Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate N515DRAFT_1560 N515DRAFT_1560 sulfate transport system permease protein
Query= reanno::Koxy:BWI76_RS01820 (296 letters) >FitnessBrowser__Dyella79:N515DRAFT_1560 Length = 274 Score = 65.5 bits (158), Expect = 1e-15 Identities = 69/218 (31%), Positives = 102/218 (46%), Gaps = 17/218 (7%) Query: 81 VLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKAT---LLKGMLIFQMFPAVLSL 137 VLL L S A + A+ + L A+ R RFP + L+ A ++L Sbjct: 52 VLLALQLSFGGALVAAVLDLLLGLLLAWVLVRYRFPLRRVCDALIDLPFALPTAVAGIAL 111 Query: 138 VALYALFDRLGQYVPFVGLN---THGGVIFAYMG-GIALHVWTIKGYFETIDGSLEEAAA 193 ALYA +GQ + +G+ T GV+ A + G+ V T++ E+++ +EEAA Sbjct: 112 TALYAPNGWVGQLLQPLGVQVAYTRLGVLLAMVFVGLPFVVRTLQPVIESLEREVEEAAL 171 Query: 194 LDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYL 253 GA+PWQ+FR VLLPL P L F L+ A+ E + ++ T V + L Sbjct: 172 TLGASPWQSFRRVLLPLLAPTLLTGFALALARAVGEYGSVIYISGNLPLRTEIVPL---L 228 Query: 254 NPQNYLWG-DFAAAAVLSAIPITVVFLL------AQRW 284 Q G D A AA+L A+ + V L+ QRW Sbjct: 229 IVQKIDAGDDTAPAALLGAVMLAVSLLVLLTVNGLQRW 266 Lambda K H 0.328 0.141 0.438 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: 239 Number of extensions: 17 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: 296 Length of database: 274 Length adjustment: 26 Effective length of query: 270 Effective length of database: 248 Effective search space: 66960 Effective search space used: 66960 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 17 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