Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate Pf6N2E2_1647 Maltose/maltodextrin ABC transporter, permease protein MalF
Query= reanno::Phaeo:GFF1304 (288 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1647 Length = 321 Score = 141 bits (355), Expect = 2e-38 Identities = 88/291 (30%), Positives = 151/291 (51%), Gaps = 13/291 (4%) Query: 9 AARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNY--------ARFL 60 AA + ++P ++ L PL T +FS GD +VG NY + L Sbjct: 29 AAWLFLSPMLLCLALVAAWPLLRTFWFSLTDASLADTGDATFVGLSNYLFHSSAGWSGIL 88 Query: 61 SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120 +W +V+ TL + + ++LG+ +ALLLN G+ +VR L++ P+ + VSA Sbjct: 89 VDPQWWNAVRNTLHFTVVSVGLEIVLGLMVALLLNVKFTGRALVRALILIPWAIPTIVSA 148 Query: 121 LVWKNMFMDPVNGLFAHLWKAFGA--EPVSWLSEASLQ--SIILIVSWQWLPFATLILLT 176 +W M D G+ HL G P++W ++A L ++I++ W+ +PF TL++L Sbjct: 149 KIWSWMLNDQF-GIINHLMLGLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLA 207 Query: 177 AIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQG 236 A+Q L S+ EAA +DG PV F ++TLP L A+ V + + + L +F I+V T Sbjct: 208 ALQMLPSDCYEAARVDGIHPVKVFWWVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSN 267 Query: 237 SFGTKTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLD 287 S T +++ Q ++E Q+VG GSA ++ ++A+ + + + L+ Sbjct: 268 SSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIAMAYLYLGRRQLE 318 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: 291 Number of extensions: 18 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: 288 Length of database: 321 Length adjustment: 27 Effective length of query: 261 Effective length of database: 294 Effective search space: 76734 Effective search space used: 76734 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