Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease
Query= reanno::Dino:3607126 (288 letters) >NCBI__GCF_000018545.1:WP_015888140.1 Length = 307 Score = 168 bits (426), Expect = 1e-46 Identities = 102/277 (36%), Positives = 157/277 (56%), Gaps = 9/277 (3%) Query: 11 FAFIGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMG 70 + + P V+ L + I P +Y + ++H + EF+G+ N+ +L+D F A+ Sbjct: 29 YLMLAPTVLILLALTIFPSIYMFYAAVHRISPNPDLPWEFVGVGNFARLLSDPQFHVALR 88 Query: 71 RTFFLLGTALPLQIALGLGIALVLHQ--PGLTLVKTLARLSLVLPMATTYAVVGLLGQVM 128 T A+ L+ LGLG+AL+L + L+ +KT+ L++PM V + +++ Sbjct: 89 NTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTV----LMIPMMLPPIAVAITWKLI 144 Query: 129 FNQKFGVVNQ---LLGGADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEV 185 + +FGV+N+ LLG W GD A II DVWQWTPFV L++LAGL +P E Sbjct: 145 YEPQFGVLNEIMFLLGLPVQAWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASLPVEP 204 Query: 186 EEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFI 245 EAA L+ S W + LPFL P + L+LR D L+LFD+VF LT GGP T+ + Sbjct: 205 YEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADRTKVL 264 Query: 246 SLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIYIR 282 SL I +V +R D G A+A ++ +L +TIVL+ +++ Sbjct: 265 SLYIYQVAYRFADPGYAAAISLFVLFVTIVLSTWFMK 301 Lambda K H 0.329 0.144 0.440 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: 266 Number of extensions: 13 Number of successful extensions: 4 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: 307 Length adjustment: 26 Effective length of query: 262 Effective length of database: 281 Effective search space: 73622 Effective search space used: 73622 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 Apr 09 2024. 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