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 | d1s0aa_ | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA | PLP-dependent transferases | PLP-dependent transferases | 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 <-- 0.638 --> HitDALI alignment (Z-score: 3.2 Raw score:328.70) d1xi3a_ 1 ------------------------------------------------------------ 1 d1s0aa_ 1 mttddlafdqrhilhpftsmtsplpvypvvsaegcelilsdgrrlvdgmsswwaaihgyn 60 d1xi3a_ 1 ------------------------------------------------------------ 1 d1s0aa_ 61 hpqlnaamksqidamshvmfggithapaielcrklvamtpqplecvfladsgsvavevam 120 d1xi3a_ 1 ----NLRN----kLKLYVITDR-------------------------------------- 14 :::: ::::::::: d1s0aa_ 121 kmalQYWQakgeaRQRFLTFRNgyhgdtfgamsvcdpdnsmhslwkgylpenlfapapqs 180 d1xi3a_ 15 ----rlkpeVESVREALEGG---ATAIQMR--IKNA---PTREmYEIGKTLRQLTREYDA 62 ::::::::::: ::::::: :::: :::: :::::::::::::::: d1s0aa_ 181 rmgewderdMVGFARLMAAHrheIAAVIIEpiVQGAggmRMYH-PEWLKRIRKICDREGI 239 d1xi3a_ 63 LFFVDD---------rvDVAL--AVDADGVQLgpeDMPIEV-akeiaPNLI--------- 101 :::::: :::: ::::::::: :::::: :::: d1s0aa_ 240 LLIADEiatgfgrtgklFACEhaEIAPDILCL---GXALTGgtmtlsATLTtrevaetis 296 d1xi3a_ 102 -------------------------------igasvysleealeaekkgadylgagsvfp 130 d1s0aa_ 297 ngeagcfmhgptfmgnplacaaanaslailesgdwqqqvadievqlreqlapardaemva 356 d1xi3a_ 131 tdarvigleglrkivesvkipvvaigginkdnarevlktgvdgiavisavmgaedvrkat 190 d1s0aa_ 357 dvrvlgaigvvetthpvnmaalqkffveqgvwirpfgkliylmppyiilpqqlqrltaav 416 d1xi3a_ 191 eelrkiveevlg 202 d1s0aa_ 417 nravqdetffcq 428 FAST alignment (Normalized score: 2.24 Raw score:659.80) d1xi3a_ 1 NLRNK------------------------------------------------------- 5 d1s0aa_ 1 -----MTTDDLAFDQRHILHPFTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAA 55 d1xi3a_ 6 ------------------------------------------------------------ 6 d1s0aa_ 56 IHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVA 115 d1xi3a_ 6 ------------------LKLYVITDRRLKP----------------------------- 18 ::::::: d1s0aa_ 116 VEVAMKMALQYWQAKGEARQRFLTF------RNGYHGDTFGAMSVCDPDNSMHSLWKGYL 169 d1xi3a_ 19 -------------------EVESVREALE---GGATAIQMRI--------KNAPTREMYE 48 :::::::::: :::::::: ::::: ::: d1s0aa_ 170 PENLFAPAPQSRMGEWDERDMVGFARLMAAHRHEIAAVII--EPIVQGAGGMRMY--HPE 225 d1xi3a_ 49 IGKTLRQLTREYDALFFVDDRV-------------DVAL--AVDADGVQLGPEDMPIEVA 93 :::::::::::::::::: :::: ::::::::: d1s0aa_ 226 WLKRIRKICDREGILLIA----DEIATGFGRTGKLFACEHAEIAPDILCL---------- 271 d1xi3a_ 94 KEIAPNLIIGASV---------------------------------------YSLEEALE 114 :::::::: d1s0aa_ 272 -------------GAALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAA 318 d1xi3a_ 115 AEKKGADYLGAGSVFPTDARVIGLEGLRKIVESVKIPVVAIGGINKDNAREVLKTGVDGI 174 ::: d1s0aa_ 319 ANA--------------------------------------------------------- 321 d1xi3a_ 175 AVISAVMGAEDVRKATEELRKIVEEVLG-------------------------------- 202 d1s0aa_ 322 ----------------------------SLAILESGDWQQQVADIEVQLREQLAPARDAE 353 d1xi3a_ 203 ------------------------------------------------------------ 203 d1s0aa_ 354 MVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLT 413 d1xi3a_ 203 --------------- 203 d1s0aa_ 414 AAVNRAVQDETFFCQ 428 TMalign alignment (TM-score: 0.43 Raw score:86.45) d1xi3a_ 1 --------------------------------------------------NLRNKLKLYV 10 d1s0aa_ 1 MTTDDLAFDQRHILHPFTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMS---------- 50 d1xi3a_ 11 ITDRR-LK---------------------PEVE--SVR----E-ALE--GG--------- 30 :: :: : : : :: :: d1s0aa_ 51 ---SWWAAIHGYNHPQLNAAMKSQIDAMS---HVM--FGGITHA-PAIELCRKLVAMTPQ 101 d1xi3a_ 31 ----ATAIQMRIKNAPTREMYEIGKTL-RQLTREYDALFF-------------------- 65 :::::::: : : :::: d1s0aa_ 102 PLECVFLADSGS-----------V--AV--------EVAMKMALQYWQAKGEARQRFLTF 140 d1xi3a_ 66 ----VDDRVDVALAVDADGVQ--LGPE--D-M--PIEVAKEIAPNLIIGASVYS------ 108 ::::: :: :::: : : ::::::: ::::::: d1s0aa_ 141 RNGYHGDTF----------GAMSVCDPDNSMHSLWKGYLPE------NLFAPAPQSRMGE 184 d1xi3a_ 109 -----L-EEALEA-EKK-GADYLGAGSVFPT-D-ARVIGLEGLRKIVESV--K-IPVVAI 155 : :::::: ::: ::::::::::::: : :::::::::::::::: : :::::: d1s0aa_ 185 WDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIAD 244 d1xi3a_ 156 G--GINK---DNA-REVLKTGVDGIAVISAVMGAE------------------------- 184 : :::: ::: ::::::::::::::::::::: d1s0aa_ 245 EIATGFGRTGKLFACEHAEIAPDILCLGAALTGGTMTLSATLTTREVAETISNGEAGCFM 304 d1xi3a_ 185 -------------DVRKATEEL-------------------------------------- 193 ::::::::: d1s0aa_ 305 HGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAI 364 d1xi3a_ 194 ------------------------------------------------------------ 194 d1s0aa_ 365 GVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDET 424 d1xi3a_ 194 ----RKIVEEVLG 202 d1s0aa_ 425 FFCQ--------- 428 HHsearch alignment (Probability: 0.11 E-value:0.01) d1xi3a_ 18 PEVESVREALEG---GATAIQMRI--KNA--PTREMYEIGKTLRQLTREYDALFFVDD 68 :::::::::::: ::::::::: ::: ::::::::::::::::::::::::::: d1s0aa_ 188 RDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADE 245