Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AO356_18220 AO356_18220 amino acid ABC transporter permease
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18220 Length = 223 Score = 125 bits (315), Expect = 9e-34 Identities = 73/217 (33%), Positives = 121/217 (55%), Gaps = 7/217 (3%) Query: 166 GLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVP 225 G+ P LWNG+++TL + A+ +V +G +LAL R S+ ++ + Y+ R +P Sbjct: 7 GVIPAIPGLWNGMVMTLKLMAMGVVGGIILGTILALMRLSHNKLISNIAGAYVNYFRSIP 66 Query: 226 LIGILFLAQVMLPLFF----AADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQV 281 L+ ++ + +P D + + ++F AAY E VR G+Q++ +GQ+ Sbjct: 67 LLLVITWFYLAVPFVLRWITGEDTPIGAFGSCVVAFMMFEAAYFCEIVRAGVQSIPKGQM 126 Query: 282 EAAKALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSIL 341 AA+ALG+N + LI+LPQA R + P L+ Q I LF+DTSL+ VGLV+ +R Sbjct: 127 GAAQALGMNYGQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNASR--- 183 Query: 342 AQPQFIGRYAEVYLFIGLIYWLFCYSMSLASRRLERQ 378 A IGR E + GL+Y+ ++ SL +RL+++ Sbjct: 184 ANGDIIGRSNEFLIVAGLVYFTISFAASLLVKRLQKR 220 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: 240 Number of extensions: 10 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: 381 Length of database: 223 Length adjustment: 26 Effective length of query: 355 Effective length of database: 197 Effective search space: 69935 Effective search space used: 69935 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: 48 (23.1 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