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_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000020045.1:WP_012402388.1 Length = 594 Score = 178 bits (452), Expect = 2e-49 Identities = 98/250 (39%), Positives = 151/250 (60%), Gaps = 3/250 (1%) Query: 10 PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69 PLL K FGG+ AV + EV G I GLIGPNGAGK+T FNL++ ++ G + Sbjct: 345 PLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGAIT 404 Query: 70 FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129 F GE I L +I ++G+ RTFQ + L ++VLEN+ + + W + ++ Sbjct: 405 FRGERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGGHLRGRAGVW--RSVARLN 462 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 EE +L +A + VGL + Y+ AG L+ G++++LE+ RAL +P L+LLDEPAAG Sbjct: 463 GAEEGRLMAEAARQIRRVGLEEHMYDEAGSLALGKQRILEIARALCCDPTLLLLDEPAAG 522 Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249 + + + +L R++GM+ L++EH+MD +M+L DR+ V+ G +A+G P ++Q Sbjct: 523 LRYQEKQQLA-TLLRKLREEGMSLLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQDVQN 581 Query: 250 NSQVLEAYLG 259 + VLEAYLG Sbjct: 582 DPAVLEAYLG 591 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: 325 Number of extensions: 12 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: 594 Length adjustment: 31 Effective length of query: 229 Effective length of database: 563 Effective search space: 128927 Effective search space used: 128927 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: 50 (23.9 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