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 | d1w0ma_ | Triosephosphate isomerase | Triosephosphate isomerase (TIM) | TIM beta/alpha-barrel | α/β |
| Hit | d1ccwa_ | Glutamate mutase, small subunit | Cobalamin (vitamin B12)-binding domain | Flavodoxin-like | α/β |
Query <-- 0.866 --> IntermediateDALI alignment (Z-score: 9.0 Raw score:886.70) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCF-----aTWSVF-DLMRDYM-- 52 ::::::::::: ::::: ::::::: d1w0ma_ 1 --------------------------mrLPILIINFKAYgeaagkRAVELaKAAERAAre 34 query 53 ----DGTTSSSlFEVRLGRERFGKETHAYSVAYGDN-------EIDEVVS-HADKIIFN- 99 ::::::: :::::::::::::::::::::::: ::::::: :::::::: d1w0ma_ 35 lgvnIVVAPNH-LELGLVSQSVDIPVYAQGADVEAGgahtahvSLENIKEaGGSGVILNh 93 query 100 -----SISQLERFADKAA--GIARGLRLNPqrlgewdvpkvervMDRINGFMIHN--NCE 150 ::::::::::::: :::::::::: ::::::::::: ::: d1w0ma_ 94 seaplKLNDLARLVAKAKslGLDVVVCAPD------prtslaaaALGPHAVAVEPpeLIG 147 query 151 NKDfglFDRMLGEIEErFGALIA---RVDWVSLGGGIHFtgddypvdAFSARLRAFSdry 207 ::: :::::::::: :::::: ::::::::::::: :::::::::: d1w0ma_ 148 TGR-avSRYKPEAIVE-TVGLVSrhfPEVSVITGAGIES-------gDDVAAALRLG--- 195 query 208 gvqIYLEPGEAS-ITKSttlevtvldtlynknlaivdssieahmldlliyretakvlpne 266 ::::::::: :::: d1w0ma_ 196 --tRGVLLASAAvKAKD------------------------------------------- 210 query 267 gshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiair 326 d1w0ma_ 211 ------------------------------------------------------------ 211 query 327 eldgsvrtvreftyadyeqsls 348 d1w0ma_ 211 -------pyakivelakplsel 225 FAST alignment (Normalized score: 3.62 Raw score:1014.00) query 1 MIETPYYLI----------------DKAKLTRNMERIAHVREKSGAKALLALKCFA---T 41 :::::::::::::::::::::::: : d1w0ma_ 1 ---------MRLPILIINFKAYGEAAGKRAVELAKAAERAARELGVNIV-------VAPN 44 query 42 WSVFDLMRD-------------------------------YMDGTTSS------------ 58 ::::::::: :::::: d1w0ma_ 45 HLELGLVSQSVDIPVYAQGADVEAGGAHTAHVSLENIKEAGGSGVI--LNHSEAPLKLND 102 query 59 SLFEVRLGRERF-GKETHAYSVAYGDNEIDEVVS-HADKIIFN---------------SI 101 :::::::::: :::::::::: ::::::::: ::::::: :: d1w0ma_ 103 LARLVAKAKS--LGLDVVVCAPD--PRTSLAAAALGPHAVAV-EPPELIGTGRAVSRYKP 157 query 102 SQLERFADK----AAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLF 157 ::::::::: ::::::::: d1w0ma_ 158 EAIVETVGLVSRHFPEVSVITG-------------------------------------- 179 query 158 DRMLGEIEER----FGALIAR-----VDWVSLGGGIHFTGDDYPVD---------AFSAR 199 ::::::: ::::: ::::: d1w0ma_ 180 ----------AGIESGDDVAAALRLGTRGVL---------------LASAAVKAKDPYAK 214 query 200 LRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRET 259 :::::: d1w0ma_ 215 IVELAK------------------------------------------------------ 220 query 260 AKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVK 319 d1w0ma_ 221 ------------------------------------------------------------ 221 query 320 MPAIAIRELDGSVRTVREFTYADYEQSLS----- 348 d1w0ma_ 221 -----------------------------PLSEL 225 TMalign alignment (TM-score: 0.36 Raw score:124.76) query 1 --MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSS 58 :: :::::: d1w0ma_ 1 MR-----------------------------LP---------------------ILIINF 10 query 59 ----------SLFEVRLGRERF--G-KETHAYSVAYG-DNEIDEVVSHADKIIFNSI--- 101 :::::::::::: : ::::::::::: ::::::: ::: ::::::: d1w0ma_ 11 KAYGEAAGKRAVELAKAAERAARELGVNIVVAPNHLELGLVSQSV-DIP-VYAQGADVEA 68 query 102 -------SQLERFADKAAGIARGLRLNPQRLGEWDVPKVER--VM-DR-INGFMIHNNCE 150 ::::::::::: : ::::::: :::::::::::: :: :: :::::::: d1w0ma_ 69 GGAHTAHVSLENIKEAGG-S-GVILNHS-EAPLKLNDLARLVAKAKSLGLDVVVCAP--- 122 query 151 NKDFGLFDRMLGEIEERFGALIARVDWVSLGG--G-----IHFTGDDYPVDAFSARLRAF 203 ::::::: :::: ::::::::: : ::::: ::: ::::::::: d1w0ma_ 123 ---------DPRTSLA-AAAL--GPHAVAVEPPELIGTGRAVSRY--KPE-AIVETVGLV 167 query 204 SDRY-GVQIYLEPGEASITK---------------STTLEVTVLDTLYNKNLAIVDSSIE 247 :::: ::::::::::::::: d1w0ma_ 168 SRHFPEVSVITGAGIESGDDVAAALRLGTRGVLLA------------------------- 202 query 248 AHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGY 307 :: d1w0ma_ 203 ----------------------------------------------------------SA 204 query 308 TMVKK---NWFNGVKMPAI------------AIRELDGSVRTVREFTYADYEQSLS 348 ::::: : d1w0ma_ 205 AVKAKDPY----------AKIVELAKPLSEL------------------------- 225 HHsearch alignment (Probability: 0.13 E-value:0.06) query 74 THAYSVAYGDNEIDEVVSHADKIIF--------------NSISQLERFADKAAGIARGLR 119 ::::::::::::::::::::::::: ::::::::::::::::::::: d1w0ma_ 116 DVVVCAPDPRTSLAAAALGPHAVAVEPPELIGTGRAVSRYKPEAIVETVGLVSRHFPEVS 175 query 120 LNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGAL 171 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1w0ma_ 176 VITGAGIESGDDVAAALRLGTRGVL--LASAAVKAKDPYAKIVELAKPLSEL 225
Intermediate <-- 1.099 --> HitDALI alignment (Z-score: 3.9 Raw score:396.70) d1w0ma_ 1 mrlpiliinfkaygeaagkravelakaaeraarelgvnivvapnhlelglvsqsvdipvy 60 d1ccwa_ 1 ------------------------------------------------------------ 1 d1w0ma_ 61 aqgadveaggahtahvslenikeaggsgvilnhseaplklndlarlvakaksLGLDVVVC 120 :::::::: d1ccwa_ 1 ----------------------------------------------------MEKKTIVL 8 d1w0ma_ 121 APD-------------------------------PRTSLAAAA-LGPHAVAVEPPELigt 148 ::: ::::::::: ::::::::::::: d1ccwa_ 9 GVIgsdchavgnkildhaftnagfnvvnigvlspQELFIKAAIeTKADAILVSSLYG--- 65 d1w0ma_ 149 gravsrYKPEAIVETVGLVSRH-FPEVSVITGAG-----ieSGDDVAAALRLGTRGVLLA 202 :::::::::::::::: ::::::::::: ::::::::::::::::::: d1ccwa_ 66 ------QGEIDCKGLRQKCDEAgLEGILLYVGGNivvgkqhWPDVEKRFKDMGYDRVYAP 119 d1w0ma_ 203 SAAvkakdpyakivelakplsel 225 ::: d1ccwa_ 120 GTP-----pevgiadlkkdlnie 137 FAST alignment (Normalized score: 4.64 Raw score:814.00) d1w0ma_ 1 MRLPILIINFKAYGEAAGKRAVELAKAAERAARELGVNIVVAPNHLELGLVSQSVDIPVY 60 d1ccwa_ 1 ------------------------------------------------------------ 1 d1w0ma_ 61 AQGADVEAGGAHTAHVSLENIKEAGGSGVILNHSEAPLKLNDLARLVAKAKSLGLDVVVC 120 :::::::: d1ccwa_ 1 ----------------------------------------------------MEKKTIVL 8 d1w0ma_ 121 A-------------------------------PDPRTSLAAA-ALGPHAVAVEPPELIGT 148 : :::::::::: :::::::::::: d1ccwa_ 9 GVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAIETKADAILVSSL----- 63 d1w0ma_ 149 GRAVS-RYKPEAIVETVGLVSR-HFPEVSVITGAGIE-------SGDDVAAALRLGTRGV 199 :::::::::::::::: :::::::::::: :::::::::::::::: d1ccwa_ 64 -----YGQGEIDCKGLRQKCDEAGLEGILLYVGGN--IVVGKQHWPDVEKRFKDMGYDRV 116 d1w0ma_ 200 LLASAAVKAKDPYAKIVELAKPLSEL------------------- 225 :: d1ccwa_ 117 YA------------------------PGTPPEVGIADLKKDLNIE 137 TMalign alignment (TM-score: 0.34 Raw score:76.34) d1w0ma_ 1 ----------------MRLPILIINFKAY--GEAAGKRAVELAKAAERAARELGVNIVVA 42 ::: d1ccwa_ 1 MEKKTIVLGVIGSDCH----------AVGNK----------------------------- 21 d1w0ma_ 43 PNHLELGLVSQSVDIPVYAQGADVEAGGAHTAHVSLENIKEAGGSGVILNHSEAPLKLND 102 : ::: ::: : ::::::::: : d1ccwa_ 22 -I-----------------LDH-----------AFT--N----AGFNVVNIG--V----- 39 d1w0ma_ 103 LARLVAKAKSLGLDVVVCAPDPRTSLAAAA-LGPHAVAVEPPELIGTGRAVSRYKPEAIV 161 :::::::::::: :::::::::: : : :::: : ::: d1ccwa_ 40 ------------------LSPQELFIKAAIETKADAILVSS---L-Y-GQGE--I--DCK 72 d1w0ma_ 162 ETVGLVSRH-FPEVSVITGAGI---E--SGDDVAAALRLGTRGVLLASAAV--KAKDPYA 213 ::::::::: :::::::::::: : :::::::::::::::::::: :: d1ccwa_ 73 GLRQKCDEAGLEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAPG-TPPE------- 124 d1w0ma_ 214 KI------------VELAKPLSEL 225 : d1ccwa_ 125 -VGIADLKKDLNIE---------- 137 HHsearch alignment (Probability: 0.94 E-value:0.00) d1w0ma_ 104 ARLVAKAKSLGLDVVV---CAPDPRTSLAAAALGPHAVAVEPPELIGTGRAVSRYKPEAI 160 :::::::::::::::: :::::::::::::::::::::: ::: ::::::: d1ccwa_ 21 KILDHAFTNAGFNVVNIGVLSPQELFIKAAIETKADAILVS--------SLY-GQGEIDC 71 d1w0ma_ 161 VETVGLVSRHF-PEVSVITGAGIES-----GDDVAAALRLGTRGVLLASAAV 206 ::::::::::: ::::::::::::: :::::::::::::::::::::: d1ccwa_ 72 KGLRQKCDEAGLEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPP 123