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_037572161.1 BS73_RS13615 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000744815.1:WP_037572161.1 Length = 266 Score = 152 bits (383), Expect = 9e-42 Identities = 87/251 (34%), Positives = 142/251 (56%), Gaps = 8/251 (3%) Query: 10 PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69 P+L SG+ S GG +++ +V +G IGPNGAGKT+LFN++S ++ GR+ Sbjct: 22 PVLWLSGVGWSVGGAVILEDVGFDVREGEFLAFIGPNGAGKTSLFNVVSGLVQATAGRIE 81 Query: 70 FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129 DG + H A+ G+ RTFQ + +SV +++ LAAQ G ++ + Sbjct: 82 LDGADLTGRPAHDRARLGLGRTFQTSSLWPGMSVADHVRLAAQAAQGGSYR--------I 133 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 + +E+ L GLA +A AG LS G+++ LE+ L+ +P+++LLDEP AG Sbjct: 134 WRRAAGYREEVRDALARTGLAGRADALAGALSHGEKRKLELAVLLVGDPRVMLLDEPMAG 193 Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249 V+ + + + I +R++G T L++EH+MDV++ L DRV V+ G LA P + Sbjct: 194 VSAEEVPALTELIGALHREEGRTVLMVEHHMDVLLGLADRVAVMHHGTLLALDDPRAVTA 253 Query: 250 NSQVLEAYLGK 260 ++ V +AYLG+ Sbjct: 254 DATVQQAYLGE 264 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: 168 Number of extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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