Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Dyella79:N515DRAFT_3950 Length = 239 Score = 132 bits (333), Expect = 5e-36 Identities = 81/248 (32%), Positives = 131/248 (52%), Gaps = 14/248 (5%) Query: 18 LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77 +L A+GL K F + V ++EG + GL+GPNGAGKTT F ++ I D G + Sbjct: 1 MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60 Query: 78 NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137 + I L H A G Q V RLTV +N++ + + + Sbjct: 61 DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIMAVLELR------------ENLS 108 Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197 ++RA +++ L+ + + A +LSGG+R+ +E+ARAL + P+ +LLDEP AGV Sbjct: 109 AKQRAGELESL--LDELKIAHIADQRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGV 166 Query: 198 NPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDP 257 +P +G+I + + +GI L+ +HN+ + +C ++L +G L+ GTP I +D Sbjct: 167 DPISVGEIQRIVRHLKERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHILADE 226 Query: 258 RVLEAYLG 265 +V E YLG Sbjct: 227 KVREVYLG 234 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: 165 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: 239 Length adjustment: 24 Effective length of query: 243 Effective length of database: 215 Effective search space: 52245 Effective search space used: 52245 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