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 PP_5023 PP_5023 Amino acid ABC transporter, permease protein
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__Putida:PP_5023 Length = 320 Score = 130 bits (327), Expect = 3e-35 Identities = 73/211 (34%), Positives = 116/211 (54%), Gaps = 14/211 (6%) Query: 28 GLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNVPLLVQLFIWYFL 87 GL T+ I++V + L +G G+ R N + ++T YVE+ R PLLVQ+FI+YF Sbjct: 121 GLWTTLWISVVSGALGLVIGLFAGLCRLSNNPTLRDLSTVYVELVRGTPLLVQIFIFYFF 180 Query: 88 VPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPYGQTSAARA 147 + +L S + V L LFT A V E VR G+Q++ GQ AAR+ Sbjct: 181 IGTVL--------------NLSREFAGVAALALFTGAYVAEIVRAGVQSIAKGQNEAARS 226 Query: 148 MGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELLAQTKQTAEFSAN 207 +G Q RHV+LPQAF+ ++PPL +F+++ K++S+ S+I + EL ++ S + Sbjct: 227 LGLNAGQSMRHVILPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELTKSGREAITTSFS 286 Query: 208 LFEAFTLATLIYFTLNMSLMLIMRLVERKVA 238 FE + +Y +N+ L I +ER++A Sbjct: 287 TFEIWFCVAGLYLLINLPLSHIASRLERRLA 317 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: 193 Number of extensions: 7 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: 320 Length adjustment: 26 Effective length of query: 222 Effective length of database: 294 Effective search space: 65268 Effective search space used: 65268 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