Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate GFF3012 HP15_2956 sugar ABC transporter, permease protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >FitnessBrowser__Marino:GFF3012 Length = 289 Score = 436 bits (1121), Expect = e-127 Identities = 215/284 (75%), Positives = 243/284 (85%), Gaps = 9/284 (3%) Query: 7 KSGISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKA 66 ++G SR+AIY LLLAA VYLIPL +ML+TSFK+P DIRTGNL++ PT IGW KA Sbjct: 6 RTGFRPSRVAIYGLLLLAALVYLIPLFIMLVTSFKTPMDIRTGNLMALPTDWTTIGWTKA 65 Query: 67 W---------DVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFG 117 W + + GYFWNS K+TVPAVLIST +GA NGYVLS W+F+GS LFFG+LLFG Sbjct: 66 WSEACTGVQCEGISGYFWNSFKMTVPAVLISTLLGAFNGYVLSKWKFKGSDLFFGMLLFG 125 Query: 118 CFLPFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAAR 177 CF+PFQ VLLP + TLGK GLANTT+GLVLVHV+YG+AFTTLFFRNYYV+IPDAL+KAAR Sbjct: 126 CFVPFQVVLLPMAATLGKLGLANTTSGLVLVHVIYGVAFTTLFFRNYYVAIPDALIKAAR 185 Query: 178 LDGAGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVN 237 LDGAGFFTIF +ILLPMS PI MV LIWQFTQIWNDFLFGVVFASGD+QPITVALNNLVN Sbjct: 186 LDGAGFFTIFFRILLPMSTPIFMVSLIWQFTQIWNDFLFGVVFASGDSQPITVALNNLVN 245 Query: 238 TSTGAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 TSTG KEYNVDMAAAMIA LPTL+VYI AGKYF+RGLT+G+VKG Sbjct: 246 TSTGVKEYNVDMAAAMIAALPTLVVYIVAGKYFIRGLTAGSVKG 289 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: 333 Number of extensions: 7 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: 289 Length adjustment: 26 Effective length of query: 255 Effective length of database: 263 Effective search space: 67065 Effective search space used: 67065 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