Align NatE, 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_048082254.1 EJ01_RS09405 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000745485.1:WP_048082254.1 Length = 222 Score = 85.9 bits (211), Expect = 6e-22 Identities = 67/218 (30%), Positives = 113/218 (51%), Gaps = 17/218 (7%) Query: 11 LLEVENVHAGYI---KDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTG 67 +LE +NV Y + V+ L G+N +E G V+GP+G+GKST L P G Sbjct: 5 VLEFKNVWKTYTMGDETVNALAGLNLALEKGSFTAVMGPSGSGKSTFLHVAGILDMPTRG 64 Query: 68 KITFKGKNIAGLKSNQIVRLG---MCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD 124 GK L + RL + ++ Q N+ L+V EN+ M I+ D+ + + D Sbjct: 65 TFQINGKETHKLSVKEQARLRRDEIGFIFQRFNLMSQLTVLENV-MLPMIKEDTKKAV-D 122 Query: 125 KIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFE 184 + M L+ + +R G LSGGE+Q +A+ +AL+ +PS+++ DEP+ L + + Sbjct: 123 LLNKM--GLAGKYNKRPGQLSGGEQQRVAIARALINDPSIILADEPTGELDTKNADSIMQ 180 Query: 185 QVKQINQ-EGTAIILVEQN------ARKALEMADRGYV 215 ++ +N+ EG +I++V N A + L M+D +V Sbjct: 181 ILQDLNRDEGVSIVMVTHNPSSAEFAGEILHMSDGNFV 218 Lambda K H 0.317 0.136 0.377 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: 8 Number of successful extensions: 2 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: 247 Length of database: 222 Length adjustment: 23 Effective length of query: 224 Effective length of database: 199 Effective search space: 44576 Effective search space used: 44576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 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