Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_156167385.1 AAV99_RS05200 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_001013305.1:WP_156167385.1 Length = 258 Score = 124 bits (311), Expect = 2e-33 Identities = 76/253 (30%), Positives = 125/253 (49%), Gaps = 16/253 (6%) Query: 7 PPLPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKG 66 PP L + KS+ + + + V +G + GL+GPNGAGKTT F + ++PD G Sbjct: 17 PPEGGLEVVSIAKSYDKRSVLSDISLSVGKGEVLGLLGPNGAGKTTCFYSIMGLVKPDSG 76 Query: 67 RVIFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQP 126 R++ DG + +L ++ A G+ Q ++V +N + Sbjct: 77 RILMDGVDVTRLPMYRRAILGLGYLPQETSIFRGMTVEQN---------------INCVL 121 Query: 127 QVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEP 186 ++V ++ + LL+ GL + A LSGG+R+ E+ RAL +P ++LLDEP Sbjct: 122 EMVEPDKATRARELERLLDEFGLTRLRSSPAMALSGGERRRCEIARALAASPSIMLLDEP 181 Query: 187 AAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAE 246 AG++P I DI D + + G+ LI +HN+ + + DR ++ GQ L G+P E Sbjct: 182 FAGIDPLSISDIRDLVADLKNR-GIGVLITDHNVRETLEIVDRACIIYGGQVLFAGSPQE 240 Query: 247 IQTNSQVLEAYLG 259 + + V YLG Sbjct: 241 LVADENVRRLYLG 253 Lambda K H 0.319 0.136 0.391 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: 132 Number of extensions: 9 Number of successful extensions: 3 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: 260 Length of database: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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