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 CA265_RS15245 CA265_RS15245 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Pedo557:CA265_RS15245 Length = 254 Score = 102 bits (255), Expect = 6e-27 Identities = 76/234 (32%), Positives = 110/234 (47%), Gaps = 23/234 (9%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 +++ L K + AVQ EV + I GL+GPNGAGKTT ++ G +I Sbjct: 7 IISVKDLVKKYDDFVAVQGLSFEVYEHEIFGLLGPNGAGKTTTLEIIETLRAKTSGEIIV 66 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130 DG + + QP I Q V+ Q A L+++E + L A + ++P Sbjct: 67 DGFSVDK-QPQDIKQIIGVQ-LQAAGYYPNLNLIELIELFA------GLYGANIKP---- 114 Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 M +LE V L KA LSGGQ++ + L+ PK+I LDEP G+ Sbjct: 115 ----------MEMLEKVNLQDKAKAKYKALSGGQKQRFSIATTLINQPKIIFLDEPTTGL 164 Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTP 244 +P+ ++ D I+ R G T +I H MD LCDRV + GQ +A TP Sbjct: 165 DPQARRNLWDLIIE-IRNAGTTVVITTHYMDEAEQLCDRVAFVERGQIIALDTP 217 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: 147 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: 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 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