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 GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__psRCH2:GFF3784 Length = 266 Score = 166 bits (419), Expect = 6e-46 Identities = 93/251 (37%), Positives = 146/251 (58%), Gaps = 11/251 (4%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 +L+A GL K FGG AV ++V + LIGPNGAGKTT+FNLL+ F++P G + Sbjct: 21 MLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLTKFLQPSAGSIRL 80 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTG--ENFWQVQLQPQV 128 I + P ++A+ G+VR+FQ++ L+VL+N+ +A Q+ G FW + Sbjct: 81 LDHDITRTDPAKVARMGLVRSFQISAVFPHLTVLDNVRVALQRPGGLATQFW-------L 133 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 ++ +L E+A+ L+ESVGLA K +E A LS G++++LE+ L PK++LLDEP A Sbjct: 134 PMRSLNRLNERALQLIESVGLADKRHELAADLSYGRKRVLEIATTLALEPKVLLLDEPMA 193 Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 G+ + + + I Q + L++EHN+ V+ LC +V VL G+ L G + Sbjct: 194 GMGHEDVHVVAEIIREVATQRAV--LMVEHNLKVVADLCHQVTVLQRGEILTSGDYRTVS 251 Query: 249 TNSQVLEAYLG 259 + +V AY+G Sbjct: 252 QDERVRVAYMG 262 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: 136 Number of extensions: 3 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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