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 WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease
Query= TCDB::Q9I403 (248 letters) >NCBI__GCF_003217355.1:WP_110804905.1 Length = 262 Score = 101 bits (252), Expect = 1e-26 Identities = 64/212 (30%), Positives = 114/212 (53%), Gaps = 9/212 (4%) Query: 28 GLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNVPLLVQL-FIWYF 86 G+G T+ + L + AL LG +L V + + +A Y E+ R VP++V L ++ + Sbjct: 43 GIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVMLLYVAFA 102 Query: 87 LVPDLLPE----GLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPYGQT 142 LVP ++ GL +D A L++++ F A E R G+ ++ GQ Sbjct: 103 LVPAVVAGWNALGLPEASVRDFPLLARAVLALILAYAAFLA----EVFRAGLLSVERGQI 158 Query: 143 SAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELLAQTKQTA 202 AA+A+G +R ++ PQAFR ++PPL ++F+ + K+SS+ S++G+ ++ K TA Sbjct: 159 EAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKVTA 218 Query: 203 EFSANLFEAFTLATLIYFTLNMSLMLIMRLVE 234 + FE + + LIY + ++L L +R +E Sbjct: 219 AGNFRYFETYNVVALIYLAMTVTLSLALRKLE 250 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: 172 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: 248 Length of database: 262 Length adjustment: 24 Effective length of query: 224 Effective length of database: 238 Effective search space: 53312 Effective search space used: 53312 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 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