Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate WP_011803054.1 PNAP_RS18455 carbohydrate ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >NCBI__GCF_000015505.1:WP_011803054.1 Length = 289 Score = 343 bits (879), Expect = 3e-99 Identities = 171/278 (61%), Positives = 209/278 (75%), Gaps = 9/278 (3%) Query: 13 SRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDV--- 69 SR +YA LL+AA +L P VML TSFK E IR+GNLLS P ++ W AW Sbjct: 12 SRALLYAVLLVAALFFLAPFYVMLATSFKDAEQIRSGNLLSPPASLNFDAWRLAWSSACT 71 Query: 70 ------VGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQ 123 + YFWNSV + +PAVLIST GA+NGYVLS+W+FRGS+L FG LLFG F+PFQ Sbjct: 72 GVDCRGLQPYFWNSVSMAIPAVLISTAWGAVNGYVLSLWKFRGSELLFGFLLFGVFMPFQ 131 Query: 124 TVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGF 183 VLLP S LG GL+++ GLVLVH + G+A TTLFFRNYY +IP LV AAR+DGAGF Sbjct: 132 VVLLPMSQVLGYLGLSSSIGGLVLVHCLAGMAGTTLFFRNYYTAIPKELVNAARMDGAGF 191 Query: 184 FTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAK 243 + IF +I+LP+S PI+MV LIWQFT IWNDFLFGV F+ D++PITV LNN+ NTS+ K Sbjct: 192 WRIFWRIVLPLSTPILMVTLIWQFTNIWNDFLFGVAFSGADSKPITVGLNNMANTSSSVK 251 Query: 244 EYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 YNVDMAAA+IAGLPT+LVY+ AG+YF++GLT+GAVKG Sbjct: 252 SYNVDMAAAVIAGLPTMLVYVLAGQYFVKGLTAGAVKG 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: 297 Number of extensions: 12 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 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