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 BPHYT_RS00160 BPHYT_RS00160 ABC transporter substrate-binding protein
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__BFirm:BPHYT_RS00160 Length = 262 Score = 163 bits (413), Expect = 3e-45 Identities = 102/245 (41%), Positives = 140/245 (57%), Gaps = 9/245 (3%) Query: 8 LLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKTECE 67 L A A+LA + ASAAD LR G E YPPF +G+ G D+D+G A+C C+ Sbjct: 10 LACAFASLAASSGASAADTLRFGLEAQYPPFESKGPNGELQGLDIDVGNAVCVAAHMTCK 69 Query: 68 VVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTDK 127 V + +DG+IPAL +KFD I ++M+ TD R+QA+DFT Y Q +A + Sbjct: 70 WVETSFDGLIPALQGRKFDAINSAMNATDARRQAIDFTTVVYRVPTQLIAKRDSGLLPTP 129 Query: 128 DSLKGKVIGAQRATIAGTWLEDNMADV-VTIKLYDTQENAYLDLSSGRLDGVLA-DKFVQ 185 SLKGK +G +A+I T+ + + VT+ Y Q Y DL +GRLD L Q Sbjct: 130 ASLKGKRVGVLQASIQETYAKAHWESAGVTVVPYQDQNQVYTDLVAGRLDATLVLAPAGQ 189 Query: 186 YDWLKSDAGKEFEFKGEPVFDNDKI---GIA--VRKGD-PLREKLNAALKEIVADGTYKK 239 +L +G+ + F GEPV D DKI GIA +RKGD LR++LNAA+ ++ ADGT K Sbjct: 190 TGFLSKPSGEGYAFVGEPVRD-DKILGSGIAYGIRKGDTALRDRLNAAIAKVQADGTVKT 248 Query: 240 INDKY 244 + KY Sbjct: 249 LAAKY 253 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: 152 Number of extensions: 8 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: 262 Length adjustment: 24 Effective length of query: 226 Effective length of database: 238 Effective search space: 53788 Effective search space used: 53788 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: 47 (22.7 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