Align Probable binding protein component of ABC transporter, 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 Ac3H11_1642 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= TCDB::Q9I402 (302 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1642 Length = 296 Score = 279 bits (714), Expect = 5e-80 Identities = 138/300 (46%), Positives = 202/300 (67%), Gaps = 4/300 (1%) Query: 1 MRIAPSLLSTAIVAALLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGKP 60 M+++ + +V LL++ VV+ + TLKK+ E+G ITL +R++S+PFSYL + PG P Sbjct: 1 MKLSAVTSAAIVVTGLLASTVVSAD---TLKKVAESGKITLAYRESSVPFSYL-SGPGVP 56 Query: 61 IGYSHDLQLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQK 120 +G++ D+ VV+AVKK +N P LKV VTSQ RIPL+ NGT+D+ECGSTTNN R K Sbjct: 57 VGFAVDISNAVVDAVKKRVNNPALKVELQAVTSQNRIPLLTNGTIDLECGSTTNNSVRGK 116 Query: 121 QVDFSVGIFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNII 180 V F+V F GTRLL+KKT+ +K++ DL K V +T+GTT+ ++++ N D+ + M+I+ Sbjct: 117 DVQFAVNYFYTGTRLLTKKTSGVKNYADLAKKKVASTSGTTNAQVIRKYNRDQNLDMDIV 176 Query: 181 SAKDHGESFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGD 240 KDH +S +++ESGRA AF MDD LL+G M + P +W V G E Y CM+RK D Sbjct: 177 LGKDHDDSLLLVESGRAEAFAMDDILLFGLMGNQRNPAEWTVVGDSLQVEPYACMLRKDD 236 Query: 241 AAFKKVVDKAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTDKAAE 300 F+ +V+ I SGE +K+Y KWF P+PP+ NLN MS+EL++ + + +DK A+ Sbjct: 237 PQFQALVNGVIGGMMKSGEFDKLYTKWFMSPVPPRNQNLNLAMSKELRENLVAQSDKPAQ 296 Lambda K H 0.314 0.132 0.370 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: 239 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: 302 Length of database: 296 Length adjustment: 27 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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