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_013525179.1 MESCI_RS31065 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000185905.1:WP_013525179.1 Length = 254 Score = 185 bits (470), Expect = 7e-52 Identities = 101/251 (40%), Positives = 147/251 (58%) Query: 9 LPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRV 68 + LL L SFGG+K + + V +G+I LIGPNGAGKT+LFN L+ F +P G + Sbjct: 1 MALLEVRDLRLSFGGLKVLHDISFSVEKGAINSLIGPNGAGKTSLFNCLTGFYKPKGGSI 60 Query: 69 IFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128 G PI L PH+I G+ RTFQ R +SVLEN + ++ L Sbjct: 61 SLSGRPITGLPPHRITALGLARTFQNIRLFKEMSVLENAMSGQHCRSRHGIVSAILHLPA 120 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 +EE+ ++ M L VG+ + A+ AGGLS G ++ LE+ RAL + P+LILLDEPAA Sbjct: 121 QRREEEAIRAIGMRWLGFVGIEQHAHRRAGGLSYGDQRRLELARALASAPELILLDEPAA 180 Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 G+N R D+ I + G+T L+IEH+M ++M + +++ V GQ +ADG P ++ Sbjct: 181 GLNEREKLDLIHLIRRIRDETGVTVLLIEHDMGLVMQVSEKIVVFDYGQKIADGAPEAVR 240 Query: 249 TNSQVLEAYLG 259 + +V+EAYLG Sbjct: 241 ADPRVIEAYLG 251 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: 148 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 236 Effective length of database: 230 Effective search space: 54280 Effective search space used: 54280 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 Apr 09 2024. 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