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_068168721.1 HTA01S_RS07505 ABC transporter permease subunit
Query= TCDB::Q9HU30 (231 letters) >NCBI__GCF_001592305.1:WP_068168721.1 Length = 226 Score = 187 bits (474), Expect = 2e-52 Identities = 102/223 (45%), Positives = 145/223 (65%), Gaps = 4/223 (1%) Query: 4 DLHGFGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVP 63 DL + QLL G W+T++L+L+++ VGL LGL+ A S LR T ++RG+P Sbjct: 3 DLWLYAGQLLQGAWVTVQLALSSLVVGLALGLVLAAGSLSGRTLLRRAVRLCTGLLRGIP 62 Query: 64 ETLWVLMIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIP 123 E L VL+ YFG + +N L G ++ SPFAAG AL + F AYA+EVFRG+ +IP Sbjct: 63 EFLIVLVCYFGLSNLIN--NHLDGAVEI--SPFAAGVFALSIVFAAYASEVFRGSFAAIP 118 Query: 124 RGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKA 183 RG EA QA GL+ + F+ + LPQ WR+ALP LGNL+ LLKDT+LVS++ L+++++K+ Sbjct: 119 RGQIEAAQAFGLTATQTFFAVRLPQAWRIALPSLGNLWQSLLKDTSLVSVVGLEDLLKKS 178 Query: 184 QVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGF 226 +A+ AT +PF F++ AA +Y +LERRAGRGF Sbjct: 179 NMAAQATHQPFLFFLAAATVYFVFLHASQPVFAWLERRAGRGF 221 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: 160 Number of extensions: 9 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: 226 Length adjustment: 23 Effective length of query: 208 Effective length of database: 203 Effective search space: 42224 Effective search space used: 42224 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 Apr 09 2024. 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