Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 7024901 Shewana3_2075 inner-membrane translocator (RefSeq)
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__ANA3:7024901 Length = 405 Score = 134 bits (336), Expect = 5e-36 Identities = 91/317 (28%), Positives = 165/317 (52%), Gaps = 9/317 (2%) Query: 31 PAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGID 90 P +L A+L + FF+ + + +L+ IL +A +L+I + VI T GID Sbjct: 65 PLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGID 124 Query: 91 LSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLG 150 LSVG +M + +L + L IAA + G L+G I+G +++ L + P +ATL Sbjct: 125 LSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLL 184 Query: 151 MMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASI 210 +M+ +G++ +I+ + I F GF+AI +G LP+P ++I L + + Sbjct: 185 LMVAGRGVAQLINQGQIITFQH-PGFAAIGVGQFLG-----LPMPVWIVIGMLTF--SQL 236 Query: 211 ILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQP- 269 +L KT G + A+G N +A R G+ K+ Y +G +AG+I + + + Sbjct: 237 LLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDAN 296 Query: 270 ALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTG 329 G ELDA+ AVVIGG +L+GG +++ +++GA I+ L + + + ++ ++ Sbjct: 297 NAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKA 356 Query: 330 VIIILAVYLDILRRRRR 346 ++I+ + L + RR+ Sbjct: 357 IVILTVLLLQSAKFRRQ 373 Lambda K H 0.326 0.139 0.398 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: 242 Number of extensions: 10 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: 347 Length of database: 405 Length adjustment: 30 Effective length of query: 317 Effective length of database: 375 Effective search space: 118875 Effective search space used: 118875 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 (21.7 bits) S2: 50 (23.9 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