Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate SMc03064 SMc03064 alpha-glucosidase
Query= uniprot:I7EUW4 (552 letters) >FitnessBrowser__Smeli:SMc03064 Length = 551 Score = 753 bits (1945), Expect = 0.0 Identities = 353/511 (69%), Positives = 409/511 (80%), Gaps = 5/511 (0%) Query: 10 AQVLAADPDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFT 69 + +L D DWWRGAVIYQIYPRS+QD+NGDGIGDL+GIT RLPHIA LG DAIWISPFFT Sbjct: 8 SSLLEPDRDWWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFT 67 Query: 70 SPMKDFGYDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESR 129 SPM+DFGYDVS+Y DVDP+FG+L +FD L+A AHRLGLRVMIDLVLSHTSD+H WF ESR Sbjct: 68 SPMRDFGYDVSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESR 127 Query: 130 QSRDNARADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHS 189 SR NA+ADWYVWAD +PDGTPPNNWLSIFGGSAWQWDP R QYYLHNFL SQPDLN H+ Sbjct: 128 SSRSNAKADWYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHN 187 Query: 190 PAVQDALLDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYNH 249 P VQ+ALL V RFWLERGVDGFRLDTINFY+HD ELR NPAL PE+RNA+ AP+VNPYN+ Sbjct: 188 PQVQEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNY 247 Query: 250 QEHLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYA 309 QEH+Y KN+PENL FL RFRA++DE+PA AAVGEVGD+QRGLEI G YT+ VHMCYA Sbjct: 248 QEHIYDKNRPENLEFLKRFRAVMDEFPAIAAVGEVGDSQRGLEIAGEYTSGGDKVHMCYA 307 Query: 310 FELLAKDVLTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWG----LNPAAQRLF 365 FE LA D LT R+AEV + R A GWACWAFSNHDV+RH SRW + A +L Sbjct: 308 FEFLAPDRLTPQRVAEVLRDFHRAAPEGWACWAFSNHDVVRHVSRWADGVTDHDAHAKLL 367 Query: 366 TTMMMCLRGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNG 425 +++M LRGT CIYQGEEL L EA++ +EDLQDPYGI+FWP+FKGRDGCRTPMVWE S Sbjct: 368 ASLLMSLRGTVCIYQGEELALAEAELDYEDLQDPYGIQFWPDFKGRDGCRTPMVWE-SLP 426 Query: 426 SGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAE 485 GGFS+ PWLP+S H+ +VA QE DP ++LHHYRR +A RKA+PALA G + + Sbjct: 427 DGGFSSATPWLPISQSHIPRAVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFVETR 486 Query: 486 GNVAFFTRQDRDEVIFCAFNLGDIPAEITLP 516 G++ F R +E +FC FN+ D A LP Sbjct: 487 GSLLGFLRSHGNEKVFCLFNMSDEAATKELP 517 Lambda K H 0.321 0.137 0.444 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1113 Number of extensions: 48 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 552 Length of database: 551 Length adjustment: 36 Effective length of query: 516 Effective length of database: 515 Effective search space: 265740 Effective search space used: 265740 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory