Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate HSERO_RS05840 HSERO_RS05840 FAD-dependent oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__HerbieS:HSERO_RS05840 Length = 433 Score = 243 bits (621), Expect = 6e-69 Identities = 147/416 (35%), Positives = 210/416 (50%), Gaps = 8/416 (1%) Query: 13 LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72 LW + A L + DV ++G G TGLS A+HL + G SV VL+A G G SG Sbjct: 13 LWAATAGEFSGAPPLQASARYDVAIVGAGYTGLSTALHLAQAGVSVCVLDAHAPGWGASG 72 Query: 73 RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132 RN G V G PD + G L +G A VF +I R GI+C+AQ G + Sbjct: 73 RNGGQVIPGLKYDPDQLRVMFGSAVADPLIAAIGSAADTVFDLIARHGIECEAQRAGWIQ 132 Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 H+ + LEAR QW GA +L+ GA+ GT D RAG+++P+ Y Sbjct: 133 PTHSPKMMRALEARARQWMAEGAPAQLMDGAEVTRRIGTGAYVGGWKDERAGSLHPLKYC 192 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGA----VRAEKVVISTGAYTEGDW 248 +GLA A RLG I + V LER GWR+ G + AE+VV++T YT+ W Sbjct: 193 RGLAQAAQRLGVVIHGDTRVTRLERRQGGWRLHGPSGEQGPHIDAERVVLATNGYTDDLW 252 Query: 249 SNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGR 308 +L++ + VA++PL +LP G+ + D+R +L RRD QGRLL+G G Sbjct: 253 PHLRQSVIAANSFIVATRPLPPALGASILPGGEVTSDSRRLLLYYRRDAQGRLLMGGRGP 312 Query: 309 VDNK--PAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVT 366 PA F +R + +P+L VE+E W+G + T D L + EPAPGL Sbjct: 313 FGEPQGPADFAH--LERSVALLFPQLAGVEYEYRWSGRVAITRDFLPHVHEPAPGLSIAL 370 Query: 367 GYNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLY 422 GYNGRG T++G+ A+ L+ + P P S ++ + L+ + +G + Y Sbjct: 371 GYNGRGIAMATMMGQRLAQRLIGPAGTAFPFPVSTIAPIPLHGLQRFYIAAGVAWY 426 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: 516 Number of extensions: 29 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: 433 Length adjustment: 32 Effective length of query: 400 Effective length of database: 401 Effective search space: 160400 Effective search space used: 160400 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