Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 185 bits (470), Expect = 1e-51 Identities = 102/227 (44%), Positives = 142/227 (62%), Gaps = 11/227 (4%) Query: 22 VSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIV----NQLTPSRRGI 77 VS E++ GE + VGPSGCGK+TLLR+IAG E + SG++ G+ V L P R + Sbjct: 27 VSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPETRSV 86 Query: 78 AMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQLTPYLERLPRQLSGG 137 MVFQ YAL+PH+TV +N+ FG+ +D++ A ++ L R P +LSGG Sbjct: 87 GMVFQDYALFPHLTVLDNVCFGL----RDRKGSAAVARQALALVGLEGLERRYPHELSGG 142 Query: 138 QRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHKTTMIYVTHDQVE 197 Q+QRVA+ RA+ P + L DEPLSNLD +R+ R E+ + R + T I VTHDQ E Sbjct: 143 QQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQA-QATAILVTHDQEE 201 Query: 198 AMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNFLS 244 A+++ DR+ V+R G EQIG P EL++ P S FVA F+ + NFL+ Sbjct: 202 ALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS--QANFLA 246 Lambda K H 0.321 0.138 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: 303 Number of extensions: 14 Number of successful extensions: 4 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: 342 Length of database: 368 Length adjustment: 29 Effective length of query: 313 Effective length of database: 339 Effective search space: 106107 Effective search space used: 106107 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 (21.9 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