Align D-lysine oxidase (EC 1.4.3.3) (characterized)
to candidate 6937363 Sama_1533 D-amino-acid dehydrogenase (RefSeq)
Query= metacyc::G1G01-3833-MONOMER (414 letters) >FitnessBrowser__SB2B:6937363 Length = 428 Score = 173 bits (439), Expect = 8e-48 Identities = 126/417 (30%), Positives = 193/417 (46%), Gaps = 13/417 (3%) Query: 4 QTLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPRQLS 63 Q +V+GAG++G++ A+ L RG +V +ID++ +G S GNAG V P A P L Sbjct: 19 QVIVIGAGVIGLANAVTLARRGFKVTVIDKEGVAAGASFGNAGHFATEQVFPLADPSLLP 78 Query: 64 ALLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEHDAL 123 L + L+ R A+ +A PW R+ P R + L R + L Sbjct: 79 KLPKMLLDPLGPFRIRPAYFHRALPWFVRFIVNMMPARRQHNGNAIKALNARSMAATKEL 138 Query: 124 IAAAGLEGLVQAKGWIEVF--RDPALFEQAKTDAKGLSRYGLRFEILECGQLQAREHQLD 181 + G L+ G + VF +DP + EQ + + G+ +L + +A E L Sbjct: 139 LTFCGRADLLVENGSLLVFETQDPRVMEQ---ELALYNDAGIAVRLLSGDEARALEPDLS 195 Query: 182 ATVVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQANGQWRVESRRGPI 241 + G + + + NP A+ A GG+ SL+ N V + G + Sbjct: 196 DAISGALWFTEVGHTPNPRAICEALADTLKALGGRIEIDSVCSLQGGNTP-SVTTETGKV 254 Query: 242 T-ADEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQLEHSICDTQGGYVLAP 300 T AD+++ C G S L LG+++PL +RGYH+ G L+ + + +++ P Sbjct: 255 TKADKLLLCAGAWSRPLALKLGHRVPLETERGYHLMMPQHSG--LKRPVASYERKFIITP 312 Query: 301 MARGVRLTTGIEFDAASAPGNQIQLGRCEALARKLFP---ALGDRLDDTPWLGRRPCLPD 357 M G RL +EF +AP + + AR L P A + W+G RP LPD Sbjct: 313 MEDGTRLAGTVEFGGLNAPMSNARADCLLPHARVLLPKVFATARVSEGKRWMGFRPSLPD 372 Query: 358 MRPVIGPAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRFD 414 PV+G + + PG++F FGH H GLT LL +L+ GE P D +PY RFD Sbjct: 373 SLPVLGES-QTPGVYFAFGHQHLGLTWAASSAELLGQLICGETPSIDLSPYCVKRFD 428 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: 452 Number of extensions: 30 Number of successful extensions: 6 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: 428 Length adjustment: 32 Effective length of query: 382 Effective length of database: 396 Effective search space: 151272 Effective search space used: 151272 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