Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate WP_086510783.1 BZY95_RS15420 carbohydrate ABC transporter permease
Query= reanno::WCS417:GFF4322 (281 letters) >NCBI__GCF_002151265.1:WP_086510783.1 Length = 292 Score = 371 bits (953), Expect = e-108 Identities = 185/279 (66%), Positives = 223/279 (79%), Gaps = 9/279 (3%) Query: 12 LSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKAWAT-- 69 L R +YAVL+LA L YL+PL VML+TS K +I+ G LLS P T W KAW Sbjct: 14 LGRAMLYAVLLLAALFYLLPLAVMLITSVKPLAEITPGTLLSLPREPTLAPWGKAWGEAC 73 Query: 70 -------VDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPF 122 + YF+NSI I VPAVLISTAIGALNGY L+ WRFKGS+L F L+LFGCF+PF Sbjct: 74 TGMRCEGIGVYFFNSIAIVVPAVLISTAIGALNGYALTKWRFKGSELLFALMLFGCFIPF 133 Query: 123 QTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAG 182 Q VLLP + TLG +GL+S+ GL+ VHV++G+AFTTLFFRN+YV++P L+ AA+LDGAG Sbjct: 134 QVVLLPMAQTLGWLGLSSSRAGLILVHVIFGIAFTTLFFRNFYVAVPTELVSAAKLDGAG 193 Query: 183 FFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGA 242 FF IF +I+LP+S PII+V +IWQFTQIWNDFLFGV FS+ ++QP+TVALNNLVNTSTGA Sbjct: 194 FFRIFWRILLPVSAPIIVVSVIWQFTQIWNDFLFGVAFSAHNTQPVTVALNNLVNTSTGA 253 Query: 243 KEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281 +EYNVDMAAAMIA LPTL+VYV+AGKYFVRGLTAG+VKG Sbjct: 254 REYNVDMAAAMIAALPTLIVYVLAGKYFVRGLTAGSVKG 292 Lambda K H 0.328 0.141 0.435 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: 276 Number of extensions: 6 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: 292 Length adjustment: 26 Effective length of query: 255 Effective length of database: 266 Effective search space: 67830 Effective search space used: 67830 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