Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate AZOBR_RS32385 AZOBR_RS32385 FAD-dependent oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__azobra:AZOBR_RS32385 Length = 434 Score = 215 bits (547), Expect = 2e-60 Identities = 133/378 (35%), Positives = 193/378 (51%), Gaps = 3/378 (0%) Query: 27 LAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVG-LVNAGTWIR 85 L G + DV V+G G+TGLS AIHL EQG V+VLEA + G GGSGRN G ++ + + Sbjct: 31 LDGAVRVDVAVVGAGVTGLSTAIHLAEQGVRVVVLEAREPGFGGSGRNNGQIIPTLSRLD 90 Query: 86 PDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEA 145 P ++ A G+ +G+ L +++G + A VF +IER + C KG + AH + E Sbjct: 91 PANLTAAYGEAKGAALARMVGGSAALVFDLIERYQMRCDGVQKGWIQPAHRPGRMKAAEQ 150 Query: 146 RHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGK 205 R QWR GA+V LL AQ + GT A++ G +NP+ + +A A LG Sbjct: 151 RVAQWRALGAEVALLDAAQTERALGTRFWHGAMVALTGGHVNPLSLAREMARAALGLGVA 210 Query: 206 IFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYYYQVAS 265 I + V + R G GW + T RG+V A++VV++T AYT+ W L++ +Q+ + Sbjct: 211 IHSDTPVVSIGRAGTGWTLTTPRGSVTADRVVLATNAYTDDLWPGLRRSVVPVLNFQMVT 270 Query: 266 KPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLG-SLGRVDNKPAWFVRSWADRI 324 +PL VLP DTR L R RL+ G +L R + +RI Sbjct: 271 EPLPAALRASVLPSDMACSDTRGDLHFFRWTADNRLVSGCTLVRSADAERRARERTRERI 330 Query: 325 QSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFA 384 + +P++G W+G + T D E APG+ GYNGRG GT +GR A Sbjct: 331 R-RVFPQIGNPAIARSWSGHLAMTADFRPHFHELAPGVTGAVGYNGRGMALGTAVGRELA 389 Query: 385 EFLLKGEADSLPIPFSPM 402 A L +PF+P+ Sbjct: 390 RHATGTGAPELALPFTPV 407 Lambda K H 0.319 0.135 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: 458 Number of extensions: 20 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: 432 Length of database: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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 (21.7 bits) S2: 51 (24.3 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