Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate CCNA_01507 CCNA_01507 cystine transport system permease protein
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Caulo:CCNA_01507 Length = 219 Score = 100 bits (249), Expect = 3e-26 Identities = 66/213 (30%), Positives = 103/213 (48%), Gaps = 25/213 (11%) Query: 89 IAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWYFAVFLGLPR 148 ++ +G+ + ++G L + RLS + L+R + VYV FR TPLL+QL Y+ Sbjct: 25 LSVIGMSIGVVLGFLLALMRLSRSALLRWPAGVYVSAFRGTPLLVQLFLIYY-------- 76 Query: 149 ADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQW 208 GL Q GLE+P A +G A+ EI+R I +V KGQW Sbjct: 77 -----------GLPQFGLEMP------PLVAAGIGFSLNVAAYSCEILRSAIAAVDKGQW 119 Query: 209 EAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPDIYFVASTTF 268 EA LG++ +R VI PQA R + PL++ +++L K++SLA I P+++ A Sbjct: 120 EAASVLGMSRGQTLRRVILPQAARTAVAPLSNSFISLVKDTSLAATIQVPELFRQAQLIT 179 Query: 269 NQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNR 301 +T + + L Y LS ++ R Sbjct: 180 ARTYEIFTLYLAAAAIYWILSTILAAAQTRLER 212 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: 150 Number of extensions: 5 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: 219 Length adjustment: 24 Effective length of query: 284 Effective length of database: 195 Effective search space: 55380 Effective search space used: 55380 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