Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS05035 Length = 285 Score = 369 bits (946), Expect = e-107 Identities = 185/281 (65%), Positives = 220/281 (78%), Gaps = 9/281 (3%) Query: 10 ISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAW-- 67 ++ SR IYA L L A +L PL VML TSFK + +RTGNLL+ PT WIKAW Sbjct: 5 MTISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPWIKAWSG 64 Query: 68 -------DVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL 120 D + +F NSV++ +PAVLIS+ IGA NGYVL+ WRFRG+ F ++L GCF+ Sbjct: 65 ACTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMILVGCFI 124 Query: 121 PFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDG 180 PFQ +LLP + G GL+NTTTGLV+VHV+YG+AFTT+FFRN+YVSIP LVKAAR+DG Sbjct: 125 PFQAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKAARIDG 184 Query: 181 AGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTST 240 AGFFTIF KILLP+S+PI MVCLIWQFTQIWNDFLFG+VF+ D+ PITVALNNLVNTST Sbjct: 185 AGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMPITVALNNLVNTST 244 Query: 241 GAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 G KEYNVDMA A+IA LPTLLVYI AG+YF+RGLT+GAVKG Sbjct: 245 GVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTAGAVKG 285 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: 328 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: 281 Length of database: 285 Length adjustment: 26 Effective length of query: 255 Effective length of database: 259 Effective search space: 66045 Effective search space used: 66045 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 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