Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate RR42_RS34300 RR42_RS34300 FAD-dependent oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Cup4G11:RR42_RS34300 Length = 424 Score = 235 bits (600), Expect = 2e-66 Identities = 144/411 (35%), Positives = 207/411 (50%), Gaps = 2/411 (0%) Query: 13 LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72 LW + P AL DV VIGGG TGLS A+HL E G V VLEA + G G SG Sbjct: 7 LWAATAPPAPPTPALRESLATDVLVIGGGFTGLSTALHLAEGGAHVCVLEANEPGWGASG 66 Query: 73 RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132 RN G VN PD++ G + L + + VF +I R GIDCQ G L Sbjct: 67 RNGGQVNPTLKHDPDELVRLFGAARAEPLLDAVSRSADLVFDLIARHGIDCQPVRSGWLQ 126 Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 ++++ + + AR EQW RRGA V++L A GT + LD RAG I P+ YT Sbjct: 127 LSYSPGAVPAMHARAEQWARRGAPVDVLDRAAVARRVGTQAFAGGWLDGRAGAIQPLAYT 186 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGA-VRAEKVVISTGAYTEGDWSNL 251 +GL A R G + ++V L R+G W T+ GA V A++VVI+T YT W L Sbjct: 187 RGLVGAAQRAGATVHGGTAVTALARQGTHWVATTSLGATVTAKQVVIATNGYTGPLWPGL 246 Query: 252 QKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311 + + VA++PL+ A +L G+ + ++ +L R+D GRLL+G G + Sbjct: 247 AQTVLSANSFIVATQPLRDAEAHGILTQGETASTSQRLLLYFRKDALGRLLMGGRGFFAD 306 Query: 312 KPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGR 371 + +R +P+LG + +E W G I T D + + EPAPG++ G NGR Sbjct: 307 PRGPQDFAHLERSLELLFPQLGPLSYEYRWAGRIAITRDFMPHVHEPAPGVIMALGCNGR 366 Query: 372 GNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLY 422 G T +G+ A L G+ P P +P++G+ L+ + +G + Y Sbjct: 367 GIALCTSLGQHIAA-RLAGKGGDFPYPITPVAGIPLHGLQRFYIAAGVAWY 416 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: 482 Number of extensions: 19 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: 424 Length adjustment: 32 Effective length of query: 400 Effective length of database: 392 Effective search space: 156800 Effective search space used: 156800 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