Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 290 bits (743), Expect = 3e-83 Identities = 173/392 (44%), Positives = 231/392 (58%), Gaps = 54/392 (13%) Query: 1 MAGIKIDKINKFY---------GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAG 51 +AG+ ++I K + G L INL+I DGEF+V VGPSGCGKSTLLR LAG Sbjct: 23 VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82 Query: 52 LEGVSSGRIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNG------- 104 LE S G I++G R V + RD+AMVFQSYALYPH++V +N+ FG++ G Sbjct: 83 LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142 Query: 105 --------------FEPDLR---KERIAEAARVLQLEDYLDRKPGQLSGGQRQRVAIGRA 147 +EP+ K R+ E A +LQL+ LDR+P QLSGGQ+QRVA+GRA Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202 Query: 148 IVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAMTMADKIVVL 207 I +NP VFL DEPLSNLDAKLR + R ++ L +QLG T +YVTHDQ EAMTM D+I VL Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262 Query: 208 NRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFSSDV--GLQDIS------------- 252 NRG ++QV SP+++Y +P +RFVA+FIGSP MN+ V LQ + Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEP 322 Query: 253 ----LDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLKGGG-QIVARV 307 D +G RPEH+E+ ++ TV E LG ++ + LK G + AR+ Sbjct: 323 VLRLYDGQTVELGIRPEHLEVGAAASKNLLITVTGVEALGSDTFIAGELKESGIAVQARL 382 Query: 308 GGDDETKVGAAVSLRFSRHRLHQFD-EAGRAI 338 ++G + L F ++H FD E G+AI Sbjct: 383 APQQCWQMGDRLWLTFKPDQIHLFDLETGKAI 414 Lambda K H 0.320 0.139 0.396 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: 380 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 338 Length of database: 417 Length adjustment: 30 Effective length of query: 308 Effective length of database: 387 Effective search space: 119196 Effective search space used: 119196 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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