Align UPF0237 protein MMP0657 (characterized, see rationale)
to candidate AO353_13070 AO353_13070 phosphoserine phosphatase
Query= uniprot:Q6LZH1 (90 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13070 Length = 404 Score = 51.2 bits (121), Expect = 1e-11 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 3/74 (4%) Query: 2 ENVVITVVGVDKPGIVAEVTKVLAQNSANIVDIRQTIMEDLFTMIMLVDISKISSDFSEL 61 E V+I + GVD+PG+ A +T VLAQ NI+DI Q ++ D + +LV+I S L Sbjct: 3 EIVLINITGVDRPGLTAAITGVLAQGGVNILDIGQAVIHDTLSFGILVEIPDTEQGSSVL 62 Query: 62 NVALEK---LGSEI 72 L K LG ++ Sbjct: 63 KDILFKAYELGQQV 76 Lambda K H 0.320 0.136 0.355 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: 67 Number of extensions: 2 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: 90 Length of database: 404 Length adjustment: 19 Effective length of query: 71 Effective length of database: 385 Effective search space: 27335 Effective search space used: 27335 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: 44 (21.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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