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_009543427.1 CCE_RS21280 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000017845.1:WP_009543427.1 Length = 245 Score = 125 bits (313), Expect = 1e-33 Identities = 75/236 (31%), Positives = 132/236 (55%), Gaps = 18/236 (7%) Query: 24 IKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQPHQI 83 + +Q ++ G + +IGPNGAGK+TL + ++ ++G++ F G+ I L+ QI Sbjct: 18 LNILQGINFRISLGELVTVIGPNGAGKSTLVKTIFGLLKTNEGQITFKGQNITGLKSDQI 77 Query: 84 AQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQEQAMFL 143 + GM Q+ + LS+ EN+ + A G +K++K+ + MF Sbjct: 78 VKLGMCYVPQIQNVFATLSIEENLEMGAFITHGS------------LKQQKE-KIYTMF- 123 Query: 144 LESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICDRIL 203 LA++ + AG LSGG+R++L MGRALM +P ++LLDEP+A ++P L++ + ++I Sbjct: 124 ---PRLAERRRQKAGTLSGGERQMLAMGRALMLDPDVLLLDEPSAALSPILVNSVFEQIK 180 Query: 204 TWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNSQVLEAYLG 259 N Q G +++E N + + DR +VL G++ +GT E+ + +V + YLG Sbjct: 181 AIN-QTGKAIVLVEQNAKKALMMADRGYVLENGRDRFEGTGEELLNDPKVGQLYLG 235 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: 154 Number of extensions: 9 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: 245 Length adjustment: 24 Effective length of query: 236 Effective length of database: 221 Effective search space: 52156 Effective search space used: 52156 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 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