Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_026129775.1 BN415_RS00760 cell division ATP-binding protein FtsE
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000341525.1:WP_026129775.1 Length = 230 Score = 103 bits (257), Expect = 3e-27 Identities = 66/227 (29%), Positives = 115/227 (50%), Gaps = 19/227 (8%) Query: 24 LSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDSIG 83 + K G A+ + + G ++GP+GAGK+T LL I+ D+G + G ++ Sbjct: 10 VKKYDNGTTALRGVTVTIHPGEFAYIVGPSGAGKSTFIRLLYREIKLDKGSLQVAGFNLA 69 Query: 84 QLAPHQIAL--RGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEER 141 ++ I + R FQ K+L + TV EN+ A + V E R Sbjct: 70 KIKKRDIPMLRRNVGVVFQDYKLLPKKTVYENIAYAME----------------VIGERR 113 Query: 142 AN-REKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPT 200 ++ +++ M +L+ VGL K + + LSGG+++ + +ARA+++NPK+++ DEP ++P Sbjct: 114 SHIKKRVMEVLDLVGLKHKVRSFPNELSGGEQQRIAIARAIVNNPKVLIADEPTGNLDPD 173 Query: 201 LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLAD 247 +I + N QG T L+ HN ++ TL H V + GR + D Sbjct: 174 NSWEIMNLLERINLQGTTVLMATHNSQIVNTLRHRVIAIENGRVVRD 220 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: 145 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: 230 Length adjustment: 24 Effective length of query: 243 Effective length of database: 206 Effective search space: 50058 Effective search space used: 50058 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 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