Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Pf1N1B4_3215 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3215 Length = 255 Score = 199 bits (506), Expect = 5e-56 Identities = 107/257 (41%), Positives = 158/257 (61%), Gaps = 13/257 (5%) Query: 18 LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77 +L LS FGGL AV+ + VKE + +IGPNGAGKTT+FN L+ F +P G ++ Sbjct: 5 ILKVTDLSMRFGGLLAVNSVALTVKEKQVVSMIGPNGAGKTTVFNCLTGFYQPTAGSIVL 64 Query: 78 NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137 +G+ I L H+IAL+G VRTFQ ++ +T +EN+L+A FL L + Sbjct: 65 DGEQIQGLPGHKIALKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFLAGLFKTPAFR 124 Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197 + ER E A LE V L A AG L+ GQ++ LE+AR +M+ P++++LDEPAAG+ Sbjct: 125 RSEREAMEYAEYWLEKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 Query: 198 NP-------TLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTP 250 NP LIG + E +T L+IEH+M ++M++ H++V+ +G LADGTP Sbjct: 185 NPRETEDLKALIGILRE------EHDVTVLLIEHDMKLVMSISDHIFVINQGTPLADGTP 238 Query: 251 EQIQSDPRVLEAYLGDS 267 EQI+ +P V++AYLG++ Sbjct: 239 EQIRDNPEVIKAYLGEA 255 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: 175 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: 255 Length adjustment: 25 Effective length of query: 242 Effective length of database: 230 Effective search space: 55660 Effective search space used: 55660 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