Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate 3607561 Dshi_0973 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Phaeo:GFF1304 (288 letters) >FitnessBrowser__Dino:3607561 Length = 288 Score = 519 bits (1336), Expect = e-152 Identities = 258/288 (89%), Positives = 276/288 (95%) Query: 1 MATQHSRSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNYARFL 60 MAT+HSRSAAR+MMAPAVILLLGWMLVPLTMTL FSFK+YLPLRGGDLGWVGFDNY RF+ Sbjct: 1 MATKHSRSAARLMMAPAVILLLGWMLVPLTMTLLFSFKQYLPLRGGDLGWVGFDNYIRFV 60 Query: 61 SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120 SSSAFWPSV ATL+IVGGVLAIT+ LGV LA+LLNQPMWGQG+VRILVIAPFFVMPTVSA Sbjct: 61 SSSAFWPSVTATLIIVGGVLAITITLGVLLAILLNQPMWGQGVVRILVIAPFFVMPTVSA 120 Query: 121 LVWKNMFMDPVNGLFAHLWKAFGAEPVSWLSEASLQSIILIVSWQWLPFATLILLTAIQS 180 LVWKNMFMDP NGL AHLW+ FGAEPVSWLSEAS+ SII+IVSWQWLPFATLILLTAIQS Sbjct: 121 LVWKNMFMDPTNGLLAHLWRFFGAEPVSWLSEASMTSIIMIVSWQWLPFATLILLTAIQS 180 Query: 181 LDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQGSFGT 240 LDSEQLEAAEMDGAPPV RF +ITLPHLSRAIT+V+LIQTIFLL+IFAEIFVTT G+FGT Sbjct: 181 LDSEQLEAAEMDGAPPVKRFAFITLPHLSRAITIVLLIQTIFLLAIFAEIFVTTGGAFGT 240 Query: 241 KTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA 288 +TLTYLI+QRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA Sbjct: 241 RTLTYLIFQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA 288 Lambda K H 0.328 0.140 0.430 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: 435 Number of extensions: 12 Number of successful extensions: 1 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: 288 Length of database: 288 Length adjustment: 26 Effective length of query: 262 Effective length of database: 262 Effective search space: 68644 Effective search space used: 68644 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: 47 (22.7 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