Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_1893 Synpcc7942_1893 ATPase
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__SynE:Synpcc7942_1893 Length = 258 Score = 323 bits (829), Expect = 2e-93 Identities = 164/251 (65%), Positives = 201/251 (80%) Query: 15 ESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGE 74 ES LL A+GLSK FGGL+AV + V EG+ITGLIGPNGAGK+TLF LLSNF++ D G+ Sbjct: 4 ESWLLEAEGLSKRFGGLQAVQDVRLQVAEGTITGLIGPNGAGKSTLFALLSNFLKADAGK 63 Query: 75 VLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFR 134 V F G +I +L P+Q+A G VRTFQVA+ LSRLTVLENMLL Q Q GEKF ++ + Sbjct: 64 VRFRGRAIEKLQPYQLAQLGLVRTFQVARSLSRLTVLENMLLGGQQQRGEKFWQVWLHPQ 123 Query: 135 RVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPA 194 ++++E+ R++A ++L VGL AKAQDYAG+LSGGQRKLLEMARALM+ P+L+LLDEPA Sbjct: 124 AIRRQEQELRDRAFSLLSDVGLAAKAQDYAGSLSGGQRKLLEMARALMAQPQLVLLDEPA 183 Query: 195 AGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQ 254 AGVNP LI +IC+HI WN+QGI+FL+IEHNMDVIM+LC VWVLAEG+NL DG P QIQ Sbjct: 184 AGVNPALIEKICDHIQTWNQQGISFLIIEHNMDVIMSLCDRVWVLAEGKNLVDGPPAQIQ 243 Query: 255 SDPRVLEAYLG 265 D +VL AYLG Sbjct: 244 QDEQVLAAYLG 254 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: 231 Number of extensions: 5 Number of successful extensions: 1 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: 258 Length adjustment: 25 Effective length of query: 242 Effective length of database: 233 Effective search space: 56386 Effective search space used: 56386 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