Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 17515 b3454 ATP-binding component of leucine transport (VIMSS)
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Keio:17515 Length = 237 Score = 116 bits (291), Expect = 4e-31 Identities = 79/260 (30%), Positives = 126/260 (48%), Gaps = 34/260 (13%) Query: 15 ESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGE 74 E +L +S +G ++A+ + + +G I LIG NGAGKTTL L R G Sbjct: 2 EKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGR 61 Query: 75 VLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLA------DQHQTGEKFLP 128 ++F+ I +I + +V SR+TV EN+ + DQ Q K++ Sbjct: 62 IVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVY 121 Query: 129 RL---INFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNP 185 L ++ RR+Q+ AG +SGG++++L + RALMSNP Sbjct: 122 ELFPRLHERRIQR-------------------------AGTMSGGEQQMLAIGRALMSNP 156 Query: 186 KLILLDEPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNL 245 +L+LLDEP+ G+ P +I QI + I QG+T ++E N + + L +VL G + Sbjct: 157 RLLLLDEPSLGLAPIIIQQIFDTIEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVV 216 Query: 246 ADGTPEQIQSDPRVLEAYLG 265 T + + ++ V AYLG Sbjct: 217 LSDTGDALLANEAVRSAYLG 236 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: 161 Number of extensions: 8 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: 237 Length adjustment: 24 Effective length of query: 243 Effective length of database: 213 Effective search space: 51759 Effective search space used: 51759 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: 46 (22.3 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