Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 194 bits (494), Expect = 2e-54 Identities = 103/225 (45%), Positives = 150/225 (66%), Gaps = 10/225 (4%) Query: 22 IDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKI----NDIEPQNRDI 77 + ++ GE L LVGPSGCGK+TLLR +AG ES SG+I + G+ + + P+ R + Sbjct: 27 VSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPETRSV 86 Query: 78 AMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELSGG 137 MVFQ YAL+PH+TV +N+ FGL+ + +AA + + L+ ++ L R P ELSGG Sbjct: 87 GMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVARQAL----ALVGLEGLERRYPHELSGG 142 Query: 138 QRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEA 197 Q+QRVAL RAL+ Q P+IL DEPLSNLD +R ++R E++ + +++T I VTHDQ EA Sbjct: 143 QQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQATAILVTHDQEEA 202 Query: 198 TTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL 242 ++ DR+AV++ G EQIG P E++ P + F+A F+ + NFL Sbjct: 203 LSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS--QANFL 245 Lambda K H 0.318 0.136 0.383 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: 267 Number of extensions: 13 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: 347 Length of database: 368 Length adjustment: 29 Effective length of query: 318 Effective length of database: 339 Effective search space: 107802 Effective search space used: 107802 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 (21.7 bits) S2: 49 (23.5 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