Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 206677 DVU1238 amino acid ABC transporter, periplasmic amino acid-binding protein
Query= TCDB::Q9HU31 (250 letters) >MicrobesOnline__882:206677 Length = 246 Score = 110 bits (274), Expect = 3e-29 Identities = 80/246 (32%), Positives = 129/246 (52%), Gaps = 11/246 (4%) Query: 5 KKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKT 64 +K+LL AA L A A + + +PP +DA+ Q VG +D A+ + Sbjct: 3 QKVLLTVAALLLSTNVAFAERTVVFAHDATWPPMEFVDANKQIVGLAVDYVDAIAKEAGF 62 Query: 65 ECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFK 124 + WDGI L A K+D I +S++IT+ERK+A+DFT PY+ K V PK+ + K Sbjct: 63 KVVHKNVAWDGIFAGLAAGKYDAIASSVTITEERKKAMDFTMPYFDVKQALVVPKTTEAK 122 Query: 125 TDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLADKFV 184 T +D +KGK +GAQ +T ++ VT K YD A DL +GR+DGV+ D V Sbjct: 123 TLED-MKGKTLGAQISTTGHFAIKRTAG--VTAKSYDEIGLAMEDLFNGRIDGVVCDDPV 179 Query: 185 QYDWLKSDAGKEFEFKGEPVF-----DNDKIGIAVRKGD-PLREKLNAALKEIVADGTYK 238 ++ +E+ K + F +++ GIAV++G+ L + +N ++ + A G Sbjct: 180 AANYALQQ--EEYAKKLKIAFIVDTPESEYYGIAVKQGNKELVDLINKGIEAVKAKGIDA 237 Query: 239 KINDKY 244 ++ K+ Sbjct: 238 QLRAKW 243 Lambda K H 0.317 0.135 0.392 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: 160 Number of extensions: 9 Number of successful extensions: 3 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: 250 Length of database: 246 Length adjustment: 24 Effective length of query: 226 Effective length of database: 222 Effective search space: 50172 Effective search space used: 50172 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: 41 (21.7 bits) S2: 46 (22.3 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