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 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q9HU29 (230 letters) >FitnessBrowser__Dino:3606890 Length = 432 Score = 95.1 bits (235), Expect = 2e-24 Identities = 70/205 (34%), Positives = 115/205 (56%), Gaps = 18/205 (8%) Query: 31 AGLALALPLGIA----RASRHWYVRAVPYAYIFFFRGTPLLLQLFIVYYGLAQFEEVRKS 86 +G+AL+LPLGIA R S ++ V +I F RG PL+ LF+ LA F S Sbjct: 234 SGIALSLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTS 293 Query: 87 AFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVGEVEAARALGMSRRQALWHIIL 146 F LR ++ +TL +AYIAE +RG + ++P G+ EA +LG+ Q++ IIL Sbjct: 294 -FDLVLR-----VIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIIL 347 Query: 147 PRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMAR-TIIART-----YESMLFFCLA 200 P+A++I +P+ N I + K + +V +++FD++GM + I++ T Y +L F A Sbjct: 348 PQALKISIPSIVNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLGF--A 405 Query: 201 GALYLVITIVLTRIFRLIERWLRVD 225 G L+ V +++ + +ER L + Sbjct: 406 GVLFFVFCYGISQYSQWLERQLATE 430 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: 304 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 230 Length of database: 432 Length adjustment: 27 Effective length of query: 203 Effective length of database: 405 Effective search space: 82215 Effective search space used: 82215 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: 48 (23.1 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