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 GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC
Query= TCDB::Q9HU29 (230 letters) >FitnessBrowser__psRCH2:GFF18 Length = 219 Score = 101 bits (251), Expect = 1e-26 Identities = 74/217 (34%), Positives = 119/217 (54%), Gaps = 9/217 (4%) Query: 7 ILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPL 66 +++ +P +LQGA +T+++ + +A AL +AR S +R + YI FRG+ L Sbjct: 1 MIELLPLLLQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSL 60 Query: 67 LLQLFIVYYGLAQFE-EVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVG 125 L+QLF +Y+ L + SAF A++ + L+ AY AE+LRGAI SV G Sbjct: 61 LVQLFWLYFVLPMPPFNIEMSAFA--------VAVVGLGLNIGAYGAEVLRGAIRSVHRG 112 Query: 126 EVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMART 185 + EA +AL M+ + IILP+A+ +P +N +I +LK +++V +TL D+ AR Sbjct: 113 QHEACQALNMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQ 172 Query: 186 IIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWL 222 + T +M F LA +Y V+ + R +ER L Sbjct: 173 LDQATLMTMEIFGLALVIYFVLAQTINFGMRQLERRL 209 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: 138 Number of extensions: 8 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: 230 Length of database: 219 Length adjustment: 22 Effective length of query: 208 Effective length of database: 197 Effective search space: 40976 Effective search space used: 40976 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 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