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 AZOBR_RS16830 AZOBR_RS16830 ABC transporter
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__azobra:AZOBR_RS16830 Length = 241 Score = 185 bits (469), Expect = 9e-52 Identities = 104/249 (41%), Positives = 147/249 (59%), Gaps = 15/249 (6%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 LL GL K F G+KAV V +G I LIGPNGAGKTT FNL++ PD+GRV Sbjct: 4 LLEVEGLSKRFRGLKAVSNVSFSVPEGRIVALIGPNGAGKTTTFNLIAGVFPPDEGRVHL 63 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130 G PI L+P+ I G+ RTFQ+ + +LSV EN+++ A + Sbjct: 64 KGAPITGLKPNHICTAGIGRTFQIVKPFGQLSVEENVIVGALARE--------------- 108 Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 + ++QA +L+ +GLA +A A L+ RK LE+ RAL T P L+LLDE AG+ Sbjct: 109 RSVAAARDQARRVLDRLGLADQANRPARSLTLPDRKRLEVARALATRPILLLLDEVLAGL 168 Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250 P +D + + + NR++GMT L+IEH M +M+L D+V VL G+ +ADG P+E+ N Sbjct: 169 RPTEVDRMVEVLRDLNRREGMTILMIEHVMRAVMALSDQVVVLDHGEKIADGLPSEVVAN 228 Query: 251 SQVLEAYLG 259 +V+E+YLG Sbjct: 229 PKVIESYLG 237 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: 152 Number of extensions: 4 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: 260 Length of database: 241 Length adjustment: 24 Effective length of query: 236 Effective length of database: 217 Effective search space: 51212 Effective search space used: 51212 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: 46 (22.3 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