Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate WP_007664885.1 BN137_RS16680 sugar ABC transporter permease
Query= reanno::WCS417:GFF4322 (281 letters) >NCBI__GCF_000319285.1:WP_007664885.1 Length = 283 Score = 115 bits (287), Expect = 1e-30 Identities = 71/211 (33%), Positives = 114/211 (54%), Gaps = 4/211 (1%) Query: 73 YFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQTVLLPASFT 132 ++WNS+KI+ ++++ + Y S +RFKG Q L L +P + L+ A F Sbjct: 75 WYWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQMIPQFSALI-AIFV 133 Query: 133 LGKM-GLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFFTIFRQII 191 L ++ GL ++ LV ++V + T + Y +IP L ++AR+DGA F IF +II Sbjct: 134 LSQLLGLINSHLALVLIYVAGMIPMNTYLMKGYLDAIPKDLDESARMDGASNFRIFIEII 193 Query: 192 LPMSTPIIMVCLIWQFTQIWNDF-LFGVVFSSGDSQPITVALNNLVNTSTGAKEYNVDMA 250 +P+S PI+ V ++ FT DF L + + D + + L NLV GA Y A Sbjct: 194 MPLSKPIVAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGA-SYTTYAA 252 Query: 251 AAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281 A++ +P ++Y+ KYFV GLT+G+ KG Sbjct: 253 GAVLIAVPVAILYLALQKYFVSGLTSGSTKG 283 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: 188 Number of extensions: 8 Number of successful extensions: 3 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: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 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 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