Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_011973908.1 MAEO_RS06085 NAAT family transporter
Query= TCDB::Q8J305 (216 letters) >NCBI__GCF_000017185.1:WP_011973908.1 Length = 217 Score = 150 bits (380), Expect = 1e-41 Identities = 79/206 (38%), Positives = 131/206 (63%), Gaps = 4/206 (1%) Query: 7 FLKYLILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQ 66 F + I + +F I NP+G VP+F T + E+ E+ K+AI+V+ TL+ FAL G Sbjct: 7 FFSFFIYSFTSIFIIMNPIGLVPLFYIWTSESEKTEKIELLRKSAIAVMLTLLTFALFGG 66 Query: 67 WIFKFFGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIP 126 IFKFFG + D+F +AGGIL+ ++A DML ++S + + ++ EE ++LE++A++P Sbjct: 67 SIFKFFGITLDSFKVAGGILMLKIAWDMLHAQVSKTRHNLKD----DEEPISLEDIAVVP 122 Query: 127 LAIPLISGPGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVG 186 +AIPL++GPG ITT ++ M S T L ++ +IIL + +L ++ I L G Sbjct: 123 MAIPLLAGPGTITTSIILMEHSITTYDTLIIMFSIILATLISVVILYLSDNIARILRVSG 182 Query: 187 IKVMTRMMGLILTSMAVQMIINGIKG 212 IK + R+MGLIL ++++++I +G+ G Sbjct: 183 IKAIVRIMGLILAAISIEIISSGVFG 208 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: 112 Number of extensions: 6 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: 217 Length adjustment: 22 Effective length of query: 194 Effective length of database: 195 Effective search space: 37830 Effective search space used: 37830 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 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