Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 193 bits (490), Expect = 7e-54 Identities = 111/298 (37%), Positives = 165/298 (55%), Gaps = 14/298 (4%) Query: 4 LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63 L LD V K ++ G + AV+++S +++ GE L LVGPSGCGK+T LRM+AG E++ G Sbjct: 7 LCLDRVCKQFS---GSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSG 63 Query: 64 ELRLEDRVL----NGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQR 119 ++L + + + R + MVFQ YAL+PH +V N+ FGL + G Sbjct: 64 SIQLAGETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSA-----AV 118 Query: 120 VEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMR 179 + ++G+ L R P +LSGGQQQRVAL RA+ P + L+DEPLSNLD ++R +R Sbjct: 119 ARQALALVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLR 178 Query: 180 TELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGF 239 EL+ + + T + VTHDQ EA+++ DRVAV+ G +Q+G P + + P + FVA F Sbjct: 179 QELRDILRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEF 238 Query: 240 IGEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSG 297 + + N GD +R D+ G G + +R EDV + G Sbjct: 239 LSQ--ANFLATEYQGDAWRTVLGDFEAPGGLEGSRTGGEPPVVMVRQEDVLLHPHPEG 294 Lambda K H 0.316 0.136 0.384 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: 378 Number of extensions: 23 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: 383 Length of database: 368 Length adjustment: 30 Effective length of query: 353 Effective length of database: 338 Effective search space: 119314 Effective search space used: 119314 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: 42 (22.0 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