Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AO353_12325 AO353_12325 ABC transporter permease
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12325 Length = 319 Score = 132 bits (331), Expect = 2e-35 Identities = 85/207 (41%), Positives = 120/207 (57%), Gaps = 10/207 (4%) Query: 174 LWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLA 233 LW GL TL ++ +S VL IG+ L R SN P +R S +YIE+VRG PL L Sbjct: 118 LW-GLWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLRDLSTVYIELVRGTPL-----LV 171 Query: 234 QVMLPLFFAADV-RLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTF 292 Q+ + FF V L R IA L LF+ AY+AE +R G+Q+++RGQ EAA++LGL+ Sbjct: 172 QIFIFYFFIGTVLNLSREFAGIAALSLFTGAYVAEIIRSGVQSIARGQNEAARSLGLSAG 231 Query: 293 FVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAE 352 + +VLPQA + V+P L GQFI L KDTSL+S++ + EL R ++ E Sbjct: 232 QSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTS---FSPFE 288 Query: 353 VYLFIGLIYWLFCYSMSLASRRLERQL 379 + + +Y L +S + RLER+L Sbjct: 289 ILFCVAGLYLLINLPLSKIASRLERRL 315 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: 331 Number of extensions: 19 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: 319 Length adjustment: 29 Effective length of query: 352 Effective length of database: 290 Effective search space: 102080 Effective search space used: 102080 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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