Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_010960978.1 MCA_RS08480 MarC family protein
Query= TCDB::Q8J305 (216 letters) >NCBI__GCF_000008325.1:WP_010960978.1 Length = 194 Score = 87.0 bits (214), Expect = 2e-22 Identities = 64/198 (32%), Positives = 99/198 (50%), Gaps = 15/198 (7%) Query: 18 LFAITNPVGAVPVFLSVTHDLSWRE-RREIASKTAISVVATLVVFALLGQWIFKFFGSST 76 LF IT+P G +P+ L+V L R + +TAI+ V LVVFA G + + + Sbjct: 10 LFLITDPFGNLPLLLTVLQRLGHAAYLRAVLRETAIAFV-VLVVFAWKGDLLLGYLNVTQ 68 Query: 77 DAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAIPLISGPG 136 + IAGG++L ++L M+ G E F + + ++P+AIP I+GP Sbjct: 69 PSLNIAGGVILTIISLKMIFGGAQ---------ETFDDRYA--NDPLVVPIAIPAIAGPA 117 Query: 137 AITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKVMTRMMGL 196 A+TTVML + L LT++ + F+L + LG G+ + R+MGL Sbjct: 118 ALTTVMLLSKQQGIPFPTLFTALTLVFLANLTTFLL--GRLLGEWLGPRGLTALERLMGL 175 Query: 197 ILTSMAVQMIINGIKGAF 214 +L +AV M + GIK F Sbjct: 176 LLNLVAVDMTMAGIKRFF 193 Lambda K H 0.327 0.141 0.396 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: 110 Number of extensions: 7 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: 216 Length of database: 194 Length adjustment: 21 Effective length of query: 195 Effective length of database: 173 Effective search space: 33735 Effective search space used: 33735 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 45 (21.9 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