Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate AZOBR_RS25655 AZOBR_RS25655 oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__azobra:AZOBR_RS25655 Length = 426 Score = 209 bits (532), Expect = 1e-58 Identities = 135/394 (34%), Positives = 187/394 (47%), Gaps = 3/394 (0%) Query: 9 RQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGH 68 R LWE + P A L +AD+ VIGGG TGLSAA+H E GK +VLEA +IG Sbjct: 4 RPDSLWEATAPPPPALPVLKDSVEADLLVIGGGFTGLSAALHAAESGKRAVVLEASEIGR 63 Query: 69 GGSGRNVGLVNAGTWIRPD--DVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQ 126 G SGRN G V T RPD D+ A GQ++G R ++ ++ +FA+I RL IDC A+ Sbjct: 64 GASGRNNGQV-IPTLTRPDPEDLIAKFGQERGERFVALIRDSAETLFALIRRLNIDCAAE 122 Query: 127 HKGTLHMAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTI 186 G + H+ IA E R +QW RGA VELL A GTD ++R G I Sbjct: 123 QTGWVQPVHSPGRIAIAERRAKQWGSRGAPVELLDRAGISALLGTDAYYGGWMNRSGGHI 182 Query: 187 NPMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEG 246 NP+ +GLA G +F S V +ER GD W +T G V +V+ T Y Sbjct: 183 NPLALARGLAGKAVEAGASVFINSPVLSVERRGDRWVARTPDGTVTTHALVLGTNGYAAA 242 Query: 247 DWSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSL 306 + ++ + +Q+A++PL +LP Q DT L +R RL+ G Sbjct: 243 VFPEIRTEVVPVLSWQMATQPLDEAQRRSILPGRQAMSDTHGDLRFMRYTADHRLVSGGA 302 Query: 307 GRVDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVT 366 V A +R + +P L + ++ W G I T D+ R+ + P Sbjct: 303 LLVPVDGADRLRRIVGLRLASMFPTLRGLRFDYVWNGRIAMTTDYTPRVHQLGPNAFTWA 362 Query: 367 GYNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFS 400 G NGRG +GR A L + L +P + Sbjct: 363 GCNGRGVALSVSLGRELAYAALGRDPAELALPLT 396 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: 477 Number of extensions: 24 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: 426 Length adjustment: 32 Effective length of query: 400 Effective length of database: 394 Effective search space: 157600 Effective search space used: 157600 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