Align glycine oxidase (EC 1.4.3.19) (characterized)
to candidate GFF3304 Psest_3368 glycine oxidase ThiO
Query= BRENDA::O31616 (369 letters) >FitnessBrowser__psRCH2:GFF3304 Length = 369 Score = 167 bits (424), Expect = 3e-46 Identities = 112/356 (31%), Positives = 175/356 (49%), Gaps = 22/356 (6%) Query: 6 EAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDF 65 E +V+GGG+IG AY LA+ K +L ESG +G + A G++ A Sbjct: 4 EVIVVGGGVIGLLSAYRLAEAGKAVSLLESGAVGSEASWAGGGIVSPLYPWRYSPAVTAL 63 Query: 66 AMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSW------ 119 A SQ Y LGE L + +GVD H G++ L D+ +++SW Sbjct: 64 AHWSQDFYPQLGERLLSETGVDPEVHVTGLYWLDLH----------DEAEALSWAERYGR 113 Query: 120 ----YSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKML-GAEIFEHTPV 174 S E V + P A +++ +V + +A +A + L + E PV Sbjct: 114 PLTSVSMETVRQAVPSLGESYKRAVYMEGVANVRNPRLLRALREALRQLPNVNVIEQCPV 173 Query: 175 LHVERDGEALF-IKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDD 233 RDG + ++T G++ A+ VVVA+G WS LGL P+KG+ + + Sbjct: 174 KGFLRDGTRIVGVQTAQGEMRADQVVVAAGAWSAQLLATLGLEIPVKPMKGQMILFKCAE 233 Query: 234 IPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMK 293 L + Y +PR+ G ++VG+T++ + +TP LES+ A +LPA+ + + Sbjct: 234 DFLPSMVLAKRRYAIPRRDGHILVGSTLEDVGFDKTPTEDALESLRATAIELLPALADAQ 293 Query: 294 VDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNK 349 V + WAGLRPG+ DG PYIG + GHFRNG++LAPA+ L+ DL++ + Sbjct: 294 VVKHWAGLRPGSPDGVPYIGPVSGFDGLWLNCGHFRNGLVLAPASCQLLVDLMLGQ 349 Lambda K H 0.320 0.137 0.419 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: 319 Number of extensions: 13 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: 369 Length of database: 369 Length adjustment: 30 Effective length of query: 339 Effective length of database: 339 Effective search space: 114921 Effective search space used: 114921 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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