Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate HSERO_RS15495 HSERO_RS15495 ABC transporter permease
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__HerbieS:HSERO_RS15495 Length = 291 Score = 129 bits (324), Expect = 8e-35 Identities = 84/275 (30%), Positives = 140/275 (50%), Gaps = 10/275 (3%) Query: 14 IGPAVIGLALVGIAPLLYALWTSLHFYNLTK-LRRVEFIGLENYWTVLTDEVFWQAM-GR 71 + PA++ L P L LW S F++ K +R F+GLENY + D VFWQA+ Sbjct: 14 LSPAMVLLIAFTHYPALATLWHS--FFSTPKGVRPSVFVGLENYRLMADDPVFWQALCNN 71 Query: 72 TFFLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFNQ 131 +F LGT +PL IAL + +AL +++ + + RL+ P V + + Sbjct: 72 LWFALGT-IPLAIALAILMALWVNEK--LAGRGVLRLAYFTPTVLPMIAVANIWLFFYTP 128 Query: 132 KFGVVNQLLGGADI---NWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEA 188 ++G++ Q+ G + NW+G+P+ ++ VW+ F + LA L + + EA Sbjct: 129 QYGLLEQITGALGLPSHNWLGNPQTVLGALMVVAVWKEAGFFMIFYLAALQQISPVLAEA 188 Query: 189 ARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLM 248 A LE S+W VQ P L+P + VLI + +L D + +T+GGP +++ + Sbjct: 189 AALEGASRWQYFWRVQFPLLMPTTLFVLINALINAFRLVDHIVVMTKGGPDNASSLLLYY 248 Query: 249 IQRVGFRGFDQGLASAQAIILLIITIVLAQIYIRV 283 I VGF +D A+A ++LL + ++A + RV Sbjct: 249 IYEVGFAFWDSSYAAALTVVLLALLGLIALVKFRV 283 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: 258 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: 288 Length of database: 291 Length adjustment: 26 Effective length of query: 262 Effective length of database: 265 Effective search space: 69430 Effective search space used: 69430 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