Align glycine oxidase (EC 1.4.3.19) (characterized)
to candidate AZOBR_RS30970 AZOBR_RS30970 glycine oxidase
Query= BRENDA::O31616 (369 letters) >FitnessBrowser__azobra:AZOBR_RS30970 Length = 374 Score = 173 bits (439), Expect = 6e-48 Identities = 123/368 (33%), Positives = 184/368 (50%), Gaps = 18/368 (4%) Query: 9 VIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEE-RDAFFDFAM 67 VIG G+IG +IA+ LA +F+ G G + AA GML A E E ++ Sbjct: 3 VIGAGVIGLSIAWRLAAAGCRVEVFDRGAAGRGASHAAGGMLAACVETEPGEESLLPLTR 62 Query: 68 HSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDS-----VSWYSK 122 SQ L+ EL A SG+ + G +A + +D ++R + D + V W S Sbjct: 63 ASQDLWPAFAAELEAASGMAVDLRGEGTMVIALNADDAAKVRFLHDFQTRLGLPVEWLSG 122 Query: 123 EEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVE-RDG 181 EV +EPY + GA F D V+ V A AA GA + E+ V +E R G Sbjct: 123 AEVRRREPYLQPGVAGALFCAGDHQVDNRKVATALHAAALRAGAVVHEYAEVSRIEVRGG 182 Query: 182 EALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLP----VKGECLSVWNDD-IPL 236 A+ I+ V A+ VV+A+G WSG GL+ A P VKG+ L + D +PL Sbjct: 183 RAVGIQVEDRLVEADQVVLAAGAWSGWID---GLSPAVRPPVRPVKGQMLCLRMDARLPL 239 Query: 237 TK-TLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVD 295 + ++ Y++PR GRL+VGAT + + + GG ++++ A LP I + ++ Sbjct: 240 LRHVVWTPGTYLIPRLDGRLLVGATTEERGFDDRLTAGGQFALLEGAWRALPGIAELPIE 299 Query: 296 RFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDW 355 WAG RPGT+D P +G E +++A GH RNGILL P T ++ L++ E + Sbjct: 300 EAWAGFRPGTRDDAPILGL-SEVEGLVYATGHHRNGILLTPVTADSVARLVLTGEAD-PV 357 Query: 356 LHAFRIDR 363 + F +DR Sbjct: 358 IRPFALDR 365 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: 376 Number of extensions: 26 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: 369 Length of database: 374 Length adjustment: 30 Effective length of query: 339 Effective length of database: 344 Effective search space: 116616 Effective search space used: 116616 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 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