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 PP_3593 PP_3593 Amino acid ABC transporter, periplasmic binding protein
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Putida:PP_3593 Length = 250 Score = 204 bits (520), Expect = 1e-57 Identities = 111/248 (44%), Positives = 150/248 (60%), Gaps = 3/248 (1%) Query: 5 KKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKT 64 K + L A L A A++A+ LR TEGAYPPFN +DA + GFD+DI ALC +MK Sbjct: 3 KSMALLGACALLLA-GAASAETLRFATEGAYPPFNYVDADNKLHGFDVDITHALCEQMKV 61 Query: 65 ECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFK 124 EC +V DW+GIIPAL A+K+D IVASM T+ER++ + FTD YY L K Sbjct: 62 ECTLVAQDWEGIIPALMARKYDAIVASMIDTEERRKKIAFTDHYYRTPLTVAVAKDSKID 121 Query: 125 TDKDSLKGKVIGAQRATIAGTWLEDNMADV-VTIKLYDTQENAYLDLSSGRLDGVLADKF 183 + + G +GAQ ++ + ED +KLY T + A DL++GRLDGV+ADKF Sbjct: 122 SAQTDFVGYTVGAQSSSTQAIYAEDVYGKAGADVKLYPTMDEANADLAAGRLDGVIADKF 181 Query: 184 VQYDWLKSDAGKEFEFKGEPVFDNDKIGIAVRKGD-PLREKLNAALKEIVADGTYKKIND 242 ++W+ + G + G+ IAVRK D LR++LN AL++IVA+GTY+KI Sbjct: 182 PLHEWMNKNGGDCCKILGDVADTKADAAIAVRKDDEALRQRLNTALQQIVANGTYQKIAS 241 Query: 243 KYFPFSIY 250 KYF F IY Sbjct: 242 KYFAFDIY 249 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: 180 Number of extensions: 6 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: 250 Length adjustment: 24 Effective length of query: 226 Effective length of database: 226 Effective search space: 51076 Effective search space used: 51076 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