Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= uniprot:A0A1N7U128 (237 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 80.5 bits (197), Expect = 5e-20 Identities = 67/228 (29%), Positives = 107/228 (46%), Gaps = 20/228 (8%) Query: 12 YLFSDGAGL--------SGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYT 63 +L G GL SG+ +TL +IS+V L I LAL R S +RW Y Sbjct: 172 WLLQGGLGLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYI 231 Query: 64 YLFRGTPLYIQLLICYTGLYSLEIVQDNAL-LNQFFRNALNCTLLAFVLNTCAYTVEIFA 122 LFRG PL + I + G + ++ D+ +++ R + T+ AY E Sbjct: 232 ELFRGLPL---VTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFL-----SAYLAETVR 283 Query: 123 GAIRNIPHGEIEAARAYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATV 182 G ++ IP G+ EAA A GL+ ++ F+V+P ALR ++PA + +L T+L + Sbjct: 284 GGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGL 343 Query: 183 ADILKVARDANAETFLT---FQAFGIAALLYMLLSFALVGLFRLAERR 227 ++L ++R A + + +LY L + L L R E+R Sbjct: 344 LELLGISRSILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQR 391 Lambda K H 0.332 0.143 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: 326 Number of extensions: 16 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: 237 Length of database: 396 Length adjustment: 27 Effective length of query: 210 Effective length of database: 369 Effective search space: 77490 Effective search space used: 77490 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