Align Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter
Query= uniprot:Q9KZP2 (149 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17540 Length = 837 Score = 85.1 bits (209), Expect = 2e-21 Identities = 52/142 (36%), Positives = 77/142 (54%), Gaps = 1/142 (0%) Query: 4 VSSPLAGRAIGLAAVPDPVFSGAMVGPGTAIDPVREPSEAVAPVDGVIVSLHPHAFVVVD 63 +S+PL+G + LA VPD VF+ +G G AIDP+ + A + + V+ HA + Sbjct: 10 LSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVARTGHAVTLRA 69 Query: 64 ESGHGVLTHLGIDTVQLNGEGFELLVNKGDTVVRGQGVVRWDPAAVEAAGKSPICPIVAL 123 ++G +L HLG+DTV+L GEGF +LV +G V GQ ++R+D V KS + +V Sbjct: 70 DNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCKSLVSLLVIT 129 Query: 124 EATAEALADLREDGDVKAGESL 145 + G VK GE L Sbjct: 130 NGEHFQARPITLKG-VKVGEPL 150 Lambda K H 0.316 0.136 0.402 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: 323 Number of extensions: 19 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: 149 Length of database: 837 Length adjustment: 28 Effective length of query: 121 Effective length of database: 809 Effective search space: 97889 Effective search space used: 97889 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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