BLAST at NCBI Find the amino acid sequence for the protein involved with your disease phenotype. Perform a Blast search on the protein. Is your protein found only in primates? All mammals? How about amphibians and reptiles? Are there homologs in bacteria? (You can search these types of organisms individually in blast). Protein is found in mammals of all kinds, fish, toads, and bacteria. Find out as much as you can about your protein and the conserved domains in your protein of interest: Examine and compile all relevant information. Save all information which you think may be useful for your presentation. Submit: 1. The FASTA file for your protein. >gi|189181666|ref|NP_000511.2| hexosaminidase A preproprotein [Homo sapiens] MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRD LLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLE TFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPS FPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSG SEPSGTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQ LESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPW YLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKLT SDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT 2. Report how far back evolutionarily you can find homologs for your protein. Could not find this. 2. List each of your conserved domains and give a brief explanation of the structure and function of these domains. Where are they located in the protein sequence molecule? (estimate the aa region using linear map of the conserved domains). If there are no conserved domains state that as well. GH-20 HexA hexb like- Catalyze removal of beta-1, results in lipid storage disorders and mutations cause deficiency in Hex A enzyme resulting in Tay-sachs. GH-20-hexosaminidase, GH-20-chitobiase-like-1, GH-20-sphex-like, GH-20-DspBLnbB-like, GH-20-Sm-chitobiase-like, GH-20- GcnA-like, Glyco-hydro-20, GH20hexosaminidase superfamily. cd06562, GH20_HexA_HexB-like, Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-... 119332 no 8e-156 Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in Tay-Sachs, mutations in the beta-subunit cause in a deficiency in both HexA and HexB enzymes and result in Sandhoff disease. In both disorders GM(2) gangliosides accumulate in lysosomes. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Cd Length: 348 Bit Score: 545.66 E-value: 8e-156 10 20 70 80 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 167 FPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPvTHIYTAQDVKEVI EYA 246 Cdd|cd06562 1 FPHRGLLLDTSRHFLSVDSIKRTIDAMAYNKLNVLHWHITDSQSFPLESPSYPELSKKGAYSPSEVYTPEDVKEIVEYA 79 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 247 RLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSE--PSGTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGDE 323 Cdd|cd06562 80 RLRGIRVIPEIDTPGHTGSWGQGYPELLTGCYAVWRkycPEPPCGQLNPTNPKTYDFLKTLFKEVSELFPDKYFHLG GDE 159 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 324 VDFTCWKSNPEIQDFMRKKGfGEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIpvnymk 402 Cdd|cd06562 160 VNFNCWNSNPEIQKFMKKNNGTDYSDLESYFIQRALDIVRSLGKTPIVWEEVFDNGVyLLPKDTIVQVWGGSD------ 232 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 403 ELELVTKAGFRALLSA--PWYLNRISYG----PDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWP 475 Cdd|cd06562 233 ELKNVLAAGYKVILSSydFWYLDCGFGGwvgpgNDWCDPYKNWPRIYSGTPEQKKLVLGGEACMWGEQVDDTNLDQR LWP 312 330 340 350 ....*....|....*....|....*....|....*. gi 189181666 476 RAGAVAERLWSNKLTSDLTFAYERLSHFRCELLRRG 511 Cdd|cd06562 313 RASALAERLWSGPSDTNLTDAEPRLVEFRCRLVRRG 348 119331 cd02742, GH20_hexosaminidase, Beta-N-acetylhexosaminidases of glycosyl hydrolase no 4e-110 family 20 (GH20) catalyze the... Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked Nacetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including Nacetylglucosides and N-acetylgalactosides. These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself. Cd Length: 303 Bit Score: 393.72 E-value: 4e-110 10 20 70 80 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 169 HRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKG--SYNPVTHIYTAQDVKEVIEY 245 Cdd|cd02742 1 IRGIMLDVSRHFLSVESIKRTIDVLARYKINTFHWHLTDDQAWRIESKKFPELAEKGgqiNPRSPGGFYTYAQLKDI IEY 80 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 246 ARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGD EVD 325 Cdd|cd02742 81 AAARGIEVIPEIDMPGHSTAFVKSFPKLLTECYAGLKLRDVFDPLDPTLPKGYDFLDDLFGEIAELFPDRYLHIGGD EAH 160 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 326 FTcwksnpeiqdfmrkkgfgEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPvNYMK ELE 405 Cdd|cd02742 161 FK-----------------QDRKHLMSQFIQRVLDIVKKKGKKVIVWQDGFDKKMKLKEDVIVQYWDYDGD-KYNVELP 221 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 406 LVTKAGFRALLSAPWYLNRISYGPDWKDFYIVEPLAFEgTPEQKALVIGGEACMWGEYVDNT-NLVPRLWPRAGAVAER 483 Cdd|cd02742 222 EAAAKGFPVILSNGYYLDIfIDGALDARKVYKNDPLAVPTPQQKDLVLGVIACLWGETVKDTkTLQYRFWPRALAVAER 300 ... gi 189181666 484 LWS 486 Cdd|cd02742 301 SWS 303 cd06570, GH20_chitobiase-like_1, A functionally uncharacterized subgroup of the Glycosyl 119338 no 2e-74 hydrolase family 20 (GH20)... A functionally uncharacterized subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the chitobiase of Serratia marcescens, a beta-N-1,4-acetylhexosaminidase that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This subgroup lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Cd Length: 311 Bit Score: 274.67 E-value: 2e-74 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 167 FPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNpvtHIYTAQDVKEVI EYA 246 Cdd|cd06570 1 FPWRGLLIDVSRHFIPVAVIKRQLDAMASVKLNVFHWHLTDDQGFRIESKKYPKLQQKASDG--LYYTQEQIREVVAYA 77 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 247 RLRGIRVLAEFDTPGHTLSWGPGIPGLLT-PCYSGSEPS-GTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGDE 323 Cdd|cd06570 78 RDRGIRVVPEIDVPGHASAIAVAYPELASgPGPYVIERGwGVFEPLlDPTNEETYTFLDNLFGEMAELFPDEYFHIG GDE 157 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 324 VDFTCWKSNPEIQDFMRKKGFgEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFdnkvkiQPD---TIIQVWREDipvn 399 Cdd|cd06570 158 VDPKQWNENPRIQAFMKEHGL-KDAAALQAYFNQRVEKILSKHGKKMIGWDEVL-----HPDlpknVVIQSWRGH---- 226 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 400 ymKELELVTKAGFRALLSAPWYLNRisygPDW- KDFYIVEPlafegtpeqkaLVIGGEACMWGEYVDNTNLVPRLWPRAG 478 Cdd|cd06570 227 --DSLGEAAKAGYQGILSTGYYIDQ----PQPaAYHYRVDP----------MILGGEATMWAELVSEETIDSRLWPRTA 289 330 340 ....*....|....*....|.. gi 189181666 479 AVAERLWSNKLTSDLTFAYERL 500 Cdd|cd06570 290 AIAERLWSAQDVRDEDDMYRRL 311 119333 cd06563, GH20_chitobiase-like, The chitobiase of Serratia marcescens is a beta-N-1,4no 1e-65 acetylhexosaminidase with a... The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetylD-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This GH20 domain family includes an N-acetylglucosamidase (GlcNAcase A) from Pseudoalteromonas piscicida and an Nacetylhexosaminidase (SpHex) from Streptomyces plicatus. SpHex lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Cd Length: 357 Bit Score: 245.95 E-value: 1e-65 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 167 FPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHI------------ 233 Cdd|cd06563 1 FSWRGLMLDVSRHFFPVDEVKRFIDLMALYKLNVFHWHLTDDQGWRIEIKKYPKLTEVGAWRGPTEIglpqgggdgt pyg 80 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 234 --YTAQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFG--PVNPSLNNTYEFMSTFFLEV 308 Cdd|cd06563 81 gfYTQEEIREIVAYAAERGITVIPEIDMPGHALAALAAYPELGCTGGPGSVVSVQGVvsnVLCPGKPETYTFLEDVL DEV 160 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 309 SSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFgEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVfdNKVKIQP DTI 388 Cdd|cd06563 161 AELFPSPYIHIGGDEVPKGQWEKSPACQARMKEEGLKDEHELQSYFIKRVEKILASKGKKMIGWDEI--LEGGLPPNAT 237 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 389 IQVWREDipvnymKELELVTKAGFRALLS--APWYLNR-ISYGPDW---------KDFYIVEPLAFEGTPEQKALVIGG 455 Cdd|cd06563 238 VMSWRGE-----DGGIKAAKQGYDVIMSpgQYLYLDYaQSKGPDEpaswagfntlEKVYSFEPVPGGLTPEQAKRILGV 311 330 340 350 360 ....*....|....*....|....*....|....*....|....*. gi 189181666 456 EACMWGEYVDNTNLVPR-LWPRAGAVAERLWSNKLTSDLTFAYERL 500 Cdd|cd06563 312 QANLWTEYIPTPERVEYmAFPRLLALAEVAWTPPEKKDWEDFRKRL 357 119336 cd06568, GH20_SpHex_like, A subgroup of the Glycosyl hydrolase family 20 (GH20) no 2e-37 catalytic domain found in... A subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the Nacetylhexosaminidase from Streptomyces plicatus (SpHex). SpHex catalyzes the hydrolysis of N-acetyl-betahexosaminides. An Asp residue within the active site plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Proteins belonging to this subgroup lack the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. Cd Length: 329 Bit Score: 152.10 E-value: 2e-37 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 167 FPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPV---THIYTAQDVKEV 242 Cdd|cd06568 1 FAYRGLMLDVARHFFTVAEVKRYIDLLALYKLNVLHLHLTDDQGWRIEIKSWPKLTEIGGSTEVgggpGGYYTQEDY KDI 80 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 243 IEYARLRGIRVLAEFDTPGHTLSWGPGIPGL----LTPCYSGSEPSgtFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYL 317 Cdd|cd06568 81 VAYAAERHITVVPEIDMPGHTNAALAAYPELncdgkAKPLYTGIEVG-FSSLDVDKPTTYEFVDDVFRELAALTPGPYI 158 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 318 HLGGDEVDFTcwksnPEiqdfmrkkgfgEDFKqlesFYIQTLLDIVSSYGKGYVVWQEVfdNKVKIQPDTIIQVWRE DIP 397 Cdd|cd06568 159 HIGGDEAHST-----PH-----------DDYA----YFVNRVRAIVAKYGKTPVGWQEI-ARADLPAGTVAQYWSDRAP 216 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 398 vnyMKELELVTKAGFRALLS--APWYLNR----------ISYGP-DWKDFYIVEPLAFE- GTPEQkaLVIGGEACMWGEY 463 Cdd|cd06568 217 --DADAAAALDKGAKVILSpaDKAYLDMkydadsplglTWAGPvEVREAYDWDPAAYGpGVPDE--AILGVEAPLWTET 291 330 340 350 ....*....|....*....|....*....| gi 189181666 464 VDNT-NLVPRLWPRAGAVAERLWSNKLTSD 492 Cdd|cd06568 292 IRNLdDLEYMAFPRLAGVAEIGWSPQEARD 321 cd06564, GH20_DspB_LnbB-like, Glycosyl hydrolase family 20 (GH20) catalytic domain of 119334 yes 2e-22 dispersin B (DspB), lacto-N-... Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6linkages of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major component of the extracellular polysaccharide matrix. Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I oligosaccharides at the nonreducing terminus to produce lacto-N-biose as part of the GNB/LNB (galacto-N-biose/lacto-N-biose I) degradation pathway. The lacto-Nbiosidase from Bifidobacterium bifidum has this GH20 domain, a carbohydrate binding module 32, and a bacterial immunoglobulin-like domain 2, as well as a YSIRK signal peptide and a G5 membrane anchor at the N and C termini, respectively. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Cd Length: 326 Bit Score: 102.75 E-value: 2e-22 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 168 PHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHL------VDDPSFPYESFTFPELMRKGSYNPVTHI-----YT 235 Cdd|cd06564 1 EVRGFMLDVGRKYYSMDFLKDIIKTMSWYKMNDLQLHLndnlifnLDDMSTTVNNATYASDDVKSGNNYYNLTandg yYT 80 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 236 AQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSlnnTYEFMSTFFLEVSSVF PDF 315 Cdd|cd06564 81 KEEFKELIAYAKDRGVNIIPEIDSPGHSLAFTKAMPELGLKNPFSKYDKDTLDISNPE--AVKFVKALFDEYLDGFNPK 157 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 316 -YLHLGGDEvdftcwksnpeiqdFMRKKGFGEDFKQlesfYIQTLLDIVSSYGKGYVVWQ--EVFDNKVKIQPDTIIQ 390 Cdd|cd06564 158 sdTVHIGADE--------------YAGDAGYAEAFRA---YVNDLAKYVKDKGKTPRVWGdgiYYKGDTTVLSKDVIIN 219 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 391 VWREDipvnYMKELELVTKaGFRaLLSAP--WY---LNRISYGPDWKDFYI--VEPLAFEGT----PEQKALVIGGEAC 458 Cdd|cd06564 220 YWSYG----WADPKELLNK-GYKIINTNdgYLyivPGAGYYGDYLNTEDIynnWTPNKFGGTnatlPEGDPQILGGMFA 293 330 340 350 ....*....|....*....|....*....|. gi 189181666 459 MWGEYVDNT----NLVPRLWPRAGAVAERLW 485 Cdd|cd06564 294 IWNDDSDAGisevDIYDRIFPALPAFAEKTW 324 cd06569, GH20_Sm-chitobiase-like, The chitobiase of Serratia marcescens is a beta-N-1,4- 119337 no 1e-21 acetylhexosaminidase with a... The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetylD-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Cd Length: 445 Bit Score: 99.67 E-value: 1e-21 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 163 DFPRFPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSY-------------- 227 Cdd|cd06569 1 DAPRFEYRGMHLDVARNFHSKETVLKLLDQMAAYKLNKLHLHLTDDEGWRLEIPGLPELTEVGAKrchdlsettcll pql 80 90 100 110 120 ....*....|....*....|....*....|....*....|.. gi 189181666 228 -------NPVTHIYTAQDVKEVIEYARLRGIRVLAEFDTPGH 262 Cdd|cd06569 81 gsgpdtnNSGSGYYSRADYIEILKYAKARHIEVIPEIDMPGH 122 119335 cd06565, GH20_GcnA-like, Glycosyl hydrolase family 20 (GH20) catalytic domain of Nno 7e-11 acetyl-beta-D-glucosaminidase... Glycosyl hydrolase family 20 (GH20) catalytic domain of N-acetyl-beta-D-glucosaminidase (GcnA, also known as BhsA) and related proteins. GcnA is an exoglucosidase which cleaves N-acetyl-beta-D-galactosamine (NAG) and Nacetyl-beta-D-galactosamine residues from 4-methylumbelliferylated (4MU) substrates, as well as cleaving NAG from chito-oligosaccharides (i.e. NAG polymers). In contrast, sulfated forms of the substrate are unable to be cleaved and act instead as mild competitive inhibitors. Additionally, the enzyme is known to be poisoned by several first-row transition metals as well as by mercury. GcnA forms a homodimer with subunits comprised of three domains, an N-terminal zincin-like domain, this central catalytic GH20 domain, and a C-terminal alpha helical domain. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Cd Length: 301 Bit Score: 64.15 E-value: 7e-11 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 169 HRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDdpSFPYESFtfPELMRkgSYNPvthiYTAQDVKEVIEYAR 247 Cdd|cd06565 1 FRGVHLDLKRNAVPkVSYLKKLLRLLALLGANGLLLYYED--TFPYEGE--PEVGR-MRGA----YTKEEIREIDDYAA 70 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 248 LRGIRVLAEFDTPGHT---LSWGPgipglltpcYSG---SEPSGTFgpvNPSLNNTYEFMSTFFLEVSSVFPDFYLHLG 320 Cdd|cd06565 71 ELGIEVIPLIQTLGHLefiLKHPE---------FRHlrevDDPPQTL--CPGEPKTYDFIEEMIRQVLELHPSKYIHIG 138 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 321 GDEVdftcwksnpeiQDFMR---KKGFGEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFdNKVKIQPDTIIQVWREDI 396 Cdd|cd06565 139 MDEA----------YDLGRgrslRKHGNLGRGELYLEHLKKVLKIIKKRGPKPMMWDDML-RKLSIEPEALSGLPKLVT 206 ... gi 189181666 397 PVN 399 Cdd|cd06565 207 PVV 209 cd06569, GH20_Sm-chitobiase-like, The chitobiase of Serratia marcescens is a beta-N-1,4- 119337 no 7e-08 acetylhexosaminidase with a... The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetylD-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Cd Length: 445 Bit Score: 53.83 E-value: 7e-08 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 290 VNPSLNNTYEFMSTFFLEVSSVFPDFY-----LHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIV 363 Cdd|cd06569 171 INPCMPSTYRFVDKVIDEIARMHQEAGqplttIHFGGDEVPEGAWGGSPACKAqLFAKEGSVKDVEDLKDYFFERVS KIL 250 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 364 SSYGKGYVVWQEVFDNKVKIQPDTI------IQVWRedipVNYMKELELVTK--AGFRALLSAPWYL------------ 422 Cdd|cd06569 251 KAHGITLAGWEDGLLGKDTTNVDGFatpyvwNNVWG---WGYWGGEDRAYKlanKGYDVVLSNATNLyfdfpyekhpee 326 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 423 ------NRI-------SYGPD--------WKDFYIVEPLAFEG---TPEQKALVIGGEACMWGEYVDNTNLVPRL-WPR 476 Cdd|cd06569 327 rgyywaGRFvdtkkvfSFMPDnlyanaevTRDGDPIDDTALNGkvrlTLEGPKNILGLQGQLWSETIRTDEQLEYMv FPR 406 ....*.... gi 189181666 477 AGAVAERLW 485 Cdd|cd06569 407 LLALAERAW 415 pfam00728, Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic domain Glycosyl hydrolase family 20, catalytic domain Cd Length: 335 Bit Score: 317.37 E-value: 3e-87 10 60 70 80 20 30 144359 40 no 3e-87 50 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 167 FPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVThIYTAQDVKEVI EYA 246 Cdd|pfam00728 1 FPYRGLMLDVARHFFSVDTIKRLIDAMAFYKLNVLHWHLTDDQGWRLEIKAYPELTEVGAYRGSDFYTQEDIREIVAYA 79 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 247 RLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGS-EPSGTFGP---VNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGG 321 Cdd|pfam00728 80 AARGIEVIPEIDMPGHARAALKAYPELGCKPEDTSwYVSVQVGPpngtLNPGNPKTYDFLDKVLDEVAELFPSEYIH IGG 159 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 322 DEVDFTCWKSNPEIQDFMRKKGFGEDfkqLESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWRedipvNY 400 Cdd|pfam00728 160 DEVNKGCWLKSPKCQAFMKQEGLKSE--LQSYFIKRVVKIVKKRGKKPIGWEEILTGGGtLLPPDTTVQSWR-----NG 231 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 401 MKELELVTKAGFRALLSAP--WYL------NRISYGPDW-----KDFYIVEPLAFEGT-PEQKALVIGGEACMWGEYV- 464 Cdd|pfam00728 232 GAQARQAANQGYKVILSPGdfLYLdhgygkWPTERGYYWagfmplKKFYAWEPPYDTWGaPLEAGNVLGGEAALWGE YIr 311 330 340 ....*....|....*....|.... gi 189181666 465 DNTNLVPRLWPRAGAVAERLWSNK 488 Cdd|pfam00728 312 DPENLEYMVFPRLAALAERAWSPP 335 pfam02838, Glyco_hydro_20b, Glycosyl hydrolase family 20, domain 2 Glycosyl hydrolase family 20, domain 2 Cd Length: 131 Bit Score: 180.30 E-value: 8e-46 10 60 70 80 20 30 111707 40 no 8e-46 50 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 35 QRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLE SVE 114 Cdd|pfam02838 1 QLIHLAPGNFVITHSLPSPAQTSCSLLKVAFARYINLIFGFKAWQFPSVNFRAETVIKSVLVPVVVTSPCDSLQSLG SDE 80 90 100 110 120 130 ....*....|....*....|....*....|....*....|....*....|. gi 189181666 115 NYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFP 165 Cdd|pfam02838 81 SYTLSIKSDGIVIKANTVWGALRGLETLSQLIVYDSEGTFVINQVSISDSP 131 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism] 33328 yes 2e-44 N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism] Cd Length: 732 Bit Score: 175.62 E-value: 2e-44 10 70 80 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 91 EKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLV-WKSAEGTFFINKTEIEDFPRFP 168 Cdd|COG3525 183 EKGLSPLQADKYYPNRKGPTLGEEAYRLAINDKAIKVTAHDLAGLFYADGTLLQLDtsADSFQGDIRFPAVTIVDAP RFA 262 90 100 110 120 130 140 150 160 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 169 HRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSY--------------NPVTHI 233 Cdd|COG3525 263 WRGLLVDVARQFHSTDDVKRLIDQLAAHKLNVLHLHLTDDEGWRLEIKRYPKLTTIGAWripdepdlpqlgygpERM GGF 342 170 180 190 200 210 220 230 240 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 234 YTAQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGL-LTPCYSGSEPSGTFGP--VNPSLNNTYEFMSTFFLEVS 309 Cdd|COG3525 343 YTQDDIRELVAYASARQITVIPEIDMPGHARAAVVAYPDLnLGRADPDSYDSVQAYLnpvLNPTLDPTYQFLDKVLD EVA 422 250 260 270 280 290 300 310 320 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 310 SVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFgEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFD----NKVKIQ 384 Cdd|COG3525 423 DLFPSTTIHIGGDEFIDGQWKaSSPLVQALMEKLGNKDTFELQSYFITQVGKTLASKGRRLIGWDEGAHggdvNGTALT 501 330 340 350 360 370 380 390 400 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.. ..| gi 189181666 385 PDTIIQVWRedipvNYMKELELVtKAGFRALLS-APWYLNRISYGPDW-------------KDFYIVEPLAFEGT-PEQ 448 Cdd|COG3525 502 ANVTVMSWY-----GKDKAIELAKQGYDVVLTpAQFVYLDMLQIAAPeepgyswatttpleRNKYAYDFAGKQPInDEL 575 410 420 430 440 450 ....*....|....*....|....*....|....*....|....*....|.... gi 189181666 449 KALVIGGEACMWGEYVDN-TNLVPRLWPRAGAVAERLWSNKLTSDLTFAYERLS 501 Cdd|COG3525 576 AKRILGVQAALWSEHIQTrGRFEYMVFPRLAAAAERAWTPMAFNDWLYYLDRLS 629 Biology Workbench Use Biology Workbench to: Import the FASTA sequence into the Biology Workbench and search for similar proteins using BLASTP. Pick a diverse group of hits to perform a ClustalW alignment. Do a multiple alignment and display the results with BOXSHADE. Do the conserved areas of the protein align with certain domains? Yes Display the evolutionary relationships in a rooted and unrooted tree. Download a PostScript version of the output Download a PostScript version of the output Examine and compile all relevant information. Save all information which you think may be useful for your presentation. (HINT: Are there mutations associated with your disease found in conserved regions?) Submit: The BOXSHADE, DRAWTREE and DRAWGRAM images for your protein.