Align D-lysine oxidase (EC 1.4.3.3) (characterized)
to candidate SMc00797 SMc00797 oxidoreductase
Query= metacyc::G1G01-3833-MONOMER (414 letters) >FitnessBrowser__Smeli:SMc00797 Length = 417 Score = 385 bits (989), Expect = e-111 Identities = 197/416 (47%), Positives = 252/416 (60%), Gaps = 4/416 (0%) Query: 1 MHCQTLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPR 60 M +VLGAGIVG+S+A+HL G+ V+L+DR G TS+GNAGLI+R V PY FP Sbjct: 1 MKTDVVVLGAGIVGISSAIHLARLGKSVVLLDRRGAGEETSYGNAGLIQREGVFPYGFPH 60 Query: 61 QLSALLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEH 120 AL RY LN D Y LP P+L RYW S + A PL++ + EH Sbjct: 61 NFGALFRYALNNTIDASYHFRALPSLVPFLARYWWHSGFTQHQKIAHLYAPLIEHSIAEH 120 Query: 121 DALIAAAGLEGLVQAKGWIEVFRDPALFEQAKTDAKGLSR-YGLRFEILECGQLQAREHQ 179 LI A+G L++ GW++VFR + A DA+ LS +G+ + L +L+ E Sbjct: 121 QDLIDASGAGDLIRKDGWMKVFRTEKERDAAYKDAERLSAGFGVNHQKLSTSELKTIEPS 180 Query: 180 LDATVVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQA--NGQWRVESR 237 + A + GG+ W DP ++ +P +L + Y A F GG+ V GDA +L WRV + Sbjct: 181 IQAELAGGLRWTDPWSIRDPHSLNKAYLAYFQSLGGRLVSGDAATLEHILEGAGWRVATP 240 Query: 238 RGPITADEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQLEHSICDTQGGYV 297 GP+ A EVV LGP + + LGY PLA+KRGYHMHY R+GAQL + + D + GY Sbjct: 241 DGPLEAREVVVALGPWADTVTRKLGYHFPLAVKRGYHMHYGIREGAQLNNWVLDAEKGYF 300 Query: 298 LAPMARGVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPD 357 LAPM RG+RLTTG EF AP +QL R E +AR+ FP L +R D+ PW+G RPC PD Sbjct: 301 LAPMLRGIRLTTGAEFALRDAPKTPVQLTRAERVAREFFP-LAERRDEEPWMGARPCTPD 359 Query: 358 MRPVIGPAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRF 413 M PVIG APRH GLWF FGHAHHG+TLGPV GR LA+ +TGE P D PY RF Sbjct: 360 MMPVIGKAPRHEGLWFAFGHAHHGMTLGPVTGRALAQAMTGEKPVIDITPYRPERF 415 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: 553 Number of extensions: 30 Number of successful extensions: 5 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: 417 Length adjustment: 31 Effective length of query: 383 Effective length of database: 386 Effective search space: 147838 Effective search space used: 147838 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