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_067909264.1 AQZ52_RS02410 ATP-binding cassette domain-containing protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_001519075.1:WP_067909264.1 Length = 327 Score = 78.6 bits (192), Expect = 2e-19 Identities = 62/230 (26%), Positives = 104/230 (45%), Gaps = 29/230 (12%) Query: 12 LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKG--RVI 69 + A GL K F G AV I V +GSI G++GPNGAGKTT +L I PD G RV+ Sbjct: 12 IEARGLVKRFDGFTAVDGVDISVPRGSIYGILGPNGAGKTTTLRMLLGIIDPDSGYRRVL 71 Query: 70 FDGEPIQQLQ--PHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQ 127 P + + + ++G+ + + ++ L+ L + L ++ G + Sbjct: 72 GHERPTEVARRIGYLPEERGLYPAMKASEAIAFLAALRGVPLKEGRRRGRD--------- 122 Query: 128 VVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPA 187 LLE GL A LS G + +++ L+ P L++ DEP Sbjct: 123 ---------------LLEQHGLGYAADRQIRQLSKGMAQQVQLLGTLVHEPDLVVFDEPF 167 Query: 188 AGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQ 237 +G++ L +R++ + G T + H + LCD++ ++A G+ Sbjct: 168 SGLD-ALNQGKLERMIRSLAERGTTVIFSTHVIAHAERLCDQIAIIAGGK 216 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: 153 Number of extensions: 4 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: 260 Length of database: 327 Length adjustment: 26 Effective length of query: 234 Effective length of database: 301 Effective search space: 70434 Effective search space used: 70434 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: 48 (23.1 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