Align Sugar ABC transporter permease (characterized, see rationale)
to candidate YP_426351.1 Rru_A1263 binding-protein dependent transport system inner membrane protein
Query= uniprot:A0A165KQ00 (289 letters) >NCBI__GCF_000013085.1:YP_426351.1 Length = 269 Score = 91.7 bits (226), Expect = 2e-23 Identities = 60/208 (28%), Positives = 106/208 (50%), Gaps = 3/208 (1%) Query: 81 FFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGSDALFGMLLFGVFMPFQVVLLPMSQV 140 +F NS+ +A+ A LIS A Y + ++ G G+L G +P +++LPM + Sbjct: 65 WFTNSMTVALAATLISLPAAATMAYASARFRTGGPVLWIGVLA-GQMLPPIILVLPMFML 123 Query: 141 LGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKELVNAARMDGASFFQIFWRIVL 200 G + +++ H L +++ + L AAR+DGAS Q RI L Sbjct: 124 FGTVLSLDGRIAIIVAHVALNLPFMAWMMTSFFEGDIRSLEEAARVDGASRLQALVRIAL 183 Query: 201 PLSTPIVMVTLIWQFTNIWNDFLFGVVFSGTDSKPVTVGLNNLANTSSSVKAYNVDMAAA 260 P++ P ++ + F WN+FL+ +V S+ + VGL L T + V+ ++ AAA Sbjct: 184 PVAAPGILAAALLGFILSWNEFLYALVLGDYSSQTLPVGLAGL-ETHAGVEIASL-AAAA 241 Query: 261 IIAGLPTMVIYVLAGKFFVRGLTAGAVK 288 ++A P +++ L K+ ++GL+ GA+K Sbjct: 242 LLALAPVLILLPLLRKYLIKGLSLGALK 269 Lambda K H 0.327 0.139 0.436 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: 229 Number of extensions: 13 Number of successful extensions: 3 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: 289 Length of database: 269 Length adjustment: 26 Effective length of query: 263 Effective length of database: 243 Effective search space: 63909 Effective search space used: 63909 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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