Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF3453 PS417_17675 ABC transporter
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__WCS417:GFF3453 Length = 249 Score = 156 bits (394), Expect = 5e-43 Identities = 92/252 (36%), Positives = 150/252 (59%), Gaps = 5/252 (1%) Query: 16 SSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEV 75 S LL + L ++G AV+ ++ V+ G+I +IGPNGAGKT+LF+ L+ + G + Sbjct: 2 SILLETKDLELAYGAFHAVNGVNLKVEAGTIHTIIGPNGAGKTSLFHCLTGERQATAGAI 61 Query: 76 LFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRR 135 F+G ++ + H G R+FQ+ + L+V EN+ LA Q + G R +NF R Sbjct: 62 HFDGKNLMRKPAHGRVGLGMARSFQLTSLFQNLSVRENLRLAAQGRDG----ARALNFWR 117 Query: 136 VQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAA 195 +R + E A +LE + L A+A AG LS GQ+++LE+ ++ S PKL++LDEP + Sbjct: 118 RVDSKREHLEMADQVLERLQLTARADTLAGELSHGQQRVLEVGMSICSKPKLLMLDEPTS 177 Query: 196 GVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255 G+ I + + I + R T L+IEHNM ++M++ + V++ G+ L +GTPE +++ Sbjct: 178 GMGIDDIPIMTQLISDLGRDH-TVLLIEHNMSIVMSISQRITVMSHGQILVEGTPEFVRA 236 Query: 256 DPRVLEAYLGDS 267 D RV AYLG++ Sbjct: 237 DERVRTAYLGEA 248 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: 166 Number of extensions: 8 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: 249 Length adjustment: 24 Effective length of query: 243 Effective length of database: 225 Effective search space: 54675 Effective search space used: 54675 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