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_110806870.1 C8J30_RS16145 ABC transporter permease subunit
Query= TCDB::Q9HU29 (230 letters) >NCBI__GCF_003217355.1:WP_110806870.1 Length = 232 Score = 177 bits (450), Expect = 1e-49 Identities = 103/232 (44%), Positives = 141/232 (60%), Gaps = 4/232 (1%) Query: 1 MSEWELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFF 60 MS E + +PK+L GA TL L + + L + R + + AYI F Sbjct: 1 MSLIESLSTNLPKLLDGAETTLILTGLGAALAAVFSPGLALIRLFGPTPAKMLLRAYISF 60 Query: 61 FRGTPLLLQLFIVYYGLAQFE-EVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAI 119 RGTPLL QLF+V+YG QF E+ W + RDP+ CA+L +++ AY EILRG I Sbjct: 61 VRGTPLLAQLFLVFYGSGQFRAELTGLGLWSFFRDPFNCAVLVFVINSCAYQTEILRGGI 120 Query: 120 HSVPVGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDI 179 +VP GE+EAARA+GM+R + L +I P A RI PA NEVIL++KASA+ VT+FD+ Sbjct: 121 EAVPPGEIEAARAIGMTRARVLARVIFPHAYRIAWPALGNEVILLMKASALASIVTVFDL 180 Query: 180 MGMARTIIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWL--RVDATQG 229 MG R I +R++E ++F A ALYL+IT+V ++R IER L + TQG Sbjct: 181 MGRTRQIFSRSFEFSVYF-EAAALYLLITVVFVFLWRQIERRLTRHMRRTQG 231 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: 147 Number of extensions: 8 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: 232 Length adjustment: 23 Effective length of query: 207 Effective length of database: 209 Effective search space: 43263 Effective search space used: 43263 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