Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate WP_007695789.1 C447_RS16065 carbohydrate ABC transporter permease
Query= reanno::WCS417:GFF4322 (281 letters) >NCBI__GCF_000336675.1:WP_007695789.1 Length = 305 Score = 173 bits (439), Expect = 4e-48 Identities = 106/292 (36%), Positives = 162/292 (55%), Gaps = 24/292 (8%) Query: 8 PAISLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTV---VTGIGWV 64 P LSR +Y +++ V +LVPL L+T+FKT + +++ L +P + T WV Sbjct: 15 PGFDLSRALLYLLILFFVAFFLVPLETGLMTAFKTTQGVTN-TLPFFPPLGEAFTFQKWV 73 Query: 65 KAWATVDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQT 124 A+ + NS+ +TVPA L+ G+ Y L+ ++G L L G F+P+Q Sbjct: 74 DAFDMLGRGLVNSMVLTVPATLLCLLFGSTAAYGLTLINWRGQIFVLVLFLIGIFIPYQA 133 Query: 125 VLLPASFTLGKMGLA----------------STTTGLVFVHVVYGLAFTTLFFRNYYVSI 168 VL+P S + L + L+ YG+ TL FR YY+S+ Sbjct: 134 VLVPLSRFWSMVPLEEWLSPLYVLSFVQPEHAQLVELIITDAAYGIPICTLLFRGYYLSL 193 Query: 169 PDALIKAARLDGAGFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGV-VFSSGDS-- 225 P LI+AA+LDGA +I+R+I+LP+STP+I V I+QFTQIWN+FLF + + S DS Sbjct: 194 PGDLIEAAKLDGASVTSIYRRIVLPLSTPMIGVVFIYQFTQIWNEFLFTLTIVGSADSPA 253 Query: 226 QPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAG 277 P+T+ L+ L ++ +G ++ + MA A IA LPTL++YV+ + F GL G Sbjct: 254 APVTLILSGLGSSLSGV-DFGMRMAGAFIAALPTLVIYVLFAEQFAEGLETG 304 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: 229 Number of extensions: 13 Number of successful extensions: 4 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: 305 Length adjustment: 26 Effective length of query: 255 Effective length of database: 279 Effective search space: 71145 Effective search space used: 71145 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: 48 (23.1 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