Align Probable permease of ABC transporter, 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 WP_081718345.1 N177_RS02595 ABC transporter permease
Query= TCDB::Q9HU30 (231 letters) >NCBI__GCF_000496075.1:WP_081718345.1 Length = 248 Score = 102 bits (254), Expect = 7e-27 Identities = 70/223 (31%), Positives = 111/223 (49%), Gaps = 2/223 (0%) Query: 8 FGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLW 67 +G ++L+G W T++L ++ +G + L A + S + L Y RG P Sbjct: 27 YGFRMLSGFWTTIELVTLSLLIGAAISLPVAAGRLSPNPVIGALAYGYVYFFRGTPLLAQ 86 Query: 68 VLMIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHR 127 ++Y+G S A D G + L AY E+ GA+ ++PR Sbjct: 87 TFLVYYGAGS-FRAELDAVGLWTFFRDAWFCAVFTFSLNTSAYQAEILAGAIRTVPRSQI 145 Query: 128 EAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVAS 187 EAGQALGLS I RIVLPQ VAL GN ++++K +A+ S+IT+ ++M + + A Sbjct: 146 EAGQALGLSRYVIATRIVLPQALVVALRPYGNEVVLMIKGSAIASIITIYDLMGETRRAF 205 Query: 188 NATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVRNE 230 + + + F Y+ AA +YL L + +ERR R VR++ Sbjct: 206 SRSFD-FQTYIWAAILYLVLVETLRRLWDVMERRLTRHLVRDD 247 Lambda K H 0.327 0.143 0.431 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: 145 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: 231 Length of database: 248 Length adjustment: 23 Effective length of query: 208 Effective length of database: 225 Effective search space: 46800 Effective search space used: 46800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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