Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate 201365 SO2213 oligo-1,6-glucosidase (NCBI ptt file)
Query= uniprot:I7EUW4 (552 letters) >FitnessBrowser__MR1:201365 Length = 540 Score = 569 bits (1467), Expect = e-167 Identities = 267/500 (53%), Positives = 345/500 (69%), Gaps = 5/500 (1%) Query: 19 WWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFGYD 78 WWRGAVIYQIYPRS D+NGDG+GDLRGI +L +IASL VDAIWISPFF SPM DFGYD Sbjct: 6 WWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMADFGYD 65 Query: 79 VSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNARAD 138 +SDY ++DP+FGS+ +FD+L+ AH+ G++V+ID VLSHTSDQHAWF ESR+SR N +AD Sbjct: 66 ISDYREIDPLFGSMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFIESRESRTNPKAD 125 Query: 139 WYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDALLD 198 WYVWADP+ DGTPPNNWL+IFGG AW+W+PRR+QYYLHNFL SQPD+NFH+P V+ A+LD Sbjct: 126 WYVWADPREDGTPPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVRQAVLD 185 Query: 199 VTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYNHQEHLYSKNQ 258 FWL++GVDGFRLD I F +HD LR NPA P E+R NPY +Q H Y+ ++ Sbjct: 186 NVEFWLKKGVDGFRLDAITFCFHDELLRDNPAKPKEKRQGRGFSEDNPYAYQYHYYNNDR 245 Query: 259 PENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFELLAKDVL 318 P+ + F+ R L++ YP +GEV A+ L +M +YT + +HM Y+FELL D Sbjct: 246 PQTIQFIEALRQLINRYPGTVTLGEV-SAEDSLAVMAAYTKGDDRLHMAYSFELLTDD-Y 303 Query: 319 TASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGLNPAAQ---RLFTTMMMCLRGT 375 +A+ + + ++ +GW CWA NHDV R +SRWG ++ M+ LRG+ Sbjct: 304 SAAYIRQTVEALENSIGDGWPCWAIGNHDVQRVASRWGRGKQTSDMAKMLNAMLCSLRGS 363 Query: 376 TCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNGSGGFSAGKPW 435 C YQGEELGL E I F +LQDP+G FWP FKGRDGCRTPM WE GFS PW Sbjct: 364 VCSYQGEELGLTEVPIEFHELQDPFGKTFWPMFKGRDGCRTPMPWEQYADFSGFSQVSPW 423 Query: 436 LPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAEGNVAFFTRQD 495 LP++ H L+V QEAD ++LH YR+ +A RK +PAL + L A + F R+ Sbjct: 424 LPIAAAHRALAVDLQEADCHSVLHGYRQFLAWRKCYPALITSEIEFLDAPEPLLVFVRKL 483 Query: 496 RDEVIFCAFNLGDIPAEITL 515 ++ + FNL D +++L Sbjct: 484 GEQKLLVCFNLLDAETQLSL 503 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: 931 Number of extensions: 45 Number of successful extensions: 4 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: 540 Length adjustment: 35 Effective length of query: 517 Effective length of database: 505 Effective search space: 261085 Effective search space used: 261085 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: 52 (24.6 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