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_011318451.1 AVA_RS08305 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000204075.1:WP_011318451.1 Length = 242 Score = 130 bits (326), Expect = 3e-35 Identities = 81/234 (34%), Positives = 123/234 (52%), Gaps = 6/234 (2%) Query: 14 VENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKG 73 +EN+H Y K V I+ VN V GE+V ++GPNGAGK+T GL P+ G++ Sbjct: 5 LENIHKSYGKRV-IVNRVNLSVAQGEIVGLLGPNGAGKTTTFYIATGLEKPNQGRVWLDS 63 Query: 74 KNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFP-- 131 +I GL ++ RLG+ Y+ Q A+VF LSV++N+ + N ++ + Sbjct: 64 LDITGLPMHKRARLGIGYLAQEASVFRQLSVQDNILLVFEQTNVPRWEWAKRLNTLLREF 123 Query: 132 RLSDRRRQRAGTLSGGERQMLAMGKALML---EPSLLVLDEPSAALSPILVTQVFEQVKQ 188 RL + + LSGGER+ + +AL P L LDEP A + PI V ++ + V Q Sbjct: 124 RLEKVAKSKGIQLSGGERRRTELARALAAGGEGPKFLFLDEPFAGVDPIAVFEIQQIVAQ 183 Query: 189 INQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 + G I++ + N R+ L + DR Y+L G+ G EL +P V + YLG Sbjct: 184 LRDRGMGILITDHNVRETLAITDRAYILREGQILAYGNADELYNNPLVRQYYLG 237 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: 144 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: 247 Length of database: 242 Length adjustment: 24 Effective length of query: 223 Effective length of database: 218 Effective search space: 48614 Effective search space used: 48614 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