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_012589117.1 MSIL_RS00330 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000021745.1:WP_012589117.1 Length = 265 Score = 183 bits (464), Expect = 4e-51 Identities = 101/251 (40%), Positives = 151/251 (60%), Gaps = 3/251 (1%) Query: 10 PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69 PLL GL +GG+ AV++ + VA+G++ LIGPNGAGKT+LFNL+S R D G + Sbjct: 5 PLLNIKGLTLRYGGLAAVEDLDLIVAEGALDALIGPNGAGKTSLFNLISGLTRQDDGEIW 64 Query: 70 FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129 G I +L P Q A++G+ RTFQ R + + +EN+L+ G + ++ + Sbjct: 65 LGGARIDRLSPSQRARRGLARTFQNLRLFTETTAIENVLVGMHLHVGGSLLEILTRFGRF 124 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 + E+ + A LL VGL+ Y AG LS G ++ LE+ RAL PKL+LLDEPAAG Sbjct: 125 RQAERAAVDAARELLAFVGLSSVEYAPAGSLSYGDQRRLEIARALAAKPKLLLLDEPAAG 184 Query: 190 VNPRLIDDICDRILTWN-RQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 +NP + R+L R ++ L++EH+M ++M LCD++ VL G+ +A+G P ++ Sbjct: 185 MNP--AETAALRLLLEKLRAQKISMLLVEHDMSLVMRLCDKITVLNFGRKIAEGPPDAVR 242 Query: 249 TNSQVLEAYLG 259 N V+EAYLG Sbjct: 243 ANPAVIEAYLG 253 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: 167 Number of extensions: 8 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: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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 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