Align D-lysine oxidase (EC 1.4.3.3) (characterized)
to candidate BPHYT_RS10270 BPHYT_RS10270 D-amino acid dehydrogenase
Query= metacyc::G1G01-3833-MONOMER (414 letters) >FitnessBrowser__BFirm:BPHYT_RS10270 Length = 413 Score = 439 bits (1129), Expect = e-128 Identities = 230/414 (55%), Positives = 271/414 (65%), Gaps = 3/414 (0%) Query: 1 MHCQTLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPR 60 M +VLGAGIVGVS+ALHLQ RGR+V L+DR PG TS GNAGLIE SSV+PYAFPR Sbjct: 1 MDFDVIVLGAGIVGVSSALHLQDRGRRVALVDRRGPGEETSFGNAGLIESSSVVPYAFPR 60 Query: 61 QLSALLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEH 120 L LLRY NR D+ + LP A WL R+W +S+P RL AA DMLPL++ V EH Sbjct: 61 NLGTLLRYARNRSTDLYWDYRALPSFAGWLARFWWESSPERLMAAAHDMLPLMRHSVAEH 120 Query: 121 DALIAAAGLEGLVQAKGWIEVFRDPALFEQAKTDAK-GLSRYGLRFEILECGQLQAREHQ 179 D LIA AGLE L KGWIE FR PA F + A+ + YGLR L+ L ARE Sbjct: 121 DVLIARAGLEQLASDKGWIEAFRTPAEFSRQSAAAEVTANTYGLRVTTLDAAALAAREPG 180 Query: 180 LDATVVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQANGQWRVESRRG 239 + G +HW DPK++ NPGALT+GYA LF + GG + GDA +L+ G W V++ G Sbjct: 181 VAEGFCGALHWQDPKSIVNPGALTQGYARLFEESGGALLTGDATTLKAEGGAWTVQTSSG 240 Query: 240 PITADEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQLEHSICDTQGGYVLA 299 I+A EVV LGP S +F+ LGY+IPL KRGYHMHY L + D+Q GYV+A Sbjct: 241 RISAKEVVVALGPWSDRVFAPLGYRIPLRAKRGYHMHYQPTQ-PMLSTPLVDSQQGYVVA 299 Query: 300 PMARGVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPDMR 359 PM +RLTTG+E A +QL R E AR F LG RLD+ PWLG RPC PDMR Sbjct: 300 PMQGRLRLTTGVEIARREAAPTGVQLERAERTARPTF-GLGARLDEHPWLGLRPCTPDMR 358 Query: 360 PVIGPAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRF 413 PVIGPAPRH GLWF FGH HHGLTLGPV GRLLAE++TG PF D P+ RF Sbjct: 359 PVIGPAPRHRGLWFAFGHNHHGLTLGPVTGRLLAEMMTGAEPFVDARPFRPERF 412 Lambda K H 0.322 0.140 0.447 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: 574 Number of extensions: 22 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: 414 Length of database: 413 Length adjustment: 31 Effective length of query: 383 Effective length of database: 382 Effective search space: 146306 Effective search space used: 146306 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 (21.9 bits) S2: 50 (23.9 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