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 | d1knwa2 | Diaminopimelate decarboxylase LysA | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1nowa1 | beta-hexosaminidase B | (Trans)glycosidases | TIM beta/alpha-barrel | α/β |
Query <-- 1.000 --> IntermediateDALI alignment (Z-score: 19.8 Raw score:1758.40) query 1 mietpyylidkaKLTRNMERIAHVRekSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::: ::::::::::::::::::::::::::::::::: d1knwa2 1 ------------DAQIIRRQIAALK--QFDVVRFAQKACSNIHILRLMREQGVKVDSVSL 46 query 61 FEVRLGRERFGK------ETHAYSVAYGDNEIDEVVSHaDKIIFNSISQLERFADKAAGI 114 :::::::::::: :::::::::::::::::::: ::::::::::::::::::::: d1knwa2 47 GEIERALAAGYNpqthpdDIVFTADVIDQATLERVSELqIPVNAGSVDMLDQLGQVSPGH 106 query 115 ARGLRLNPQ----------------RLGEW--DVPKVERVMD----RINGFMIHNNCeNK 152 ::::::::: ::::: :::::::::: ::::::::::: :: d1knwa2 107 RVWLRVNPGfghghsqktntggensKHGIWytDLPAALDVIQrhhlQLVGIHMHIGS-GV 165 query 153 DFGLFDRMLGEIEERFGALIARVDWVSLGGGIHF----tgDDYPVDAFSARLRAFSDRYG 208 :::::::::::::::::::::::::::::::::: :::::::::::::::::::: d1knwa2 166 DYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVpyqqgeEAVDTEHYYGLWNAAREQIA 225 query 209 ------VQIYLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakv 262 :::::::::::::: d1knwa2 226 rhlghpVKLEIEPGRFLVAQ---------------------------------------- 245 query 263 lpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpa 322 d1knwa2 246 ------------------------------------------------------------ 246 query 323 iaireldgsvrtvreftyadyeqsls 348 d1knwa2 246 ------------------------sg 247 FAST alignment (Normalized score: 11.38 Raw score:3336.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG--AKALLALKCFATWSVFDLMRDYM--DGTT 56 ::::::::::::: ::::::::::::::::::::: :::: d1knwa2 1 ---------DAQIIRRQIAALK-------QFDVVRFAQKACSNIHILRLMRE--QGVKVD 42 query 57 SSSLFEVRLGRERFGK-----------ETHAYSVAYGDNEIDEVVSHA--DKIIFNSISQ 103 ::::::::::: ::::::::::::::::::: :::::::::: d1knwa2 43 SVSLGEIERAL-----AAGYNPQTHPDDIVFTADVIDQATLERVSE--LQIPVNAGSVDM 95 query 104 LERFADKAAGIARGLRLNP-----------------QRLGEW---DVPKVERVMD----- 138 :::::::::::::::::: ::::: :::::::: d1knwa2 96 LDQLGQVSPGHRVWLRVN-PGFGHGHSQKTNTGGENSKHGI-WYTDLPAALDV--IQRHH 151 query 139 -RINGFMIHNNCE---NKDFGLFDRMLGEIEERFGALIA----RVDWVSLGGGIHFTGD- 189 :::::::: ::::::::::::::::::: :::::::::: d1knwa2 152 LQLVGIHMH----IGSGVDYAHLEQVCGAMVRQVI----EFGQDLQAISAGGG------L 197 query 190 ---------DYPVDAFSARLRAFSDRY-------GVQIYLEPGEASITKSTTLEVTVLDT 233 ::::::::::::::::: ::::::::::::::: d1knwa2 198 SVPYQQGEEAVDTEHYYGLWNAAREQ-IARHLGHPVKLEIEPGRFLVAQ----------- 245 query 234 LYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEEL 293 d1knwa2 246 ------------------------------------------------------------ 246 query 294 KVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-- 348 d1knwa2 246 -------------------------------------------------------SG 247 TMalign alignment (TM-score: 0.53 Raw score:185.85) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 :::::::::::: ::: : :::::::::::::::::::::::::::::: d1knwa2 1 ---------DAQIIRRQIAAL-KQF---D-VVRFAQKACSNIHILRLMREQGVKVDSVSL 46 query 61 FEVRLGRERFG----K--ETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGI 114 ::::::::::: : :::::::::::::::::::::::::::::::::::::::::: d1knwa2 47 GEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGH 106 query 115 ARGLRLNPQ----------------RLGE-WD-VPKVERVMD---RIN-GFMIHNNCENK 152 ::::::::: :::: :: ::::::::: ::: :::::::: :: d1knwa2 107 RVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGS-GV 165 query 153 DFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFT----GDDYPVDAFSARLRAFSDRYG 208 ::::::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1knwa2 166 DYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIA 225 query 209 ------VQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKV 262 :::::::::::::::: d1knwa2 226 RHLGHPVKLEIEPGRFLVAQSG-------------------------------------- 247 query 263 LPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPA 322 d1knwa2 248 ------------------------------------------------------------ 248 query 323 IAIRELDGSVRTVREFTYADYEQSLS 348 d1knwa2 248 -------------------------- 248 HHsearch alignment (Probability: 1.00 E-value:0.00) query 10 DKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRER 69 :::::::::::::::: ::::::::::::::::::::::::::::::::::::::: d1knwa2 1 DAQIIRRQIAALKQFD-----VVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAA 55 query 70 FGKET------HAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQ 123 ::::: ::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa2 56 GYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLRVNPG 115 query 124 ----------------RLGEWDVPKV------ERVMDRINGFMIHNNCENKDFGLFDRML 161 :::::::::: :::::::::::::::::: ::::::::: d1knwa2 116 FGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGV-DYAHLEQVC 174 query 162 GEIEERFGALIARVDWVSLGGGIHFTGDD----YPVDAFSARLRAFSDRY------GVQI 211 ::::::::::::::::::::::::::::: ::::::::::::::::: :::: d1knwa2 175 GAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHLGHPVKL 234 query 212 YLEPGEASITKST 224 ::::::::::::: d1knwa2 235 EIEPGRFLVAQSG 247
Intermediate <-- 0.933 --> HitDALI alignment (Z-score: 7.7 Raw score:919.20) d1knwa2 1 daqiirrqiaalkqFDVVRFAQK-------acsNIHILRLMREQGV-KVDSVS------- 45 ::::::::: ::::::::::::: :::::: d1nowa1 1 --------------FSHRGILIDtsrhylpvkiILKTLDAMAFNKFnVLHWHIvddqsfp 46 d1knwa2 46 ----------------------lgeiERALaAGYNpqthpdDIVFTADV----------- 72 :::: :::: :::::::: d1nowa1 47 yqsitfpelsnkgsyslshvytpndvRMVI-EYAR--lrgiRVLPEFDTpghtlswgkgq 103 d1knwa2 73 -------------------------iDQATLERVSELQ--IPVNAG-------------- 91 :::::::::::: :::::: d1nowa1 104 kdlltpcysldsfgpinptlnttysfLTTFFKEISEVFpdQFIHLGgdevefkcwesnpk 163 d1knwa2 92 ---------------------SVDMLDQLGQVSpgHRVWLRVNpgfghghsqktntggen 130 :::::::::::: :::::::: d1nowa1 164 iqdfmrqkgfgtdfkklesfyIQKVLDIIATIN--KGSIVWQE----------------- 204 d1knwa2 131 skhgIWYTDlPAALdviqrhhlQLVGIHMHIgsgvdyahLEQVCGAMVRQVIefgQDLQa 190 ::::: :::: ::::::::: ::::::::::::: :::: d1nowa1 205 ----VFDDK-AKLA--------PGTIVEVWK--------DSAYPEELSRVTA---SGFP- 239 d1knwa2 191 ISAG--GGLSVPYQqgEEAV-DTEHYYglWNAAreQIARHLghPVKLEIEPGR------- 240 :::: :::::::: :::: :::::: :::: :::::: :::::::::: d1nowa1 240 VILSapWYLDLISY--GQDWrKYYKVE--PLDF--GGTQKQ-kQLFIGGEACLwgeyvda 292 d1knwa2 241 flVAQS--------------------------------------------------g 247 :::: d1nowa1 293 tnLTPRlwprasavgerlwsskdvrdmddaydrltrhrcrmvergiaaqplyagycn 349 FAST alignment (Normalized score: 3.76 Raw score:1105.00) d1knwa2 1 D----------------AQIIRRQIAALK--QFDVVRFAQKA------------------ 24 :::::::::::: :::::::: d1nowa1 1 -FSHRGILIDTSRHYLPVKIILKTLDAMAFNKFNVLHWH---IVDDQSFPYQSITFPELS 56 d1knwa2 25 ---------CSNIHILRLMRE------QGVKVDSV------------------------- 44 :::::::::::: ::::::: d1nowa1 57 NKGSYSLSHVYTPNDVRMVIEYARLRGIRVLPEF-DTPGHTLSWGKGQKDLLTPCYSLDS 115 d1knwa2 45 ------------------SLGEIERALAAGYNPQTHPD----DIVFTADVI--------- 73 ::::::: ::::: d1nowa1 116 FGPINPTLNTTYSFLTTFFKEISEV-------------FPDQFIHLG----GDEVEFKCW 158 d1knwa2 74 --------------------------DQATLERVSELQIPVNAGSVDMLDQLGQ----VS 103 ::::::::::::::::: :::::: :: d1nowa1 159 ESNPKIQDFMRQKGFGTDFKKLESFYIQKVLDIIATINKGSIV-WQEVFD----DKAKLA 213 d1knwa2 104 PGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGS 163 ::::::: ::::::::::::::::::: d1nowa1 214 PGTIVEV------------------------WKDSAYPEELSRVTASGFP---------- 239 d1knwa2 164 GVDY---------------AHLEQVCGAMVR--QVIEFGQ--------DLQAISAGGGLS 198 ::::::: ::::: ::::::: d1nowa1 240 ----VILSAPWYLDLISYGQDWRKYY-----KVEPLDF--GGTQKQKQLFIGGEA----- 283 d1knwa2 199 VPYQQGEEAV------------------DTEHYYGLWNAAREQIARHLGHPVKLEIEPGR 240 ::::::::: d1nowa1 284 ----------CLWGEYVDATNLTPRLWPRASAVGERL----------------------- 310 d1knwa2 241 FLVAQSG--------------------------------------- 247 d1nowa1 311 -------WSSKDVRDMDDAYDRLTRHRCRMVERGIAAQPLYAGYCN 349 TMalign alignment (TM-score: 0.52 Raw score:127.60) d1knwa2 1 -----------------------------------------------DAQ---------- 3 ::: d1nowa1 1 FSHRGILIDTSRHYLPVKIILKTLDAMAFNKFNVLHWHIVDDQSFPYQSITFPELSNKGS 60 d1knwa2 4 ------IIRRQIAALK-QF----DVVRFAQK---AC--S--------------------- 26 :::::::::: :: :::::::: :: : d1nowa1 61 YSLSHVYTPNDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTPCYSLDSFGPIN 120 d1knwa2 27 --------NI-HILRLMREQGV--KVDSVS------------------------------ 45 :: ::::::::::: :::::: d1nowa1 121 PTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQDFMRQKGFGTDFKKL 180 d1knwa2 46 -L-GEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAG----SVDMLDQL 99 : :::::::: :::::: ::::::::::::: :: ::::::::: :::::::: d1nowa1 181 ESFYIQKVLDI--IATINK--GSIVWQEVFDDKA--KL-APGTIVEVWKDSAYPEELSRV 233 d1knwa2 100 GQVSPGHRVWLRVNPGFGHGHSQ--KTNTGG---ENSKHGIWYTDLPAALDVIQRHHLQL 154 :::: ::::::::: ::::::: : ::::::::: :::::::::: d1nowa1 234 TASG--FPVILSAPW-YLDLISYGQ-----DWRK------YYKVEPLDF-GGTQKQKQLF 278 d1knwa2 155 VGIHMHIG---SGV--DYAHLEQVCGAMVRQVIEFGQ---------------------DL 188 :::::::: ::: ::::::::::::::::::::: d1nowa1 279 IGGEACLWGEYVDATNLTPRLWPRASAVGERLWSSKDVRDMDDAYDRLTRHRCRMVER-- 336 d1knwa2 189 QAISAGGGLSVPYQQGEEAVDTEHYYGL-----------WNAAREQIARHLGHPVKLEIE 237 :: d1nowa1 337 --------------------------GIAAQPLYAGYCN--------------------- 349 d1knwa2 238 PGRFLVAQSG 247 d1nowa1 350 ---------- 350 HHsearch alignment (Probability: 0.93 E-value:0.00) d1knwa2 92 SVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHH 151 ::::::::::::::: ::::::::::::::: ::::::::: :::: d1nowa1 68 TPNDVRMVIEYARLR--GIRVLPEFDTPGHTL--------SWGKGQKDL-------LTPC 110 d1knwa2 152 LQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQ-------- 203 :::: :::: :::::::::::::::::::::: :::::::::::: ::::: d1nowa1 111 YSLD--SFGP-INPTLNTTYSFLTTFFKEISEV-FPDQFIHLGGDE-VEFKCWESNPKIQ 165 d1knwa2 204 -----GEEAVDTEHYYGLWNAAREQIARHLGHPVKLEIEP 238 ::::::::::::::::::::::::::::::::::: d1nowa1 166 DFMRQKGFGTDFKKLESFYIQKVLDIIATINKGSIVWQEV 205