Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 132 bits (331), Expect = 9e-36 Identities = 82/248 (33%), Positives = 128/248 (51%), Gaps = 18/248 (7%) Query: 22 QGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDS 81 + + KS+G V+ + V +G + GL+GPNGAGKTT F + + RPD+G V + Sbjct: 14 ENVRKSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLDETE 73 Query: 82 IGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEER 141 + +L Q A G Q A + LTV+EN+LL Q QTG + R Sbjct: 74 LTRLPMTQRARLGIGYLAQEASIFRHLTVVENLLLVLQ-QTGIR--------------GR 118 Query: 142 ANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARAL---MSNPKLILLDEPAAGVN 198 R++ +L L A +SGG+R+ E+ARAL PK +LLDEP AG++ Sbjct: 119 EQRQRVEELLSEFRLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGID 178 Query: 199 PTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPR 258 P + ++ E I Q + L+ +HN+ + + ++L +G LA G+ E++ S+P Sbjct: 179 PIAVAEVQEIIARLRAQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPL 238 Query: 259 VLEAYLGD 266 V + YLG+ Sbjct: 239 VRQYYLGE 246 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: 133 Number of extensions: 4 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: 267 Length of database: 250 Length adjustment: 24 Effective length of query: 243 Effective length of database: 226 Effective search space: 54918 Effective search space used: 54918 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