Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 249 bits (636), Expect = 1e-70 Identities = 159/366 (43%), Positives = 210/366 (57%), Gaps = 29/366 (7%) Query: 14 GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPA 73 G+V VL+ INL+I GE +V VGPSGCGKSTLLR++AGLE + G +++ V+ +P Sbjct: 45 GEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAK 104 Query: 74 QRGIAMVFQSYALYPHMTVRENMSFALK-------------IAKKS-----------QAE 109 R IAMVFQSYALYPH++V +N++F L+ +A +S +A Sbjct: 105 ARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEAR 164 Query: 110 IDAAVEAAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALR 169 I V A LQL LDR PK LSGGQ+QRVA+GR+I R+P+V+L DEPLSNLDA LR Sbjct: 165 IKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLR 224 Query: 170 VATRLEIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENE 229 TR +I L+ + +T+ YVTHDQ EAMT+ RI VL G + QV SPLE+Y++P N Sbjct: 225 AETRAQIVSLQRQLGVTTL-YVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANR 283 Query: 230 FVAQFIGSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDM- 288 FVAQFIGSP MNL+P + Q T E + P G V +G+RPE + Sbjct: 284 FVAQFIGSPPMNLIP-VTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLE 342 Query: 289 VEAAPGGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEP 348 V AA + + V EALG T + E +L G LT +P Sbjct: 343 VGAAASKNLLI--TVTGVEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKP 400 Query: 349 AKVHVF 354 ++H+F Sbjct: 401 DQIHLF 406 Lambda K H 0.316 0.135 0.379 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: 423 Number of extensions: 14 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: 373 Length of database: 417 Length adjustment: 31 Effective length of query: 342 Effective length of database: 386 Effective search space: 132012 Effective search space used: 132012 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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