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_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000017845.1:WP_009545830.1 Length = 238 Score = 123 bits (309), Expect = 3e-33 Identities = 84/252 (33%), Positives = 133/252 (52%), Gaps = 21/252 (8%) Query: 12 LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71 L + K++G V ++VA G I GL+GPNGAGKTT F + + I+P+KGRV + Sbjct: 3 LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62 Query: 72 GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131 + + +L ++ A+ G+ Q LSV EN+ +A + QT F Sbjct: 63 QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQVALE-QTNVPF------------ 109 Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRAL---MTNPKLILLDEPAA 188 +Q ++ LL+ L K A+ +SGG+R+ E+ R+L P +LLDEP A Sbjct: 110 --RQRPQRLHTLLKEFRLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFA 167 Query: 189 GVNPRLIDDICDRIL-TWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247 GV+P + +I I +RQ G+ LI +HN+ +++ +R +++ +GQ LA G+ EI Sbjct: 168 GVDPIAVSEIQTMIAQLCDRQMGI--LITDHNVQATLAITNRAYIMRDGQILAAGSAEEI 225 Query: 248 QTNSQVLEAYLG 259 N V + YLG Sbjct: 226 YNNPLVRQYYLG 237 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: 131 Number of extensions: 8 Number of successful extensions: 4 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: 238 Length adjustment: 24 Effective length of query: 236 Effective length of database: 214 Effective search space: 50504 Effective search space used: 50504 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 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