Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease
Query= reanno::Dino:3607127 (272 letters) >NCBI__GCF_003217355.1:WP_110804034.1 Length = 382 Score = 115 bits (288), Expect = 1e-30 Identities = 75/242 (30%), Positives = 130/242 (53%), Gaps = 16/242 (6%) Query: 38 VALEAPPVWIFEPTLSNYREALFEDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFE 97 V APP T NY + +G+ R +N++ + I T + +++ AA+ALA Sbjct: 148 VTTVAPP----RLTTGNYARVITAEGIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMR 203 Query: 98 FRGKKDLWFWFITNRMISPIVLAL-PFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVT 156 F G+ L I ++ P+ LAL P + +GL ++ + L + F LP+ I+++ Sbjct: 204 FPGRA-LLVATIVGLLVVPLQLALIPLLKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLLR 262 Query: 157 DQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGLIL-- 214 + G+P ++ E+AR++GA++F I R+I LPL+ P +A AIF F++ WN+L+ + Sbjct: 263 NYMVGLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFLG 322 Query: 215 --TRSEAKTAPAMAVSFMEGYNLPYGKIMATSTL--IVIPVLIFALIASKQLVRGLTMGA 270 T ++ T A+ G + +I+A S I +P+++F + K LVRGL G+ Sbjct: 323 NATDTQVMTGALRALLGSRGGD---WEILAASAFVSIAVPLIVFFAL-QKYLVRGLLAGS 378 Query: 271 VK 272 VK Sbjct: 379 VK 380 Lambda K H 0.331 0.143 0.431 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: 281 Number of extensions: 12 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: 272 Length of database: 382 Length adjustment: 28 Effective length of query: 244 Effective length of database: 354 Effective search space: 86376 Effective search space used: 86376 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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