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_011317839.1 AVA_RS04995 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000204075.1:WP_011317839.1 Length = 247 Score = 476 bits (1224), Expect = e-139 Identities = 245/247 (99%), Positives = 246/247 (99%) Query: 1 MSGSAQNFTPLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFG 60 MSGSAQNFTPLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFG Sbjct: 1 MSGSAQNFTPLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFG 60 Query: 61 LLTPHTGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQ 120 LLTPHTGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQ Sbjct: 61 LLTPHTGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQ 120 Query: 121 PLKDKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVT 180 PLK+KIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVT Sbjct: 121 PLKEKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVT 180 Query: 181 QVFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELY 240 QVFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELY Sbjct: 181 QVFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELY 240 Query: 241 LGAGKGH 247 LGAGK H Sbjct: 241 LGAGKRH 247 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: 347 Number of extensions: 3 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: 247 Length of database: 247 Length adjustment: 24 Effective length of query: 223 Effective length of database: 223 Effective search space: 49729 Effective search space used: 49729 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 Apr 09 2024. 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