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 H281DRAFT_05291 H281DRAFT_05291 amino acid ABC transporter membrane protein 1, PAAT family
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__Burk376:H281DRAFT_05291 Length = 240 Score = 177 bits (448), Expect = 2e-49 Identities = 93/224 (41%), Positives = 141/224 (62%), Gaps = 1/224 (0%) Query: 7 GFGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETL 66 G+G LL MT+ L+LAA+ VG + G L A AK S+ LR +G YTT+ RGVPE L Sbjct: 13 GWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRLRTLRVIGDIYTTVFRGVPELL 72 Query: 67 WVLMIYFGTVSGLNALGDLFGKPD-LALSPFAAGTLALGLCFGAYATEVFRGALLSIPRG 125 + + YFG + + +G FG + + PF G LA+G+ GAY EV+R A+L++ RG Sbjct: 73 VIYLFYFGGSTLVTTVGQWFGAEGFVGVPPFVIGALAVGMISGAYQAEVYRSAVLAVSRG 132 Query: 126 HREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQV 185 EA +++G+ + RI++PQ+ R ALPG+GN++ + LKD+AL+S+ L E++R +QV Sbjct: 133 ELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQV 192 Query: 186 ASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVRN 229 A+ +T + FTF++ A+YL +T + + E R GR F RN Sbjct: 193 AAGSTHQYFTFFVVGGALYLLMTSISNRVFNHAEARVGRSFKRN 236 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: 151 Number of extensions: 10 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: 240 Length adjustment: 23 Effective length of query: 208 Effective length of database: 217 Effective search space: 45136 Effective search space used: 45136 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