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_RS13290 AZOBR_RS13290 ABC transporter
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__azobra:AZOBR_RS13290 Length = 259 Score = 182 bits (461), Expect = 8e-51 Identities = 94/249 (37%), Positives = 153/249 (61%) Query: 12 LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71 L+ L SFGG+ A+ + I V G I G+IGPNGAGKTTL N++S +RP G + D Sbjct: 4 LSIERLSLSFGGLAALSDVDIAVPAGEIRGIIGPNGAGKTTLLNVVSGLVRPTGGEIRLD 63 Query: 72 GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131 G+P+ +L+ ++A +G+ RTFQ + ++VLEN++ + + + V++ Sbjct: 64 GQPLTRLKASEVAARGVGRTFQTSLLFKGMTVLENVMAGMHQGLRTSVLGAAIGLPGVLR 123 Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVN 191 EE+Q +E+A L VG+ A LS GQ++L+E+ R+L+ PK++LLDEPA G++ Sbjct: 124 EERQARERAREALAFVGMLSFAERDGASLSFGQQRLVEIARSLVAEPKVLLLDEPAVGLS 183 Query: 192 PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNS 251 P + ++ + + + G+T +++EH + ++M +CDR+ VL G+ +ADGTP I + Sbjct: 184 PPRVAELDELLRRIRDKRGITIIMVEHVIRLVMGVCDRITVLNSGRKIADGTPDVILADP 243 Query: 252 QVLEAYLGK 260 V EAYLGK Sbjct: 244 FVKEAYLGK 252 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: 156 Number of extensions: 5 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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