Align D-lysine oxidase (EC 1.4.3.3) (characterized)
to candidate BPHYT_RS26530 BPHYT_RS26530 amino acid dehydrogenase
Query= metacyc::G1G01-3833-MONOMER (414 letters) >FitnessBrowser__BFirm:BPHYT_RS26530 Length = 409 Score = 165 bits (418), Expect = 2e-45 Identities = 123/415 (29%), Positives = 191/415 (46%), Gaps = 19/415 (4%) Query: 7 VLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPRQLSALL 66 ++GAG +G+++A+ L G +V L D G G S GNAG + IP P L Sbjct: 6 IIGAGFIGLASAVALMRDGHRVTLFDPAGVGQGASFGNAGTFAHYACIPVNNPSVFRDLP 65 Query: 67 RYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEHDALIAA 126 R+ L+ Q R +LP PWL R+ S P R +A + L+ D + L+A Sbjct: 66 RFLLSNQSPFRLRWGYLPHLTPWLVRFMMSSLPQRYETSAGALAALLDCAQDGYAPLLAN 125 Query: 127 AGLEGLVQAKGWIEVFRDPALFEQAKTDAKGLSRYGLRFEILECGQLQAREHQLDATVVG 186 A L V+ + + ++ + A F+ A+ + G+ FE+L+ ++A E L Sbjct: 126 AELARFVRPRECLYLYSNAASFDAARPALDLRHKLGVAFEVLDGAAIRALEPALAPIFER 185 Query: 187 GI------HWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQANGQWRVESRRGP 240 G+ H+ DP+ G L Y L Q G + +++ + Sbjct: 186 GVLFSNSWHFSDPQ-----GFLQTLYEQLAAQ-GLKLERSTVDAVQPGTDSASLTVGGMT 239 Query: 241 ITADEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQ--LEHSICDTQGGYVL 298 D VV G +SA S G +PL +RGYH+ + GAQ + + + G+ + Sbjct: 240 RRFDHVVVATGARSAQFASQCGDSVPLDTERGYHVRF---PGAQQLVSRPVGWAERGFYM 296 Query: 299 APMARGVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPDM 358 PM+ G+R+ +E N+ L +++ PAL D+ WLG RP LPD Sbjct: 297 TPMSDGLRVAGTVELAGFGDTRNRSLLDLLTFSSKRALPALD--TPDSDWLGFRPTLPDG 354 Query: 359 RPVIGPAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRF 413 PV+ + + + FGH H GLTL V GR++A+L+ P D APY+ATRF Sbjct: 355 VPVLARSRASARVIYAFGHQHLGLTLAGVSGRIVADLIAQRAPPLDLAPYAATRF 409 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: 465 Number of extensions: 21 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: 409 Length adjustment: 31 Effective length of query: 383 Effective length of database: 378 Effective search space: 144774 Effective search space used: 144774 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