Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate RR42_RS02580 RR42_RS02580 amino acid ABC transporter permease
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Cup4G11:RR42_RS02580 Length = 242 Score = 114 bits (286), Expect = 2e-30 Identities = 68/224 (30%), Positives = 115/224 (51%), Gaps = 15/224 (6%) Query: 73 DTYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLL 132 +TY + GL ++ + I+ ++G + G+ R N + ++ YVEIFRN PLL Sbjct: 18 ETYLDWMISGLKVTIALGLSSWIIALVIGSVLGVLRTVPNKWLSGLAATYVEIFRNIPLL 77 Query: 133 LQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFI 192 +QL WYF + LP ++ + F+ +F A +L L +T A + Sbjct: 78 VQLFIWYFVMPELLPGGESFKQMN---------------PFAQQFLAAMLCLGTFTAARV 122 Query: 193 AEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLA 252 E VR GI S+ GQ AG ++G + R V+ P + RVI+PPLTS++LN+ KNS++A Sbjct: 123 CEQVRSGINSLPPGQRNAGLAMGFTLAQTYRYVLLPMSFRVIVPPLTSEFLNIFKNSAVA 182 Query: 253 IAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIM 296 IG ++ + T + E + + + Y +++ + L+M Sbjct: 183 STIGLLELAAQGRQLVDYTARPYESFIAVTIMYALINIVVMLLM 226 Lambda K H 0.328 0.143 0.430 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: 183 Number of extensions: 8 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: 308 Length of database: 242 Length adjustment: 25 Effective length of query: 283 Effective length of database: 217 Effective search space: 61411 Effective search space used: 61411 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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