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 WP_011386136.1 AMB_RS19155 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9I402 (302 letters) >NCBI__GCF_000009985.1:WP_011386136.1 Length = 302 Score = 228 bits (581), Expect = 1e-64 Identities = 132/296 (44%), Positives = 175/296 (59%), Gaps = 2/296 (0%) Query: 5 PSLLSTAIVAALLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGKPIGYS 64 P +L + A++S A TL K+K TG++ LG R+AS P SYL + KPIGY Sbjct: 3 PFVLPLFLALAVISTGGAA-RAEPTLDKVKRTGSVVLGVREASYPLSYLDGDK-KPIGYH 60 Query: 65 HDLQLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQKQVDF 124 D+ +V EAVK +L L L+VR +VTS+TRIP + +G +D+ECGSTTNN RQ QV F Sbjct: 61 VDICRRVTEAVKAQLGLAALEVRTEVVTSKTRIPRLLDGGIDLECGSTTNNAARQTQVAF 120 Query: 125 SVGIFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNIISAKD 184 + + R+ KK A+I L GK V TTAG+TS +LLKA + + + + D Sbjct: 121 APTTYVASVRIAVKKAAHIGKLSQLDGKAVATTAGSTSVQLLKARVQGRDIKVTELFGND 180 Query: 185 HGESFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGDAAFK 244 H ESF MLES +A AF+MDD LL G +A + P D+ + + E M+RKGD FK Sbjct: 181 HAESFKMLESDQAAAFVMDDNLLAGLIASSAAPKDYQILPQTLNTEPIAIMLRKGDPEFK 240 Query: 245 KVVDKAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTDKAAE 300 +VD+ + SGEV ++Y KWF PIPP L+FPMS L LI P D AE Sbjct: 241 ALVDRTVKAMMESGEVGRLYAKWFQSPIPPMNAALDFPMSPVLLSLIKFPGDDPAE 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: 227 Number of extensions: 5 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: 302 Length adjustment: 27 Effective length of query: 275 Effective length of database: 275 Effective search space: 75625 Effective search space used: 75625 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