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 WP_086510658.1 BZY95_RS14690 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_002151265.1:WP_086510658.1 Length = 251 Score = 184 bits (468), Expect = 1e-51 Identities = 104/245 (42%), Positives = 151/245 (61%), Gaps = 11/245 (4%) Query: 17 LCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQ 76 L KSF G KAV + I V G+I LIG NGAGKTT FNLL+ F+ P G + F G I Sbjct: 11 LTKSFRGFKAVNDISIRVEPGTIHALIGANGAGKTTCFNLLTKFLEPSAGSIFFKGRDIT 70 Query: 77 QLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGE--NFWQVQLQPQVVVKEEK 134 +L+P Q+A+ GMVR+FQ++ S+L+VLEN+ LA Q++ GE +FW Q + Sbjct: 71 RLKPDQVARLGMVRSFQISAVFSQLTVLENVKLALQRRRGESYDFWATQ-------RRLD 123 Query: 135 QLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRL 194 + +E+AM LLE VGL++ A A L G+++ LE+ L +P+L+LLDEP AG+ Sbjct: 124 EYRERAMDLLEEVGLSEWADTPAAELPYGRKRALELATTLALDPELMLLDEPLAGMGTED 183 Query: 195 IDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNSQVL 254 + + I Q T L++EHN+ V+ LCDR+ VLA G+ L +G A + + +V+ Sbjct: 184 VGRTAELIRRVAAQ--RTVLMVEHNLGVVAELCDRITVLARGEVLVEGDYATVSRDERVI 241 Query: 255 EAYLG 259 E+Y+G Sbjct: 242 ESYIG 246 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: 149 Number of extensions: 6 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: 251 Length adjustment: 24 Effective length of query: 236 Effective length of database: 227 Effective search space: 53572 Effective search space used: 53572 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 24 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