Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 181 bits (460), Expect = 2e-50 Identities = 97/228 (42%), Positives = 143/228 (62%), Gaps = 8/228 (3%) Query: 13 YPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVT-- 70 + G+ V + + E+ GE L LVGPSGCGK+T LRM+AG E++ G+I + + V Sbjct: 16 FSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATA 75 Query: 71 --HVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEF 128 + P R + MVFQ+YAL+PH+TV +N+ F L+ S +A A +GL Sbjct: 76 QRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVAR----QALALVGLEGL 131 Query: 129 LERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVT 188 R P LSGGQ+QRVA+ RA+ P + L+DEPLSNLD ++R++ R ++ + R+ T Sbjct: 132 ERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQAT 191 Query: 189 TVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFI 236 + VTHDQ EAL++ DR+AV++ G +Q+G P EL+ PA+ FVA F+ Sbjct: 192 AILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFL 239 Lambda K H 0.316 0.135 0.380 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: 303 Number of extensions: 12 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: 376 Length of database: 368 Length adjustment: 30 Effective length of query: 346 Effective length of database: 338 Effective search space: 116948 Effective search space used: 116948 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: 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