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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1j93a_ | Uroporphyrinogen decarboxylase, UROD | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
| Hit | d1nowa1 | beta-hexosaminidase B | (Trans)glycosidases | TIM beta/alpha-barrel | α/β |
Query <-- 0.875 --> IntermediateDALI alignment (Z-score: 2.8 Raw score:517.50) query 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 query 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 query 1 ------------sLQLRLALN-qidSTVG---------------------------DIAG 20 :::::::: :::: :::: d1j93a_ 121 gealtilrkevnnQAAVLGFVgapfTLASyvveggssknftkikrlafaepkvlhaLLQK 180 query 21 NAEAILRWTRHSAEQGAHLVAFPEMaltgypvedLALRSSFVEASRTALRELAARLAEEg 80 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDS------watELSPVDFEEFSLPYLKQIVDSVKLT- 233 query 81 FGELPVLVGY---lDRSEsaqpkygqpagaprnaaavlhrgRVALTFAKHhlpnygvfde 137 :::::::::: :::: ::::::::: d1j93a_ 234 HPNLPLILYAsgsgGLLE------------------rlpltGVDVVSLDW---------- 265 query 138 fryfvPGDTMpivrlhgvdialaiceDLWQD----ggrvPAARSAGaglllsvnaspyer 193 ::::: ::::: ::::::: d1j93a_ 266 -----TVDMAdgrrrlgpnvaiqgnvDPGVLfgskefitNRINDTV---kkagkgkhiln 317 query 194 dkddtRLELvRKRAQEAGcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcv 253 :::: :::::::: d1j93a_ 318 lghgiKVGTpEENFAHFF------------------------------------------ 335 query 254 vldldlpaaEAEPptgvvddglridrlviseeplpayeaelaggyadrl 302 :::: d1j93a_ 336 -----eiakGLRY------------------------------------ 343 FAST alignment (Normalized score: 2.91 Raw score:937.50) query 1 S----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 2 ------------------------------------------------------------ 2 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 2 --------------LQLRLALNQIDSTV-------------------------------- 15 :::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 query 16 --GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL--------RSSFV-EA 64 ::::::::::::::::::::::::::: ::::: :: d1j93a_ 174 LHALLQKFATSMAKYIRYQADSGAQAVQI---------------FDSWATELSPVDFEEF 218 query 65 SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG------ 118 :::::::::::::: :::::::::: d1j93a_ 219 SLPYLKQIVDSVKL-THPNLPLILY-----------------------------ASGSGG 248 query 119 --------RVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVD-------------- 156 ::::::: d1j93a_ 249 LLERLPLTGVDVVSL-------------------------------DWTVDMADGRRRLG 277 query 157 ---IALAICEDLWQDG------------------GRVPAARSAGA---GLLLSV---NAS 189 ::::: ::::: ::::: ::: d1j93a_ 278 PNVAIQGN--------VDPGVLFGSKEFITNRINDTVKK------AGKGKHIL-NLGHGI 322 query 190 PYERDKD-----DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVAR 244 : ::::::::::: d1j93a_ 323 K------VGTPEENFAHFFEIAK------------------------------------- 339 query 245 APQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL-- 302 d1j93a_ 340 ----------------------------------------------------------GL 341 query 303 -- 303 d1j93a_ 342 RY 343 TMalign alignment (TM-score: 0.44 Raw score:131.70) query 1 SLQLRL------------------------------------------------------ 6 ::::: d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 7 ------ALNQIDSTVGDIAGN--------------------------------A---E-A 24 ::::::::::::::: : : : d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 25 ILRWTRHSAE--QGAHLVAFPEMAL-TG-YP-----VE--D-LAL---------RSSFVE 63 :::::::::: ::::::::::::: :: :: :: : ::: :::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 query 64 ASRTALRELAARLAEEGFGELPVLVGYLDRS--ESAQPKYGQPAGAPR-NAA-AV--LHR 117 :::::::::::::::: : ::::::::::: : :::::::::: ::: :: ::: d1j93a_ 180 KFATSMAKYIRYQADS-G--AQAVQIFDSWATE---L-SPVDFEEFSLPYLKQIVDSVKL 232 query 118 GRV-ALTFA-KHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::: ::::: :::::: : :::::::::: ::::::::::::::::: d1j93a_ 233 THPNLPLILYASGSGG------L--LERLPLTGVD--------VVSLDWTVDMADGRRRL 276 query 176 RSAGAGLLLSVNASPYERDKDD--TRLELVRKRAQEAGCT-TAYLA-MIGGQDELVFD-G 230 ::: : ::::::: ::::::: :::::::::::::::: ::::: ::: :::: : d1j93a_ 277 GPN-V--AIQGNVD-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI----KVGTPE 328 query 231 --DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLP 288 ::::: ::::: ::: d1j93a_ 329 ENFAHFF---EIAKG-------------LRY----------------------------- 343 query 289 AYEAELAGGYADRL 302 d1j93a_ 344 -------------- 344 HHsearch alignment (Probability: 0.14 E-value:0.02) query 18 IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLA 77 ::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD------FEEFSLPYLKQIVDSVK 231 query 78 EEGFGELPVLV 88 :::: :::::: d1j93a_ 232 LTHP-NLPLIL 241
Intermediate <-- 1.218 --> HitDALI alignment (Z-score: 11.7 Raw score:1405.40) d1j93a_ 1 tqpllldavrgkeverPPVWLMRQAgrymksyqllcekyplfrdRSENvdlvVEISLQPW 60 ::::::::: :::: :::::::: d1nowa1 1 ----------------FSHRGILID----------------tsrHYLP----VKIILKTL 24 d1j93a_ 61 KVFR---PDGVILFSDIL-----tplsGMNI--PFDIikgkgpvifdplrtaadvekvre 110 :::: ::::::::::: :::: :::: d1nowa1 25 DAMAfnkFNVLHWHIVDDqsfpyqsitFPELsnKGSY----------------------- 61 d1j93a_ 111 fipeksvPYVGEALTILRKEVNN-QAAVLGFVGApFTLA--------sYVVEggsskNFT 161 :::::::::::::::: :::::::::: :::: :::: ::: d1nowa1 62 ---slshVYTPNDVRMVIEYARLrGIRVLPEFDT-PGHTlswgkgqkdLLTP--cysLDS 115 d1j93a_ 162 KIkrlafaepkvLHALLQKFATSMAKYIRYQAdsGAQAVQIFDSWaTELS---------- 211 :: :::::::::::::::::::: ::::::::::: :::: d1nowa1 116 FG------pinpTLNTTYSFLTTFFKEISEVF--PDQFIHLGGDE-VEFKcwesnpkiqd 166 d1j93a_ 212 --------pVDFEEfSLPYLKQIVDSVKLTHpnLPLILYASgsggLLERLpLTGV-DVVS 262 ::::: :::::::::::::::: :::::::: ::::: :::: :::: d1nowa1 167 fmrqkgfgtDFKKL-ESFYIQKVLDIIATIN--KGSIVWQE---vFDDKA-KLAPgTIVE 219 d1j93a_ 263 LDWTVDMADGRRRL-GPNVAIQG-NVDPG---vlfGSKEFITNRinDTVKK----aGKGK 313 :::::::::::::: :::::::: ::::: ::::::::: ::::: :::: d1nowa1 220 VWKDSAYPEELSRVtASGFPVILsAPWYLdlisygQDWRKYYKV--EPLDFggtqkQKQL 277 d1j93a_ 314 HILNlGHGI---------kvGTPEENFAHFFEIAKGLR---------------------- 342 :::: :::: :::::::::::::::::: d1nowa1 278 FIGG-EACLwgeyvdatnltPRLWPRASAVGERLWSSKdvrdmddaydrltrhrcrmver 336 d1j93a_ 343 ------------y 343 d1nowa1 337 giaaqplyagycn 349 FAST alignment (Normalized score: 5.26 Raw score:1819.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS--------ENVDLV 52 :::::: :::::: d1nowa1 1 ---------------FSHRGI-------------------------LIDTSRHYLPVKII 20 d1j93a_ 53 VEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFI 112 ::::::: ::::::::::: d1nowa1 21 LKTLDAM-AFNKFNVLHWH----------------------------------------- 38 d1j93a_ 113 PEKS------------------------------VPYVGEALTILRKEVNN-QAAVLGFV 141 ::::::::::::: :::::::: d1nowa1 39 ----IVDDQSFPYQSITFPELSNKGSYSLSHVYTPNDVRMVIEYARL----RGIRVLPEF 90 d1j93a_ 142 GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV---------------------------L 174 ::::: : d1nowa1 91 DTPGH---------------------------TLSWGKGQKDLLTPCYSLDSFGPINPTL 123 d1j93a_ 175 HALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFE------------------ 216 ::::::::::::::::: ::::::::::: d1nowa1 124 NTTYSFLTTFFKEISEV---FPDQFIHLGGD-----------EVEFKCWESNPKIQDFMR 169 d1j93a_ 217 ---------EFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGV--------- 258 :::::::::::::::: ::::::: d1nowa1 170 QKGFGTDFKKLESFYIQKVLDIIAT--INKGSIV-----------------WQEVFDDKA 210 d1j93a_ 259 -----DVVSLDWT---VDMADGRRRLG---PNVAIQGNVDPGVLFG-------------- 293 ::::: ::::::::: :::::: d1nowa1 211 KLAPGTIVEV---WKDSAYPEELSR--VTASGFPVI----------LSAPWYLDLISYGQ 255 d1j93a_ 294 SKEFITNRINDTVKKA-------GKGKHILNLGHGIKVGT-------------------P 327 ::::::: :::: :::::: : d1nowa1 256 DWRKYYK--VEPL---DFGGTQKQKQLFI-----------GGEACLWGEYVDATNLTPRL 299 d1j93a_ 328 EENFAHFFEIAKGLRY-------------------------------------- 343 :::::::::::: d1nowa1 300 WPRASAVGERLW----SSKDVRDMDDAYDRLTRHRCRMVERGIAAQPLYAGYCN 349 TMalign alignment (TM-score: 0.59 Raw score:202.34) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :::::::::::: : :: :: ::::::: d1nowa1 1 ---------------FSHRGILIDTSR----H------------YL----PV-KIILKTL 24 d1j93a_ 61 KVFR---PDGVILFSDI---L-T-P--LSGMNIPFDII--KGKGPVIFDPLRTAADVEKV 108 :::: :::::::::: : : : ::::::::::: : d1nowa1 25 DAMAFNKFNVLHWHIVDDQSFPYQSITFPELSNKGSYSLS----H--------------- 65 d1j93a_ 109 REFIPEKSVPYVGEALTILRKE-VNNQAAVLGFVGAPFTLASYV------VEGGSS-KNF 160 :::: ::::::::: ::::::::::::::::::::: ::: : :: d1nowa1 66 --------VYTP-NDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTP--CY-SL 113 d1j93a_ 161 TKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQ-AVQIFDSWATEL--S------ 211 :::: : ::::: :::::::::::::::::::: :::::::::::: : d1nowa1 114 DSFG--P-----INPTL-NTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQ 165 d1j93a_ 212 ---------PVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTG-VDVV 261 :::::: :::::::::::::::: ::::::: : ::::::::: :::: d1nowa1 166 DFMRQKGFGTDFKKL-ESFYIQKVLDIIATIN--KGSIVWQ--E--VFDDKAKLAPGTIV 218 d1j93a_ 262 SLDWTVDMADGRRRL-GPNVAIQG-NVDPG-VLF--GSKEFITNRINDTVKK-----AGK 311 ::::::::::::::: :::::::: ::::: ::: ::::::::: : :::: ::: d1nowa1 219 EVWKDSAYPEELSRVTASGFPVILSAPWYLDLISYGQDWRKYYKV-E-PLDFGGTQKQKQ 276 d1j93a_ 312 GKHILNLGHGI-KV---G---TPEENFAHFFEIAKGLRY--------------------- 343 ::::::::::: :: : :::::::::::::::::: d1nowa1 277 LFIGGEACLWGEYVDATNLTPRLWPRASAVGERLWSSKDVRDMDDAYDRLTRHRCRMVER 336 d1j93a_ 344 ------------- 344 d1nowa1 337 GIAAQPLYAGYCN 349 HHsearch alignment (Probability: 0.06 E-value:0.04) d1j93a_ 169 AEPKVLHALLQKFATSMAKYIRYQADSGAQAV 200 :::::::::::::::::::::::::::::::: d1nowa1 122 TLNTTYSFLTTFFKEISEVFPDQFIHLGGDEV 153