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_006747154.1 THITH_RS14200 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_000227685.2:WP_006747154.1 Length = 261 Score = 129 bits (325), Expect = 4e-35 Identities = 74/220 (33%), Positives = 118/220 (53%), Gaps = 5/220 (2%) Query: 27 ILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVR 86 +L V+ + GE+V ++GPNGAGK+T + GL+ P G+I G+++ + R Sbjct: 38 VLSEVDVHLRHGEVVGLLGPNGAGKTTCFYILVGLIQPDAGRIELAGRDVTRAPVHLRAR 97 Query: 87 LGMCYVPQIANVFPSLSVEENLEMGAFIRND----SLQPLKDKIFAMFPRLSDRRRQRAG 142 LG+ Y+PQ A++F L+V +NL+ +R D + D + F +L R Sbjct: 98 LGLGYLPQEASIFRRLTVWQNLQAVLELRRDLDRAGRRETGDALIEEF-QLETVRDSPGI 156 Query: 143 TLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAIILVEQN 202 LSGGER+ + +AL P + LDEP A + PI V ++ + + + Q G +++ + N Sbjct: 157 ALSGGERRRAEIARALAGNPQFVCLDEPFAGVDPISVVEIQDVIGHLKQRGIGVLISDHN 216 Query: 203 ARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 R+ L + DR Y+L GR G ELL D +V +YLG Sbjct: 217 VRETLGICDRAYILSEGRLLSEGTPAELLADHRVRTVYLG 256 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: 172 Number of extensions: 9 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: 261 Length adjustment: 24 Effective length of query: 223 Effective length of database: 237 Effective search space: 52851 Effective search space used: 52851 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: 47 (22.7 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