Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate WP_013402055.1 CALHY_RS00400 carbohydrate ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >NCBI__GCF_000166355.1:WP_013402055.1 Length = 281 Score = 118 bits (295), Expect = 2e-31 Identities = 82/277 (29%), Positives = 144/277 (51%), Gaps = 10/277 (3%) Query: 11 SFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKA---- 66 SF+ + Y L+L A ++PL+ +L SFK +I N + P+ + + + Sbjct: 9 SFADVIKYLILVLWACTTILPLLWVLNNSFKESNEILL-NPMKLPSKLSFFNYSQLISYG 67 Query: 67 -WDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTV 125 ++ G F NS+ I+ VL+ G YV++ + F+ + + +P ++ Sbjct: 68 NMNIFRG-FLNSLIISGSVVLLVLLFGGFAAYVIARFDFKLTGIVKIFFTGAMLVPAFSI 126 Query: 126 LLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFT 185 ++P+ L K GL + L+L L F TL + ++P L +AA +DGAG Sbjct: 127 VIPSLVILRKLGLNGSYLALILPQTAGLLPFATLTLAGFMKTLPVELEEAAIIDGAGVLR 186 Query: 186 IFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFAS-GDAQPITVALNNLVNTSTGAKE 244 IF +I++P+SIP ++ I+ F +ND ++F + QPI V L +LV++ G Sbjct: 187 IFFRIIVPLSIPGLVTAAIFVFLWSYNDLFMSLIFIPIREKQPICVLL-SLVSSIYGT-N 244 Query: 245 YNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 Y MAA +I LP +++Y+F +Y ++G+T+GA+KG Sbjct: 245 YGAMMAALIITVLPVIILYVFLQEYVIKGMTAGAIKG 281 Lambda K H 0.329 0.143 0.447 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: 228 Number of extensions: 18 Number of successful extensions: 5 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: 281 Length of database: 281 Length adjustment: 26 Effective length of query: 255 Effective length of database: 255 Effective search space: 65025 Effective search space used: 65025 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 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