Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AZOBR_RS26565 AZOBR_RS26565 branched-chain amino acid ABC transporter permease
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__azobra:AZOBR_RS26565 Length = 567 Score = 185 bits (470), Expect = 2e-51 Identities = 101/254 (39%), Positives = 150/254 (59%) Query: 12 GSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPD 71 G+P ++ A LSK FGG++AV I +K G I GLIGPNGAGKTT FNLLS F+RP Sbjct: 314 GTPGEVVVSATSLSKHFGGIQAVKDLTIDLKRGEIVGLIGPNGAGKTTAFNLLSGFLRPT 373 Query: 72 QGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLI 131 G +L+ G + L PH++ G R+FQ K+ ++LTV+EN+L++ Q G++ L Sbjct: 374 GGTILYRGRDMTTLKPHEVVAAGLARSFQDLKLFTKLTVVENILVSLPAQPGDRPLDVYF 433 Query: 132 NFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLD 191 V++ +R N +A+ + VGL AKA + A LS + KLL +AR L + ++LLD Sbjct: 434 RPGLVRRADRENVARALEIASFVGLLAKADETAANLSYAEEKLLVIARLLATGADVLLLD 493 Query: 192 EPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPE 251 EP +G++ + +IC I + R +IEHN++VI +C + + EGR L G P+ Sbjct: 494 EPLSGLDTVTVERICGVIRDLARANKAVCIIEHNLEVIRGVCDEIVFIDEGRVLTKGPPD 553 Query: 252 QIQSDPRVLEAYLG 265 + D + E Y G Sbjct: 554 TLMRDRELAERYFG 567 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: 328 Number of extensions: 13 Number of successful extensions: 1 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: 567 Length adjustment: 30 Effective length of query: 237 Effective length of database: 537 Effective search space: 127269 Effective search space used: 127269 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