Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane 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 WP_004326833.1 C665_RS18760 amino acid ABC transporter permease
Query= TCDB::Q9HU29 (230 letters) >NCBI__GCF_000310185.1:WP_004326833.1 Length = 216 Score = 127 bits (320), Expect = 1e-34 Identities = 75/217 (34%), Positives = 124/217 (57%), Gaps = 9/217 (4%) Query: 5 ELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGT 64 + IL + + +G+ +TL+L I ++ + L L L + R SR AYI+ RGT Sbjct: 2 DYILSILGPLAEGSLVTLQLFLITLLLAVPLGLALALVRISRFRVASQAVNAYIWLMRGT 61 Query: 65 PLLLQLFIVYYGLAQFEEVRKSAFWPYLRDP-YWCALLTMTLHTAAYIAEILRGAIHSVP 123 PL+LQ+ +YY L + +R P + A++ L+ AAY AEI R I S+ Sbjct: 62 PLMLQMLFIYYALPFVPGIG-------IRLPDFPAAIVAFALNYAAYFAEIFRAGIQSID 114 Query: 124 VGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMA 183 G+ E A+ LG S Q + I+LP+ V+ LP SNE I ++K ++++Y + L D++ A Sbjct: 115 RGQYEGAKVLGFSYGQTMRRIVLPQVVKRILPPMSNETITLVKDTSLIYVLALNDLLRAA 174 Query: 184 RTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIER 220 R I+ R + ++ F +A A YL++T+VLT +F+ +E+ Sbjct: 175 RGIVQRDF-TITPFIVAAAFYLIMTLVLTWLFQRLEK 210 Lambda K H 0.332 0.142 0.443 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: 121 Number of extensions: 7 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: 230 Length of database: 216 Length adjustment: 22 Effective length of query: 208 Effective length of database: 194 Effective search space: 40352 Effective search space used: 40352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 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