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_084087424.1 N800_RS09205 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000768355.1:WP_084087424.1 Length = 560 Score = 75.5 bits (184), Expect = 2e-18 Identities = 70/230 (30%), Positives = 105/230 (45%), Gaps = 30/230 (13%) Query: 16 GLCKSFGGIKAVQEA-RIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEP 74 G+ ++ G A+ E+ + + G + GPNGAGK+TL +LL F+ PD+GRV+ DG Sbjct: 339 GVGFAYPGRPALYESLNLSIRVGETVAITGPNGAGKSTLAHLLLRFVAPDQGRVLLDGVD 398 Query: 75 IQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEK 134 I +L+ + + + QV L +VL+N+ P E + Sbjct: 399 ISELRLSNLRSHVGLVSQQV--LLFHGTVLDNIAYG--------------HPTAGQAEVE 442 Query: 135 QLQEQAMFLLESVGLAKKAYEYAGG----LSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 AM VGL G LSGGQR+ + + R L+ NP +I+LDE A Sbjct: 443 AAANAAMAHDFIVGLPDGYRTVVGDQGVRLSGGQRQRIALARVLLRNPAVIVLDEATAMF 502 Query: 191 NP---RLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQ 237 +P R C +L +G T L+I H ++L DRV L G+ Sbjct: 503 DPEAERAFIARCHAVL-----EGRTVLLITHR-PASLALADRVLRLDGGR 546 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: 267 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 560 Length adjustment: 30 Effective length of query: 230 Effective length of database: 530 Effective search space: 121900 Effective search space used: 121900 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: 50 (23.9 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