Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PP_2748 PP_2748 putative Branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Putida:PP_2748 Length = 266 Score = 165 bits (418), Expect = 8e-46 Identities = 99/266 (37%), Positives = 153/266 (57%), Gaps = 5/266 (1%) Query: 1 MSDRITPAENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTL 60 M+ RI+ A + S+LL + +S SF G++A+ V+ G I LIGPNGAGK++L Sbjct: 1 MAARISGARGM----SALLEVRNVSLSFKGVKAISDLSFSVRRGEICALIGPNGAGKSSL 56 Query: 61 FNLLSNFIRPDQGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQH 120 N+L+ R D G++ F + + + P Q A G RTFQ + +++VL+N+L Sbjct: 57 LNILNGVYRADAGQLFFATEPLRRPHPLQAARLGIGRTFQNNALFKKMSVLDNLLTGLSR 116 Query: 121 QTGEKFLPRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARA 180 FL + + R ++E RA E+A +L + L G+L+ G +K +E+ RA Sbjct: 117 FQRSYFLEQALGLPRARREARAFAERAEQVLAFLELQPWRDVAVGSLAYGLQKRVELGRA 176 Query: 181 LMSNPKLILLDEPAAGVNPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVL 239 L++ P L+LLDEP AG+N + I + NR G T ++IEH++ V+M L HV VL Sbjct: 177 LIAQPTLLLLDEPMAGMNAEEKQDMSRFIADINRDLGTTVILIEHDIQVVMGLSSHVVVL 236 Query: 240 AEGRNLADGTPEQIQSDPRVLEAYLG 265 GR + DGTP ++Q++P V+ AYLG Sbjct: 237 DYGRKVGDGTPAEVQANPDVIAAYLG 262 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: 170 Number of extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 242 Effective length of database: 241 Effective search space: 58322 Effective search space used: 58322 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