Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= reanno::pseudo5_N2C3_1:AO356_09905 (231 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 102 bits (253), Expect = 1e-26 Identities = 70/212 (33%), Positives = 115/212 (54%), Gaps = 17/212 (8%) Query: 14 AGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVRGIPELLWVLLIYF 73 +G L+T+ AL ++ L LG+L AL + S ++WL TY L RG+P V +++F Sbjct: 189 SGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLP---LVTILFF 245 Query: 74 GTVNLMRALGEYLGMPDLALNAFAAGVIALGLCFGAYATEVFRGAILAIPKGHREAGVAL 133 G V + L + ++ ++ L + AY E RG + AIP+G EA AL Sbjct: 246 GQVMVPLMLDS-----EWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAAL 300 Query: 134 GLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHAQIGVTVSKQP 193 GL+ ++ + +++PQ RI++P + LF+ L++DT L+S++GL E+ +G++ S Sbjct: 301 GLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLEL-----LGISRSILA 355 Query: 194 FTFYMVA-ALMYLGLTVLAML---GMHLLERR 221 Y+ A +YL L VL L G+ L RR Sbjct: 356 NPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRR 387 Lambda K H 0.329 0.143 0.435 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: 344 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: 231 Length of database: 396 Length adjustment: 27 Effective length of query: 204 Effective length of database: 369 Effective search space: 75276 Effective search space used: 75276 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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