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_011384430.1 AMB_RS10235 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000009985.1:WP_011384430.1 Length = 245 Score = 172 bits (436), Expect = 6e-48 Identities = 100/251 (39%), Positives = 146/251 (58%), Gaps = 14/251 (5%) Query: 10 PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69 P+L+ L KSF G++AV + EV +G I LIGPNGAGKTT FNL++ + P G+V+ Sbjct: 6 PMLSVENLGKSFRGLRAVNQVAFEVPRGDIVALIGPNGAGKTTTFNLIAGALPPSDGKVV 65 Query: 70 FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129 DG I L I + G+ RTFQ+ + + LSV EN+++ A + + Sbjct: 66 LDGHDITGLGQAAICRAGVGRTFQIVKPFAGLSVEENVMVGALRHDNGD----------- 114 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 V + + + LLE L KA + A L+ RK LE+ +AL T PKL+LLDE AG Sbjct: 115 VDKARAASRATLDLLE---LGDKARDPAQTLTLPDRKRLEVAKALATRPKLLLLDEVMAG 171 Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249 + P D + + N++ G+T L+IEH M +M+L D V VL G+ +A+GTPAE+ + Sbjct: 172 LRPVECDRMVAILTGLNKETGLTILLIEHVMRAVMALSDHVVVLHHGEKIAEGTPAEVTS 231 Query: 250 NSQVLEAYLGK 260 + +VLE YLG+ Sbjct: 232 HPKVLECYLGE 242 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: 159 Number of extensions: 5 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: 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 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