Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 189 bits (480), Expect = 1e-52 Identities = 108/258 (41%), Positives = 157/258 (60%), Gaps = 1/258 (0%) Query: 8 AENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNF 67 A + G E L L +G+ F GL+A++ D+ V+ G+I GLIGPNG+GK+T+ N+L+ Sbjct: 382 AVHAGGTEDILQL-RGILMQFSGLKALNDVDLTVQRGTIHGLIGPNGSGKSTMMNVLTGI 440 Query: 68 IRPDQGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFL 127 P G + + G S+ QIAL G RTFQ ++ +T LEN+L+ H Sbjct: 441 YVPTAGTLEYRGASLAGKTSAQIALSGIARTFQNVQLFGEMTALENVLVGLHHTFNANLA 500 Query: 128 PRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKL 187 + R ++EERA RE+A ML VGL A + A L G+++LLE+ARAL +P+L Sbjct: 501 DVGLMSSRYRREERAARERAFGMLRFVGLDNVAAEEARNLPYGKQRLLEIARALALDPQL 560 Query: 188 ILLDEPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLAD 247 +LLDEPAAG+ I ++ I GIT ++IEH+MDV+M++C V VL G+ +A+ Sbjct: 561 LLLDEPAAGLTAPDIKELVAIIRKVRDHGITVVLIEHHMDVVMSVCDRVSVLDFGQKIAE 620 Query: 248 GTPEQIQSDPRVLEAYLG 265 G P IQS+ +V+EAYLG Sbjct: 621 GKPADIQSNEKVIEAYLG 638 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: 366 Number of extensions: 16 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: 646 Length adjustment: 31 Effective length of query: 236 Effective length of database: 615 Effective search space: 145140 Effective search space used: 145140 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: 50 (23.9 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