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_067078017.1 MCUHO_RS10540 ATP-binding cassette domain-containing protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_001602375.1:WP_067078017.1 Length = 316 Score = 89.7 bits (221), Expect = 7e-23 Identities = 67/229 (29%), Positives = 110/229 (48%), Gaps = 18/229 (7%) Query: 20 SFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQ 79 +FG AV+ V +G I +GPNGAGK+T N+L+ + KG V G + + + Sbjct: 15 AFGDFTAVRGISFTVKKGEIFSFLGPNGAGKSTTINILTTLLPVQKGAVRVAGYDVAR-E 73 Query: 80 PHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQEQ 139 P ++ ++ + FQ L+V E M + ++ ++ + + Sbjct: 74 PRKV-RKAIGIVFQDDVLDRDLTVRETM---------------EFHGRLYGIPREERRRR 117 Query: 140 AMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDIC 199 LL V L K E LSGG ++ L++ R LMT P ++ LDEP G++P+ I Sbjct: 118 IDDLLRIVELEFKRDERTKNLSGGMKRRLQIARGLMTQPGVLFLDEPTQGLDPQTRMRIW 177 Query: 200 DRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 D I N + G T + H M+ L DR+ ++ G+ + GTPAE++ Sbjct: 178 DYIRQVN-EAGTTIFLTTHYMEEADMLSDRISIIDHGRIVVSGTPAELK 225 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: 161 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 316 Length adjustment: 26 Effective length of query: 234 Effective length of database: 290 Effective search space: 67860 Effective search space used: 67860 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 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