Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= TCDB::Q8YPM7 (381 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 98.2 bits (243), Expect = 5e-25 Identities = 63/175 (36%), Positives = 105/175 (60%), Gaps = 6/175 (3%) Query: 174 LWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLA 233 L GL TL+++ +S VL +G++LA+ S +RW + +Y +I RG+P + ++ + Sbjct: 359 LKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVILVV 418 Query: 234 QVML-PLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTF 292 + + P+ L A+A L L +AAY+ E R G+Q+V GQ+EA++A+G + Sbjct: 419 GLGIGPVVKNLTGNNPYWLGAVA-LALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSYR 477 Query: 293 FVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLV----ELTGIARSILAQ 343 + L+V+PQ +R V+PAL+ QFI L KD+SL+ +GL+ EL + R + AQ Sbjct: 478 QSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRDLNAQ 532 Lambda K H 0.332 0.145 0.452 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: 451 Number of extensions: 13 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: 381 Length of database: 589 Length adjustment: 33 Effective length of query: 348 Effective length of database: 556 Effective search space: 193488 Effective search space used: 193488 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 51 (24.3 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