Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_011337827.1 RSPH17029_RS07790 MarC family protein
Query= TCDB::Q8J305 (216 letters) >NCBI__GCF_000015985.1:WP_011337827.1 Length = 206 Score = 130 bits (326), Expect = 2e-35 Identities = 71/204 (34%), Positives = 119/204 (58%), Gaps = 7/204 (3%) Query: 10 YLILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIF 69 +LI + LF + +P+G VP+F+++T ++ ERR I + V L F LLG+ + Sbjct: 6 FLITAFATLFVVVDPLGLVPLFIALTPGMTREERRAIGLRACFVAVGILTTFGLLGEAVL 65 Query: 70 KFFGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAI 129 F G S AF IAGGILLF ALDML + + + + + ++ PLAI Sbjct: 66 GFIGISMSAFRIAGGILLFLTALDMLFERRTQRREGQTAADHD-------HDPSVFPLAI 118 Query: 130 PLISGPGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKV 189 PLI+GPGAI +++L + + LAV L +++ + + + A ++ LGR+G V Sbjct: 119 PLIAGPGAIASMILLVGSAEDWTGVLAVHLVMLVTVASAFLLFLVAGPLERLLGRIGTLV 178 Query: 190 MTRMMGLILTSMAVQMIINGIKGA 213 +TR++G++L +++VQ +I+GI+G+ Sbjct: 179 ITRLLGMLLAALSVQFVIDGIRGS 202 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: 124 Number of extensions: 4 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: 216 Length of database: 206 Length adjustment: 21 Effective length of query: 195 Effective length of database: 185 Effective search space: 36075 Effective search space used: 36075 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 Apr 10 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