Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__PS:Dsui_0627 Length = 267 Score = 194 bits (493), Expect = 2e-54 Identities = 101/249 (40%), Positives = 156/249 (62%), Gaps = 1/249 (0%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 LL AS + K FGG+KA++ + + +G I GLIGPNGAGKTT FN L+ P+ GR++F Sbjct: 7 LLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVF 66 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130 G + PH++A +G+ RTFQ R + ++ LEN+++ ++T + + Sbjct: 67 AGAELDTSAPHKVAARGIARTFQNIRLFAHMTALENVMVGRHQRTRAGVFGAIFRTPGTR 126 Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 EE +Q +A LL VG+A +A++ A LS G ++ LE+ RAL T PKL+ LDEPAAG+ Sbjct: 127 AEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKLLALDEPAAGM 186 Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250 N ++ ++ R+DG+T L+IEH++ ++M LCDRV VL G+ + + PA +Q + Sbjct: 187 NASETGEL-RTLIEGIRKDGITVLLIEHDVKLVMGLCDRVAVLDYGEKICEDVPAVVQKD 245 Query: 251 SQVLEAYLG 259 +V+ AYLG Sbjct: 246 PRVITAYLG 254 Lambda K H 0.319 0.136 0.391 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: 160 Number of extensions: 7 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: 260 Length of database: 267 Length adjustment: 25 Effective length of query: 235 Effective length of database: 242 Effective search space: 56870 Effective search space used: 56870 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