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_110806878.1 C8J30_RS16140 ABC transporter permease subunit
Query= TCDB::Q9HU29 (230 letters) >NCBI__GCF_003217355.1:WP_110806878.1 Length = 235 Score = 112 bits (281), Expect = 5e-30 Identities = 75/222 (33%), Positives = 110/222 (49%), Gaps = 8/222 (3%) Query: 10 WMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPLLLQ 69 W ++L G +TL L A + GL L + A SR +RA+ + Y RG P +L Sbjct: 12 WGDELLAGVWVTLRLAAATLPVGLLLGFVVAAASLSRRPVLRAMGWGYTTVMRGMPEILT 71 Query: 70 LFIVYYGLAQFEEVRKSAFWPYLR----DPYWCALLTMTLHTAAYIAEILRGAIHSVPVG 125 LFIVY GL F P + P+ ++ + L AA+ AE+LRGA +VP G Sbjct: 72 LFIVYNGLGLGLNRLLDHFAPQIGAVDFPPFAAGVIALALVFAAFAAEVLRGAFQAVPEG 131 Query: 126 EVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMART 185 +V A A+GM+ RQ W I LP+ R LP N + +LK +A+V + L D+M + Sbjct: 132 QVLAGLAIGMTGRQVFWRIKLPQLWRFALPGMGNLWLNLLKDTALVSVIALDDLMRATKV 191 Query: 186 IIARTYESMLFFCLAGALY----LVITIVLTRIFRLIERWLR 223 + T + F+ A +Y L +VLTR+ R +R Sbjct: 192 AVGVTKQPFTFYLAACLIYWGLCLGSELVLTRLEARANRGVR 233 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: 143 Number of extensions: 10 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: 235 Length adjustment: 23 Effective length of query: 207 Effective length of database: 212 Effective search space: 43884 Effective search space used: 43884 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