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 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q9HU29 (230 letters) >MicrobesOnline__882:206399 Length = 337 Score = 122 bits (305), Expect = 1e-32 Identities = 69/212 (32%), Positives = 124/212 (58%), Gaps = 10/212 (4%) Query: 14 MLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPLLLQLFIV 73 +L+G +TLE+ +A++ G+ L + G+AR S + +R + YI RG+PLL+Q+F+ Sbjct: 127 LLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVFLW 186 Query: 74 YYGL-----AQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVGEVE 128 Y+ + A FE+V SA P W ++ + + T AY+AEI+R I SV G++E Sbjct: 187 YFVVGTLLNALFEKVGLSAI-----PPLWYGVMALAIFTGAYVAEIVRAGIQSVHRGQME 241 Query: 129 AARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMARTIIA 188 AAR+LGMS Q++ +ILP+A R +P + + I ++K S+++ + + ++ R ++ Sbjct: 242 AARSLGMSYAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVVT 301 Query: 189 RTYESMLFFCLAGALYLVITIVLTRIFRLIER 220 + + + + LYLV+T L+ + +ER Sbjct: 302 TSLQPFELWIVCALLYLVLTFTLSLCVQYLER 333 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: 195 Number of extensions: 12 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: 337 Length adjustment: 25 Effective length of query: 205 Effective length of database: 312 Effective search space: 63960 Effective search space used: 63960 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: 47 (22.7 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