Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_066605708.1 V473_RS13055 MarC family protein
Query= TCDB::Q8J305 (216 letters) >NCBI__GCF_001046645.1:WP_066605708.1 Length = 206 Score = 129 bits (323), Expect = 5e-35 Identities = 70/207 (33%), Positives = 125/207 (60%), Gaps = 2/207 (0%) Query: 8 LKYLILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQW 67 ++ I + LF + +P G P++ S+T+ S +RR +A + A L+VFAL G+ Sbjct: 2 IELFISAFVTLFVVIDPPGCAPIYASLTNGASPAQRRAMAIRAVGIAAAILLVFALWGKQ 61 Query: 68 IFKFFGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPL 127 + G + D+F IAGGI+LF +A+DM+ K + + + + S E +E+V++ P+ Sbjct: 62 LLGVLGIALDSFRIAGGIMLFMIAMDMVFEKRTQRR--EDRANKISTEEPHVEDVSVFPM 119 Query: 128 AIPLISGPGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGI 187 A+P+I+GPG+I TVML M+++ +R V+ ++L + L +A + A LGR Sbjct: 120 AMPMIAGPGSIATVMLLMSRANGMAERGVVLGAVVLTLALMLGALIAAGPLMALLGRKIE 179 Query: 188 KVMTRMMGLILTSMAVQMIINGIKGAF 214 V+TR++G++L ++A Q +I+G+K +F Sbjct: 180 AVITRLLGVLLAALAAQFVIDGLKASF 206 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: 104 Number of extensions: 3 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 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