Align L-amino-acid oxidase (EC 1.4.3.2); L-arginine oxidase (EC 1.4.3.25) (characterized)
to candidate Synpcc7942_0946 Synpcc7942_0946 UDP-galactopyranose mutase
Query= BRENDA::P72346 (495 letters) >FitnessBrowser__SynE:Synpcc7942_0946 Length = 495 Score = 999 bits (2584), Expect = 0.0 Identities = 495/495 (100%), Positives = 495/495 (100%) Query: 1 MRFSRRRFLQSSLGAAATTGLAGTLAAGGQAQTRSTPVRKRSVLVLGAGMAGLTAALSLL 60 MRFSRRRFLQSSLGAAATTGLAGTLAAGGQAQTRSTPVRKRSVLVLGAGMAGLTAALSLL Sbjct: 1 MRFSRRRFLQSSLGAAATTGLAGTLAAGGQAQTRSTPVRKRSVLVLGAGMAGLTAALSLL 60 Query: 61 RRGHQVTVIEYQNRIGGRLLSVPLKGGQFSEAGGGHFRANMPYVLSYIRHFKLPLLTLND 120 RRGHQVTVIEYQNRIGGRLLSVPLKGGQFSEAGGGHFRANMPYVLSYIRHFKLPLLTLND Sbjct: 61 RRGHQVTVIEYQNRIGGRLLSVPLKGGQFSEAGGGHFRANMPYVLSYIRHFKLPLLTLND 120 Query: 121 GLPRYLFDGKTADAADLSRWPWDLAPQERRVSVASLLNTYLILNGLDTDTVLDANWPDAQ 180 GLPRYLFDGKTADAADLSRWPWDLAPQERRVSVASLLNTYLILNGLDTDTVLDANWPDAQ Sbjct: 121 GLPRYLFDGKTADAADLSRWPWDLAPQERRVSVASLLNTYLILNGLDTDTVLDANWPDAQ 180 Query: 181 AIQQLDNLTLSQLIRQVGGSEAFIQLLDAHGGTFTSSSPALGVIPDLAYHFGDQNLFRIQ 240 AIQQLDNLTLSQLIRQVGGSEAFIQLLDAHGGTFTSSSPALGVIPDLAYHFGDQNLFRIQ Sbjct: 181 AIQQLDNLTLSQLIRQVGGSEAFIQLLDAHGGTFTSSSPALGVIPDLAYHFGDQNLFRIQ 240 Query: 241 GGNDRLPKAMAAAIGSERFILDAPVVAIDQQANRATVTVKDGRTFQGDAIISTIPFTVLP 300 GGNDRLPKAMAAAIGSERFILDAPVVAIDQQANRATVTVKDGRTFQGDAIISTIPFTVLP Sbjct: 241 GGNDRLPKAMAAAIGSERFILDAPVVAIDQQANRATVTVKDGRTFQGDAIISTIPFTVLP 300 Query: 301 EVAVRPGWSAGKRRMFAEMEWEQTVKVIAQTRSPVWLAQNVHGWPMAGSDRPWERVIDIT 360 EVAVRPGWSAGKRRMFAEMEWEQTVKVIAQTRSPVWLAQNVHGWPMAGSDRPWERVIDIT Sbjct: 301 EVAVRPGWSAGKRRMFAEMEWEQTVKVIAQTRSPVWLAQNVHGWPMAGSDRPWERVIDIT 360 Query: 361 GNEGGGYGNTFFYLNGRNKDAMLARPKSERAQAIVDQFRSDLPDLFDEVVTLADFAWGEQ 420 GNEGGGYGNTFFYLNGRNKDAMLARPKSERAQAIVDQFRSDLPDLFDEVVTLADFAWGEQ Sbjct: 361 GNEGGGYGNTFFYLNGRNKDAMLARPKSERAQAIVDQFRSDLPDLFDEVVTLADFAWGEQ 420 Query: 421 PWIRGSFGGPPLGGAWMIREWTTPEGLIHFAGDFTTMKSGWVEGAIESGLRAARQIDPGA 480 PWIRGSFGGPPLGGAWMIREWTTPEGLIHFAGDFTTMKSGWVEGAIESGLRAARQIDPGA Sbjct: 421 PWIRGSFGGPPLGGAWMIREWTTPEGLIHFAGDFTTMKSGWVEGAIESGLRAARQIDPGA 480 Query: 481 QPEADTFLRQEQRCN 495 QPEADTFLRQEQRCN Sbjct: 481 QPEADTFLRQEQRCN 495 Lambda K H 0.320 0.136 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: 1090 Number of extensions: 33 Number of successful extensions: 1 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: 495 Length of database: 495 Length adjustment: 34 Effective length of query: 461 Effective length of database: 461 Effective search space: 212521 Effective search space used: 212521 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 (21.8 bits) S2: 52 (24.6 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