvnrlyrindlsktqmspggkginvsialsklg 53 d1xi3a_ 17 ------------------------------------------------------------ 17 d1o14a_ 54 vpsvatgfvggymgkilveelrkisklittnfvyvegetrenieiideknktitainfpg 113 d1xi3a_ 17 --------kpeVESVREALEgGATAIQMRIKNAPtREMYeIGKTLRQLTREYDALFFVDD 68 ::::::::: ::::::::::::: :::: :::::::::::::::::::: d1o14a_ 114 pdvtdmdvnhfLRRYKMTLS-KVDCVVISGSIPPgVNEG-ICNELVRLARERGVFVFVEQ 171 d1xi3a_ 69 ---RVDVALAV--DADGVQLGPE-------------dmpIEVAKEI-APNL-IIGAsvys 108 :::::::: :::::::::: ::::::: :::: :::: d1o14a_ 172 tprLLERIYEGpeFPNVVKPDLRgnhasflgvdlktfddYVKLAEKlAEKSqVSVV---- 227 d1xi3a_ 109 leEALEaekKGAD----------------------------------------------- 121 :::: :::: d1o14a_ 228 syEVKN---DIVAtregvwlirskeeidtshllgagdayvagmvyyfikhganflemakf 284 d1xi3a_ 122 ylgAGSVF--ptdARVIGLEGLRKIVESVKipvvaigginkdnarevlktgvdgiavisa 179 ::::: ::::::::::::::::: d1o14a_ 285 gfaSALAAtrrkeKYMPDLEAIKKEYDHFT------------------------------ 314 d1xi3a_ 180 vmgaedvrkateelrkiveevlg 202 d1o14a_ 315 ------------------vervk 319 FAST alignment (Normalized score: 1.92 Raw score:486.30) d1xi3a_ 1 NLRNKLKLYVITDRRLKPEVESVREALEGG------------------------------ 30 d1o14a_ 1 ------------------------------MVLTVTLNPALDREIFIEDFQVNRLYRIND 30 d1xi3a_ 31 ---------------------ATAIQMRIKNAPTREMYEIGKTLRQLTREYDALFFVDD- 68 :::::::: d1o14a_ 31 LSKTQMSPGGKGINVSIALSKLGVPSVAT------------------------------G 60 d1xi3a_ 69 ------------------------------------------------------------ 69 d1o14a_ 61 FVGGYMGKILVEELRKISKLITTNFVYVEGETRENIEIIDEKNKTITAINFPGPDVTDMD 120 d1xi3a_ 69 ---RVDVALAV---DADGVQLGPEDM-----------PIEVAKEIA---PNLIIGASVYS 108 ::::::: ::::::: :::::::: ::::::::: : d1o14a_ 121 VNHFLRRYKM-TLSKVDCVVI-----SGSIPPGVNEGICNELVRL-ARERGVFVFVEQ-T 172 d1xi3a_ 109 LEEALEAEKK--GADYLGAGSVFPTDARV---------------IGLEGLRKIVESVK-- 149 :::::::::: :::::: :::::::::::: d1o14a_ 173 PRLLERIYEGPEFPNVVK-----------PDLRGNHASFLGVDLKTFDDYVKLAEK--LA 219 d1xi3a_ 150 ---IPVVAIGGINKDNAREVLKTGVDGIAVISAVMGAEDVRKATEELRKIVEEVLG---- 202 ::::::: d1o14a_ 220 EKSQVSVVSY----------------------------------------------EVKN 233 d1xi3a_ 203 ------------------------------------------------------------ 203 d1o14a_ 234 DIVATREGVWLIRSKEEIDTSHLLGAGDAYVAGMVYYFIKHGANFLEMAKFGFASALAAT 293 d1xi3a_ 203 -------------------------- 203 d1o14a_ 294 RRKEKYMPDLEAIKKEYDHFTVERVK 319 TMalign alignment (TM-score: 0.47 Raw score:94.39) d1xi3a_ 1 -----------------------------------------NLRNKLKLYVITDR-RLKP 18 :::: :: d1o14a_ 1 MVLTVTLNPALDREIFIEDFQVNRLYRINDLSKTQMSPGGK----------GINVS--IA 48 d1xi3a_ 19 EVESVREALEGGATAIQMRI--K-------NAPTRE-MYEIGK----------------- 51 :: ::: : ::::: : :::::: :::::: d1o14a_ 49 LS-KLG--V------PSVATGFVGGYMGKILVEELRKISKLITTNFVYVEGETRENIEII 99 d1xi3a_ 52 ---------------------------TLRQLTREYDALFFVDDRVDVALAVDADGVQLG 84 :::::::::::::::: d1o14a_ 100 DEKNKTITAINFPGPDVTDMDVNHFLR-----------------RYKMTLSKVDCVVISG 142 d1xi3a_ 85 PED------MPIEVAKEIA-PNLIIGASVYSLEEALEAEKK--GADYLGAGSVFPTDARV 135 ::: :::::::::: ::::::::::: ::::::::: ::::::::: : ::: d1o14a_ 143 SIPPGVNEGICNELVRLARERGVFVFVEQTP-RLLERIYEGPEFPNVVKPDL--R--GNH 197 d1xi3a_ 136 -------IGLE-GLRKIVESV-K-I-PVVAIGGINKDNAREVLKT----GV--------- 171 :::: ::::::::: : : :::::::: :: :::: :: d1o14a_ 198 ASFLGVDLKTFDDYVKLAEKLAEKSQVSVVSYEV---KN--DIVATREGVWLIRSKEEID 252 d1xi3a_ 172 --------------------------D--GI-AV-ISAVMGAE-----DVRKATEELRKI 196 : :: :: :::::::: :::::::::::: d1o14a_ 253 TSHLLGAGDAYVAGMVYYFIKHGANFLEMAKFGFASALAATRRKEKYMPDLEAIKKEYDH 312 d1xi3a_ 197 VEEVLG- 202 :::::: d1o14a_ 313 FTVERVK 319 HHsearch alignment (Probability: 0.01 E-value:0.47) d1xi3a_ 117 KKGADYLGAGSVFPTDARVIGLEGLRKIVESVKIP 151 ::::::::::::::::::::::::::::::::::: d1o14a_ 132 LSKVDCVVISGSIPPGVNEGICNELVRLARERGVF 166