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_012647880.1 GEOB_RS13900 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000022265.1:WP_012647880.1 Length = 247 Score = 141 bits (355), Expect = 1e-38 Identities = 83/240 (34%), Positives = 132/240 (55%), Gaps = 11/240 (4%) Query: 21 FGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQP 80 +G + A++ I + QG I LIG NGAGKTT+ N +S G ++F+ EP+Q L P Sbjct: 11 YGKVHALKNVSIHLGQGEIVTLIGANGAGKTTILNTISGVTPAAGGEILFEKEPVQALSP 70 Query: 81 HQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQEQA 140 +I + G+ + + + LSV +N+ L A + Q K + +Q Sbjct: 71 DRIVRLGIAQVPEGRQVFKPLSVEDNLDLGAYLR----------HRQREAKSRIRQDKQE 120 Query: 141 MFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICD 200 +F L L ++ + AG LSGG++++L +GRA+MT PKL+LLDEP+ G+ P ++ +I Sbjct: 121 IFTLFP-RLEERRKQPAGTLSGGEQQMLAIGRAMMTRPKLMLLDEPSMGLAPLVVQEIFR 179 Query: 201 RILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNSQVLEAYLGK 260 I RQ G T L++E N ++L DR +VL G+ + +G + + N V AYLG+ Sbjct: 180 VIDNLRRQHGTTILLVEQNAKAALNLADRGYVLETGKVILEGLSSNLLENKDVQRAYLGR 239 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: 163 Number of extensions: 9 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: 247 Length adjustment: 24 Effective length of query: 236 Effective length of database: 223 Effective search space: 52628 Effective search space used: 52628 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