Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate WP_084260334.1 Q394_RS0103655 carbohydrate ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >NCBI__GCF_000621325.1:WP_084260334.1 Length = 281 Score = 138 bits (347), Expect = 2e-37 Identities = 79/260 (30%), Positives = 142/260 (54%), Gaps = 7/260 (2%) Query: 28 VICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGVPVWDYFRNSLI 87 +I P L++ +++ + ++ +A P VW+ T + + + + +G +DY NS+I Sbjct: 29 IIFFPLLFMFVTAFKTELQAIAVPSVWV-FTPTWENFALVQERSGY-----FDYAWNSVI 82 Query: 88 VSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYARTGII 147 SV ST++ L I + Y+ A K I + + T+ +P + LP+++L G++ Sbjct: 83 TSVGSTILGLLIAVPAAYSMAFSPTKRTKDILMWMLSTKMMPAVGALLPIYVLCQTFGLL 142 Query: 148 DTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPLAGPGI 207 D SLI+ + +N+P +W++ F+ +P ++ EAA++DG + + F V PLA G+ Sbjct: 143 DNVISLIIIFTMMNLPIMVWMLYSNFKDIPIEILEAARMDGASLSEEFRHVLLPLAMGGM 202 Query: 208 ASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAVVMIVPAL 267 AS G+ + SWNE +T + N+ TL + Y++ + W + A++V+ I P + Sbjct: 203 ASTGLLCLVLSWNEAFWVLNLT-AANAGTLASLVASYSSPEGLFWAKLSAVSVLAIAPIV 261 Query: 268 TLTFIIQKHLVSGLTFGAVK 287 + QK LV GLTFGAVK Sbjct: 262 VFGWFSQKQLVQGLTFGAVK 281 Lambda K H 0.328 0.141 0.442 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: 235 Number of extensions: 11 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: 281 Length adjustment: 26 Effective length of query: 262 Effective length of database: 255 Effective search space: 66810 Effective search space used: 66810 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: 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