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_055435882.1 ASC41_RS06790 ATP-binding cassette domain-containing protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_001418085.1:WP_055435882.1 Length = 308 Score = 111 bits (278), Expect = 2e-29 Identities = 74/237 (31%), Positives = 121/237 (51%), Gaps = 31/237 (13%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 LL A + K+FG A+ I V +GSI GL+GPNGAGKTTL +++ PDKG+V+ Sbjct: 4 LLEAQSVSKNFGDFTALNNVSISVEKGSIFGLLGPNGAGKTTLIRIINQITMPDKGQVLL 63 Query: 71 DGEPIQQLQPHQIA----QQGMVRTFQVARTLSRLSVLENMLLA-AQKQTGENFWQVQLQ 125 DGEP+Q+ I ++G+ +T +V L+ L+ + A A+K+ E F ++++ Sbjct: 64 DGEPLQRHHIQNIGYLPEERGLYKTMKVGEQALYLAQLKGLDKAEAKKRLHEWFERLEIG 123 Query: 126 PQVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDE 185 K++QE LS G + ++ ++ PKL++ DE Sbjct: 124 DW----WNKKIQE---------------------LSKGMAQKIQFVVTVLHQPKLLIFDE 158 Query: 186 PAAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADG 242 P +G +P D I + IL R+DG T + H M+ + LCD + ++ + + DG Sbjct: 159 PFSGFDPINADIIKNEILRL-REDGATVIFSTHRMESVEELCDHIALIHKSNKILDG 214 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: 145 Number of extensions: 6 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: 308 Length adjustment: 26 Effective length of query: 234 Effective length of database: 282 Effective search space: 65988 Effective search space used: 65988 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