Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate WP_084260334.1 Q394_RS0103655 carbohydrate ABC transporter permease
Query= reanno::Dino:3607127 (272 letters) >NCBI__GCF_000621325.1:WP_084260334.1 Length = 281 Score = 189 bits (481), Expect = 4e-53 Identities = 95/266 (35%), Positives = 154/266 (57%) Query: 7 LFSQIALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLR 66 L S+ L I + FP +M T+ KT++ A+ P VW+F PT N+ G Sbjct: 16 LVSRTLLAWAITFIIFFPLLFMFVTAFKTELQAIAVPSVWVFTPTWENFALVQERSGYFD 75 Query: 67 TLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLI 126 NS+I ++ +T L L++ VPAA+++A + KD+ W ++ +M+ + LP +++ Sbjct: 76 YAWNSVITSVGSTILGLLIAVPAAYSMAFSPTKRTKDILMWMLSTKMMPAVGALLPIYVL 135 Query: 127 ARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICL 186 + GLLD I+LI+I+ NLPI++W++ F+ IP ++ EAAR++GAS R + L Sbjct: 136 CQTFGLLDNVISLIIIFTMMNLPIMVWMLYSNFKDIPIEILEAARMDGASLSEEFRHVLL 195 Query: 187 PLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTL 246 PLAM G+A + + + SWNE + L LT + A T ++ S+ L + K+ A S L Sbjct: 196 PLAMGGMASTGLLCLVLSWNEAFWVLNLTAANAGTLASLVASYSSPEGLFWAKLSAVSVL 255 Query: 247 IVIPVLIFALIASKQLVRGLTMGAVK 272 + P+++F + KQLV+GLT GAVK Sbjct: 256 AIAPIVVFGWFSQKQLVQGLTFGAVK 281 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: 262 Number of extensions: 11 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: 272 Length of database: 281 Length adjustment: 25 Effective length of query: 247 Effective length of database: 256 Effective search space: 63232 Effective search space used: 63232 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: 47 (22.7 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