Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_043531489.1 JH15_RS14395 ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000759345.1:WP_043531489.1 Length = 256 Score = 210 bits (534), Expect = 3e-59 Identities = 108/251 (43%), Positives = 162/251 (64%), Gaps = 1/251 (0%) Query: 16 SSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEV 75 S+++ Q K+FGGL +D I V+ GSITG+IGPNGAGK+TLFN+++ + D G V Sbjct: 2 SAIIEVQHARKAFGGLTVIDDCSIQVERGSITGMIGPNGAGKSTLFNIIAGTLPLDSGRV 61 Query: 76 LFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRR 135 L +G+ I L + +G +RTFQ+A S +T LEN+++ Q GE Sbjct: 62 LLDGEDITSLPADVLFHKGLLRTFQIAHEFSHMTALENLMMVPPRQEGESLFSAWFKPGE 121 Query: 136 VQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAA 195 V+++E R +A+ +++ +GL + AG LSGGQ+KLLE+ R +M+ +++LLDE AA Sbjct: 122 VRRQEDEVRRRALEVIDFIGLAHVRNELAGNLSGGQKKLLELGRTMMTEARVVLLDEIAA 181 Query: 196 GVNPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQ 254 GVN TL+G + +I NR+ G TFLVIEH+MD+I LC V VLA+G + +G+ + +Q Sbjct: 182 GVNRTLLGDLMTNIERLNRELGYTFLVIEHDMDMIARLCDPVIVLAQGSVMMEGSIKDVQ 241 Query: 255 SDPRVLEAYLG 265 ++P V+EAY G Sbjct: 242 NNPEVIEAYFG 252 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: 176 Number of extensions: 7 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: 256 Length adjustment: 25 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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 24 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