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 Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= TCDB::Q9HU29 (230 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 80.9 bits (198), Expect = 3e-20 Identities = 43/126 (34%), Positives = 75/126 (59%), Gaps = 4/126 (3%) Query: 100 LLTMTLHTAAYIAEILRGAIHSVPVGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSN 159 LL + +T A+I EI+RG I SVP G+ EAA ALG++R Q LW I++P+A+R+ +P+ ++ Sbjct: 249 LLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNS 308 Query: 160 EVILMLKASAVVYTVTLFDIMGMARTIIARTYESMLFFCLAGALYLVITIVLTR----IF 215 + + K S++ V D+ A+T + +T + F + YL I V++ + Sbjct: 309 QYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQ 368 Query: 216 RLIERW 221 + ++RW Sbjct: 369 QRLQRW 374 Score = 42.4 bits (98), Expect = 1e-08 Identities = 19/62 (30%), Positives = 34/62 (54%) Query: 14 MLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPLLLQLFIV 73 ++ G +L ++AI ++ + G+A S +W +R + Y+ R TPLLLQL + Sbjct: 82 LVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVW 141 Query: 74 YY 75 Y+ Sbjct: 142 YF 143 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: 244 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 230 Length of database: 377 Length adjustment: 26 Effective length of query: 204 Effective length of database: 351 Effective search space: 71604 Effective search space used: 71604 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 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