Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 109 bits (272), Expect = 5e-29 Identities = 67/214 (31%), Positives = 115/214 (53%), Gaps = 13/214 (6%) Query: 26 IAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNVPLLVQLFIWY 85 ++ + WT+A++ + +I +G ++ + RT + V AT Y+++F+ PLL+QLF+ + Sbjct: 13 LSAVQWTLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQGTPLLMQLFLVF 72 Query: 86 FLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPYGQTSAA 145 F T DLNP +A L L L +A + E R IQA+P GQ AA Sbjct: 73 FGA---------TVMGLDLNPWAAAALG----LTLNASAFLGEIWRGCIQAVPRGQWEAA 119 Query: 146 RAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELLAQTKQTAEFS 205 A+G R P + R+V+LPQA ++ +PP + + K++S+A++IG EL + + Sbjct: 120 SALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTELTRAGQIVNNAT 179 Query: 206 ANLFEAFTLATLIYFTLNMSLMLIMRLVERKVAV 239 F F + ++YF + L L+ +ER+ A+ Sbjct: 180 FQPFLVFGIVAVLYFLMCWPLSLLSARLERRYAL 213 Lambda K H 0.327 0.141 0.433 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: 144 Number of extensions: 6 Number of successful extensions: 3 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: 248 Length of database: 216 Length adjustment: 23 Effective length of query: 225 Effective length of database: 193 Effective search space: 43425 Effective search space used: 43425 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: 46 (22.3 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