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_1954 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= TCDB::Q9I402 (302 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1954 Length = 299 Score = 212 bits (540), Expect = 7e-60 Identities = 112/285 (39%), Positives = 169/285 (59%), Gaps = 3/285 (1%) Query: 13 VAALLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGKPIGYSHDLQLKVV 72 + LL+A V A + L+++ G + + HR++S+PFSY+ ++ GKP+GY+ DL L++ Sbjct: 15 LGCLLAASVQAATV---LERVSAGGKLVIAHRESSVPFSYVDSQSGKPVGYAVDLCLRMA 71 Query: 73 EAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQKQVDFSVGIFEVG 132 E V+K+ +++V + VT RI +++ G D+ECGSTTNN ER+++V F++ F G Sbjct: 72 EVVRKKTGKKDMEVEFVAVTPANRITMIEEGKADMECGSTTNNAERRQKVAFTIPHFITG 131 Query: 133 TRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNIISAKDHGESFMML 192 RLL K + I +DL GK +V+T GTT + N ++ MG+ I+ A DH ++ M+ Sbjct: 132 ARLLVKSASPIDKVEDLNGKKLVSTKGTTPLKAADQANRERLMGITIMEAPDHAKAVEMV 191 Query: 193 ESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGDAAFKKVVDKAIT 252 E G A AF+MDD LLYG A P V G + E M+ K D FKK+VD+ + Sbjct: 192 EKGEADAFVMDDVLLYGLAAGRPDPKALKVVGRFMTTEPLAIMLPKNDPEFKKLVDEEMR 251 Query: 253 DTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTDK 297 S ++ IYDKWF +PIPP LN P+S L+ PTD+ Sbjct: 252 RLITSRDIYPIYDKWFNKPIPPNNTVLNLPVSYLLRDFWKYPTDQ 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: 237 Number of extensions: 14 Number of successful extensions: 1 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: 299 Length adjustment: 27 Effective length of query: 275 Effective length of database: 272 Effective search space: 74800 Effective search space used: 74800 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