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_110804794.1 C8J30_RS05895 amino acid ABC transporter permease
Query= TCDB::Q9HU29 (230 letters) >NCBI__GCF_003217355.1:WP_110804794.1 Length = 434 Score = 86.7 bits (213), Expect = 7e-22 Identities = 67/213 (31%), Positives = 106/213 (49%), Gaps = 10/213 (4%) Query: 17 GAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPLLLQLFIVYYG 76 G L L + A+V L L + L + R S V+A+ I F RG PL+ LF Sbjct: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMVMVKALSVGMIEFIRGVPLITLLFTASL- 284 Query: 77 LAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVGEVEAARALGMS 136 L Q+ + F LR ++ +TL AAYIAE++RG + ++P G+ EAA ALG+ Sbjct: 285 LLQYFLPPGTTFDLILR-----VVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLD 339 Query: 137 RRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFD----IMGMARTIIARTYE 192 QA II+P+A++I +P + I + K + +V V LFD I G+ R+ +A Sbjct: 340 YWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVTFVGLFDPLKGISGVVRSDMAWKGT 399 Query: 193 SMLFFCLAGALYLVITIVLTRIFRLIERWLRVD 225 + ++ + ++R +ER L+ D Sbjct: 400 YWEPYIFVAVIFFLFNFSMSRYSMYLERKLKRD 432 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: 284 Number of extensions: 15 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: 434 Length adjustment: 27 Effective length of query: 203 Effective length of database: 407 Effective search space: 82621 Effective search space used: 82621 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 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