Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate WP_007664885.1 BN137_RS16680 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >NCBI__GCF_000319285.1:WP_007664885.1 Length = 283 Score = 119 bits (299), Expect = 6e-32 Identities = 83/273 (30%), Positives = 139/273 (50%), Gaps = 17/273 (6%) Query: 18 YATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGN-LLSWPTVIDGIGWIKAWDVVGG---- 72 + +L + + + PL+ + S + GN LLS + + + + D+ G Sbjct: 19 WLVILTVSVIIIYPLIWTIGAS------LNAGNSLLSSSIIPENLSFQHYADLFNGQVNY 72 Query: 73 --YFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPAS 130 ++WNS+KI+ ++++ + Y S +RF+G Q L L +P + L+ A Sbjct: 73 VTWYWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQMIPQFSALI-AI 131 Query: 131 FTLGKF-GLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLK 189 F L + GL N+ LVL++V + T + Y +IP L ++AR+DGA F IF++ Sbjct: 132 FVLSQLLGLINSHLALVLIYVAGMIPMNTYLMKGYLDAIPKDLDESARMDGASNFRIFIE 191 Query: 190 ILLPMSIPIVMVCLIWQFTQIWNDF-LFGVVFASGDAQPITVALNNLVNTSTGAKEYNVD 248 I++P+S PIV V ++ FT DF L + + D + + L NLV GA Y Sbjct: 192 IIMPLSKPIVAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGA-SYTTY 250 Query: 249 MAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 A A++ +P ++Y+ KYF+ GLTSG+ KG Sbjct: 251 AAGAVLIAVPVAILYLALQKYFVSGLTSGSTKG 283 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: 203 Number of extensions: 9 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: 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