Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_0427 Synpcc7942_0427 ATPase
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__SynE:Synpcc7942_0427 Length = 282 Score = 120 bits (300), Expect = 4e-32 Identities = 75/238 (31%), Positives = 125/238 (52%), Gaps = 17/238 (7%) Query: 17 SLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVL 76 S ++ + +SK FG + V+ + G GL+GPNGAGK+T +++ RP QG++ Sbjct: 2 SAVVLESVSKQFGDRKVVNQLSFALAPGESFGLLGPNGAGKSTTIRMITTLTRPSQGQIT 61 Query: 77 FNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRV 136 G + + + G V Q V + TV EN+ ++ RL + Sbjct: 62 IAGYDVQRDRDRVRSQLGVV--LQQVSVKNDFTVWENL----------EYHGRLHHIPDR 109 Query: 137 QKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAG 196 +++ER NR L+ V L + D LSGG ++ L++ARAL+ P ++LLDEP G Sbjct: 110 ERQERINR-----WLDYVELSDRRNDRVQTLSGGMKRRLQIARALLHEPSILLLDEPTVG 164 Query: 197 VNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQ 254 ++P +I E I + NRQG+T L+ H M+ + +LC + +L G+ +A GT +++ Sbjct: 165 LDPQTRRRIWEIIRDLNRQGMTVLLTTHYMEEVESLCDRIGILDGGQLIALGTLAELR 222 Lambda K H 0.319 0.136 0.389 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: 174 Number of extensions: 3 Number of successful extensions: 2 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: 267 Length of database: 282 Length adjustment: 25 Effective length of query: 242 Effective length of database: 257 Effective search space: 62194 Effective search space used: 62194 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 (21.7 bits) S2: 47 (22.7 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