Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_041677064.1 R2APBS1_RS14330 ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000230695.2:WP_041677064.1 Length = 307 Score = 107 bits (266), Expect = 4e-28 Identities = 75/235 (31%), Positives = 116/235 (49%), Gaps = 22/235 (9%) Query: 21 AQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGD 80 A+GL++ FG L AVDH D+ V + G +GPNG+GK+T +L + P +GE+ + Sbjct: 3 ARGLTRRFGKLVAVDHVDLEVPARRVYGFLGPNGSGKSTTIRMLCGLLTPSEGEI----E 58 Query: 81 SIGQLAPHQI-ALRGSVRTF-QVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQK 138 +G P Q ALR + Q + L V EN+ +FL + + + Sbjct: 59 VLGLRVPAQADALRPHIGYMTQNFSLFEDLGVRENL----------EFLAAIQGVPKAKT 108 Query: 139 EERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVN 198 R + ++ G + + AG LSGGQ++ L +A A++ P+L+LLDEP + V+ Sbjct: 109 RRRIDE-----LIGQYHFGDRQKQLAGTLSGGQKQRLALAGAVIHEPELLLLDEPTSAVD 163 Query: 199 PTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQI 253 P E + G T LV H MD CH + +L G +ADGTP ++ Sbjct: 164 PESRRDFWEKLFELADIGTTLLVSTHLMDE-AERCHRLAILDRGVLVADGTPHEL 217 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: 210 Number of extensions: 12 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: 307 Length adjustment: 26 Effective length of query: 241 Effective length of database: 281 Effective search space: 67721 Effective search space used: 67721 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