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 PP_3595 PP_3595 Amino acid ABC transporter, membrane protein
Query= TCDB::Q9HU29 (230 letters) >FitnessBrowser__Putida:PP_3595 Length = 236 Score = 162 bits (409), Expect = 7e-45 Identities = 82/216 (37%), Positives = 138/216 (63%), Gaps = 2/216 (0%) Query: 5 ELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGT 64 +L+ ++ P+ + G +T +L+AI+ G L L L +AR SR ++ + Y++FFRG+ Sbjct: 14 DLLERYGPRFIDGLLVTAKLVAISFSLGAVLGLLLALARLSRSLVLQRMAAGYVYFFRGS 73 Query: 65 PLLLQLFIVYYGLAQFEEVRKSA-FWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVP 123 PLL QLF++YYGL + + W + RD ++C LL TL+TAAY AEI RG++ +V Sbjct: 74 PLLAQLFLLYYGLGSLKGFWQDVGLWWFFRDAWFCTLLAFTLNTAAYQAEIFRGSLMAVA 133 Query: 124 VGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMA 183 G+ EAARAL + R + +ILP+++ + + NE+ILM+KASA+ VT++D+MG+ Sbjct: 134 PGQHEAARALNLKRSTTFFKVILPQSLLVAIGPLGNELILMIKASAIASLVTIYDLMGVT 193 Query: 184 RTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIE 219 + +R+++ ++ A LYLVI ++ R+ + +E Sbjct: 194 KLAFSRSFDFQIYL-WAAVLYLVIVELVRRLLKHLE 228 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: 136 Number of extensions: 7 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: 236 Length adjustment: 23 Effective length of query: 207 Effective length of database: 213 Effective search space: 44091 Effective search space used: 44091 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