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 H281DRAFT_05882 H281DRAFT_05882 amino acid ABC transporter substrate-binding protein, PAAT family
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Burk376:H281DRAFT_05882 Length = 262 Score = 161 bits (408), Expect = 1e-44 Identities = 94/246 (38%), Positives = 144/246 (58%), Gaps = 7/246 (2%) Query: 7 ILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKTEC 66 +L+AA A + + + LR G E AYPPF +GQ GFD+D+G A+CAK+ +C Sbjct: 10 LLVAATAASLSTVTTQSQETLRFGIEAAYPPFESKSPTGQLQGFDVDVGNAVCAKLGMKC 69 Query: 67 EVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTD 126 V + +DG+IPAL A+KFD I ++M+IT++RKQ+++FT P Y + VA ++ D Sbjct: 70 VWVENAFDGLIPALQARKFDVINSAMNITEKRKQSIEFTKPIYVVPIVMVARRASGLLPD 129 Query: 127 KDSLKGKVIGAQRATIAGTWLEDNMADV-VTIKLYDTQENAYLDLSSGRLDGVLAD-KFV 184 SL+GK +G +A+ +L+ + A VT+ Y Q+ Y DL +GRLD + + + V Sbjct: 130 VKSLQGKRVGVLQASSQEDFLKRHWAPAGVTVVPYADQDQVYADLVAGRLDAAVQEAQTV 189 Query: 185 QYDWLKSDAGKEFEFKGEPVFD----NDKIGIAVRKGDP-LREKLNAALKEIVADGTYKK 239 Q +L AG E+ G+P+ D + G +RKGD L K++AAL + DGT Sbjct: 190 QDGFLVKPAGHEYAIVGKPLSDPATLGEGTGWGLRKGDKVLVAKVDAALDALKKDGTLSS 249 Query: 240 INDKYF 245 ++ KYF Sbjct: 250 LSQKYF 255 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: 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