Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate Ac3H11_1957 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1957 Length = 221 Score = 110 bits (275), Expect = 4e-29 Identities = 64/210 (30%), Positives = 118/210 (56%), Gaps = 5/210 (2%) Query: 170 VSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGI 229 +S+ + GL +L++ I+ + G LLAL R S + + +Y+ +R +PL+ + Sbjct: 13 ISNFVLKGLYFSLMLTVIATIGGVFFGTLLALMRLSGKKWLDVPATIYVNGMRSIPLVMV 72 Query: 230 LFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGL 289 + +++P + + + A+ + F AAY +E +R G+Q++ RGQV A +ALG+ Sbjct: 73 ILWFFLLVPAIIGRPIGAE--VSAVITFIAFEAAYFSEIMRAGIQSIPRGQVHAGQALGM 130 Query: 290 NTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGR 349 + L+VLPQA R ++P L+ Q I LF+DTSL+ +G ++ + + GR Sbjct: 131 TYGQNMKLVVLPQAFRNMLPVLLTQTIILFQDTSLVYAIGAYDM---LKGFEVAGKNFGR 187 Query: 350 YAEVYLFIGLIYWLFCYSMSLASRRLERQL 379 E YL ++Y++ CY++S A +RL +++ Sbjct: 188 PIEAYLAAAVLYFVMCYALSWAVKRLHQKI 217 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: 221 Number of extensions: 17 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: 221 Length adjustment: 26 Effective length of query: 355 Effective length of database: 195 Effective search space: 69225 Effective search space used: 69225 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 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