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_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= TCDB::Q9HU29 (230 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 92.4 bits (228), Expect = 1e-23 Identities = 69/218 (31%), Positives = 113/218 (51%), Gaps = 27/218 (12%) Query: 17 GAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPLLLQLFIVYYG 76 G LTL I++V L L + L + R S +R + YI FRG PL+ LF Sbjct: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILF----- 244 Query: 77 LAQFEEVRKSAFWPYLRDPYWC------ALLTMTLHTAAYIAEILRGAIHSVPVGEVEAA 130 F +V P + D W A++ +T+ +AY+AE +RG + ++P G+ EAA Sbjct: 245 ---FGQVMV----PLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAA 297 Query: 131 RALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMARTIIA-- 188 ALG++ Q I+LP+A+RI +PA + +L+ + ++ V L +++G++R+I+A Sbjct: 298 AALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANP 357 Query: 189 ----RTYESMLFFCLAGALYLVITIVLTRIFRLIERWL 222 R E LF G LY + L ++ R +E+ L Sbjct: 358 AYLGRYAEVYLFL---GVLYWLCCYGLAQLSRRLEQRL 392 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: 303 Number of extensions: 20 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: 396 Length adjustment: 27 Effective length of query: 203 Effective length of database: 369 Effective search space: 74907 Effective search space used: 74907 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