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 | d1v6sa_ | Phosphoglycerate kinase | Phosphoglycerate kinase | Phosphoglycerate kinase | 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 <-- 0.766 --> HitDALI alignment (Z-score: 2.8 Raw score:316.70) d1xi3a_ 1 ------------------------------------------------------------ 1 d1v6sa_ 1 mrtlldldpkgkrvlvrvdynvpvqdgkvqdetrileslptlrhllaggaslvllshlgr 60 d1xi3a_ 1 ------------------------------------------------------------ 1 d1v6sa_ 61 pkgpdpkyslapvgealrahlpearfapfppgseearreaealrpgevlllenvrfepge 120 d1xi3a_ 1 ----------------------------------------------------------nl 2 d1v6sa_ 121 ekndpelsaryarlgeafvldafgsahrahasvvgvarllpayagflmekevralsrllk 180 d1xi3a_ 3 rnklKLYVITDRR-lkPEVESVREALEgGATAIQMRIK----------------NAPTRE 45 ::::::::: ::::::::::: :::::::::: :::::: d1v6sa_ 181 dperPYAVVLGGAkvsDKIGVIESLLP-RIDRLLIGGAmaftflkalggevgrsLVEEDR 239 d1xi3a_ 46 mYEIGKTLRQLTREYDALFFVDD----------------rvdvalavdadgvqLGPEdmp 89 :::::::::::::::::::::: :::: d1v6sa_ 240 -LDLAKDLLGRAEALGVRVYLPEdvvaaerieagvetrvfparaipvpymgldIGPK--- 295 d1xi3a_ 90 ievakeiapnlIIGAsvysleealeaekkgadylgagsvfptdarvigleglrkivesvk 149 :::: d1v6sa_ 296 ---------trEAFA--------------------------------------------- 301 d1xi3a_ 150 ipvvaigginkdnarevlktgvdgIAVIS------------------------------- 178 ::::: d1v6sa_ 302 -----------------ralegarTVFWNgpmgvfevppfdegtlavgqaiaalegaftv 344 d1xi3a_ 179 -------------------------avmGAEDVRKateelrkiveevlg 202 ::::::: d1v6sa_ 345 vgggdsvaavnrlglkerfghvstgggaSLEFLEK---gtlpglevleg 390 FAST alignment (Normalized score: 1.71 Raw score:480.90) d1xi3a_ 1 NLRNKL------------------------------------------------------ 6 d1v6sa_ 1 ------MRTLLDLDPKGKRVLVRVDYNVPVQDGKVQDETRILESLPTLRHLLAGGASLVL 54 d1xi3a_ 7 ------------------------------------------------------------ 7 d1v6sa_ 55 LSHLGRPKGPDPKYSLAPVGEALRAHLPEARFAPFPPGSEEARREAEALRPGEVLLLENV 114 d1xi3a_ 7 ------------------------------------------------------------ 7 d1v6sa_ 115 RFEPGEEKNDPELSARYARLGEAFVLDAFGSAHRAHASVVGVARLLPAYAGFLMEKEVRA 174 d1xi3a_ 7 ----------KLYVITDRRLK------PEVESVREALEGGATAIQMRIKNA--------- 41 :::::: ::::::::::: ::::::: d1v6sa_ 175 LSRLLKDPERPYAVVL-----GGAKVSDKIGVIESLLP-RIDRLLI-----GGAMAFTFL 223 d1xi3a_ 42 -----------PTREMYEIGKTLRQLTREYDALFFVDDRVDVALAVDADGVQLGPEDMPI 90 ::::::::::::::::::::::::: d1v6sa_ 224 KALGGEVGRSLVEEDRLDLAKDLLGRAEALGVRVYL------------------------ 259 d1xi3a_ 91 EVAKEIAPNLIIGASVYSLEEALEAEKKGADYLGAGSVFPTDARVIGLEGLRKIVESVKI 150 d1v6sa_ 260 ------------------------------------------------------------ 260 d1xi3a_ 151 PVVAIGGINKDNAREVLKTGVD-------------------------------------- 172 d1v6sa_ 260 ----------------------PEDVVAAERIEAGVETRVFPARAIPVPYMGLDIGPKTR 297 d1xi3a_ 173 ----------GIAVISAVMGAEDVRKATEELRKIVEEVLG-------------------- 202 :::: d1v6sa_ 298 EAFARALEGARTVF--------------------------WNGPMGVFEVPPFDEGTLAV 331 d1xi3a_ 203 ----------------------------------------------------------- 203 d1v6sa_ 332 GQAIAALEGAFTVVGGGDSVAAVNRLGLKERFGHVSTGGGASLEFLEKGTLPGLEVLEG 390 TMalign alignment (TM-score: 0.42 Raw score:84.58) d1xi3a_ 1 --------N---LRNKLKLYVITDRRLKPEVESVREALEGGATAIQMRIKNAPTREMYEI 49 : ::: : ::::: ::::::: :: : d1v6sa_ 1 MRTLLDLDPKGKRVL-V-RVDYN------------------------VPVQDGK-VQ--D 31 d1xi3a_ 50 GKTLRQLTREYDALF----------F-V-------------DDR-VDVALAVDADGVQLG 84 ::::: ::: :::: : : ::: :::::: :::::::: d1v6sa_ 32 ETRIL-ESL--PTLRHLLAGGASLVLLSHLGRPKGPDPKYSLAPVGEALRA-HLPEARFA 87 d1xi3a_ 85 PEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKKG---ADYLGAGSVFPTDARVI---GL 138 :: :::: :::::::::: :::::::: :::::: :: d1v6sa_ 88 PF------------------PPGS-EEARREAEALRPGEVLLLENV---RFEPGEEKNDP 125 d1xi3a_ 139 EGLRKIVESVKIPVVA-I--GGINKDNA--REV-LKTGVDGIA--V-------------- 176 ::::::: :::::::: : :::::: ::: ::::::::: : d1v6sa_ 126 ELSARYA-RLGEAFVLDAFG--SAHRAHASVVGVARLLPAYAGFLMEKEVRALSRLLKDP 182 d1xi3a_ 177 ------------------------------------------------------------ 177 d1v6sa_ 183 ERPYAVVLGGAKVSDKIGVIESLLPRIDRLLIGGAMAFTFLKALGGEVGRSLVEEDRLDL 242 d1xi3a_ 177 ------------------------------------------------------------ 177 d1v6sa_ 243 AKDLLGRAEALGVRVYLPEDVVAAERIEAGVETRVFPARAIPVPYMGLDIGPKTREAFAR 302 d1xi3a_ 177 ------------------------------------------------------------ 177 d1v6sa_ 303 ALEGARTVFWNGPMGVFEVPPFDEGTLAVGQAIAALEGAFTVVGGGDSVAAVNRLGLKER 362 d1xi3a_ 177 -----ISAVMGAEDVRKA--TEEL-RKIVEEVLG 202 :::::::::: ::: ::::::: d1v6sa_ 363 FGHVS---TGGGASLEFLEK-GTLPGLEVLEG-- 390 HHsearch alignment (Probability: 0.74 E-value:0.00) d1xi3a_ 13 DRRLKPEVESVREALEGGATAIQMRIKNA----PT-REMYEIGKTLRQLTREYDALFFVD 67 ::::::::::::::::::::::::::::: :: :::::::::::::: ::::::: d1v6sa_ 32 ETRILESLPTLRHLLAGGASLVLLSHLGRPKGPDPKYSLAPVGEALRAHL---PEARFAP 88 d1xi3a_ 68 DRV--DVA----LAVDADGVQLGPEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKKGAD 121 ::: ::: :::::::::: ::::::::: ::::::::::: :::::: d1v6sa_ 89 FPPGSEEARREAEALRPGEVLL------LENVRFEPG-----EEKNDPELSAR-YARLGE 136 d1xi3a_ 122 YLGA---GSV-------------FPTDA---RVIGLEGLRKIVESVKIPVVA-IGGINKD 161 :::: ::: ::::: ::::::::::::::::::::: ::::::: d1v6sa_ 137 AFVLDAFGSAHRAHASVVGVARLLPAYAGFLMEKEVRALSRLLKDPERPYAVVLGGAKVS 196 d1xi3a_ 162 NAREVL---KTGVDGIAVISAVMG 182 :::::: ::::::::::::::: d1v6sa_ 197 DKIGVIESLLPRIDRLLIGGAMAF 220