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 PP_0226 PP_0226 sulfur compound ABC transporter - permease subunit
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__Putida:PP_0226 Length = 222 Score = 121 bits (303), Expect = 1e-32 Identities = 76/213 (35%), Positives = 111/213 (52%), Gaps = 14/213 (6%) Query: 12 LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71 LL G T+ LS+ + GL+LG A+ + SK L +L Y + RG P + + +I Sbjct: 16 LLKGAGYTVLLSVGGMFFGLVLGFALALMRLSKILPLNWLARVYVSFFRGTPLLVQLFVI 75 Query: 72 YFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQ 131 YFG + +G + L P A + L L AY E+ R A+ SI RG EA Sbjct: 76 YFG----MPQIG-------IELDPIPASLIGLSLNMAAYICEILRAAISSIDRGQWEAAA 124 Query: 132 ALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATK 191 ++G++ + R +LPQ R ALP LGN ++ L+KDTAL + I + E+ R+AQ+ + T Sbjct: 125 SIGMTRVQAMRRAILPQALRTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTF 184 Query: 192 EPFTFYMTAAAIYLSLTVVIMVALHFLERRAGR 224 E FT Y+ A IY V+ + HF R R Sbjct: 185 EVFTMYVAVAVIY---WVLCSILAHFQNRMEAR 214 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: 110 Number of extensions: 5 Number of successful extensions: 2 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: 222 Length adjustment: 22 Effective length of query: 209 Effective length of database: 200 Effective search space: 41800 Effective search space used: 41800 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 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