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_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= TCDB::Q9I404 (222 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 84.3 bits (207), Expect = 3e-21 Identities = 63/205 (30%), Positives = 102/205 (49%), Gaps = 4/205 (1%) Query: 17 GMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIPLLLVITWFYFA 76 G+ T M++ VLGG+ L + A H L + I L L + Sbjct: 168 GITGTALPMIVTVLGGLTLTLITAWRGHLHKASLCTLGTIVAGSALWIVLDLGLAR---D 224 Query: 77 VPFILRW-ITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAIPKGQMGAAQALGMTY 135 VP R+ TG T F + L +++ +A+ EIVR G+ +P+GQ A++ALG++ Sbjct: 225 VPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSK 284 Query: 136 GQTMRLVILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLMDFLNSARSRGDIIGQANEFL 195 Q++RLVI+PQA R + P + Q I + ++++L VG D A + + GQ E + Sbjct: 285 RQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGV 344 Query: 196 IFAGLVYFVVSFTASFAVKRLQKRL 220 LV+F ++ S A+ RL R+ Sbjct: 345 AILMLVFFTLASAISLAMNRLNARV 369 Score = 33.9 bits (76), Expect = 4e-06 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 4/61 (6%) Query: 14 LWEGMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIPLLLVITWF 73 L + +TL ++VL + GV + AL R S L +AG +V+ R++PL++ + ++ Sbjct: 79 LGNSIALTLLIIVLSTMAGVPI----ALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFW 134 Query: 74 Y 74 Y Sbjct: 135 Y 135 Lambda K H 0.331 0.143 0.426 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: 169 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 222 Length of database: 374 Length adjustment: 26 Effective length of query: 196 Effective length of database: 348 Effective search space: 68208 Effective search space used: 68208 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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