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 N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Dyella79:N515DRAFT_3950 Length = 239 Score = 137 bits (346), Expect = 2e-37 Identities = 86/250 (34%), Positives = 135/250 (54%), Gaps = 15/250 (6%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 +L+A GL K F + V++ + +G + GL+GPNGAGKTT F ++ I D G + Sbjct: 1 MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130 D I L H A+ G+ Q RL+V +N++ A + EN Sbjct: 61 DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIM--AVLELRENL----------- 107 Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 KQ + LL+ + +A A + LSGG+R+ +E+ RAL P+ +LLDEP AGV Sbjct: 108 -SAKQRAGELESLLDELKIAHIADQRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGV 166 Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250 +P + +I RI+ ++ G+ LI +HN+ + +CDR ++L +G+ L+ GTPA I + Sbjct: 167 DPISVGEI-QRIVRHLKERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHILAD 225 Query: 251 SQVLEAYLGK 260 +V E YLG+ Sbjct: 226 EKVREVYLGR 235 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: 122 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: 239 Length adjustment: 24 Effective length of query: 236 Effective length of database: 215 Effective search space: 50740 Effective search space used: 50740 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: 46 (22.3 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