Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate PP_5023 PP_5023 Amino acid ABC transporter, permease protein
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Putida:PP_5023 Length = 320 Score = 133 bits (334), Expect = 8e-36 Identities = 81/212 (38%), Positives = 123/212 (58%), Gaps = 13/212 (6%) Query: 169 PVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIG 228 P++ LW L ++++ A+ +V IG+ L R SN P +R S +Y+E+VRG PL Sbjct: 117 PLAWGLWTTLWISVVSGALGLV----IGLFAGLCRLSNNPTLRDLSTVYVELVRGTPL-- 170 Query: 229 ILFLAQVMLPLFFAADV-RLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKAL 287 L Q+ + FF V L R +A L LF+ AY+AE VR G+Q++++GQ EAA++L Sbjct: 171 ---LVQIFIFYFFIGTVLNLSREFAGVAALALFTGAYVAEIVRAGVQSIAKGQNEAARSL 227 Query: 288 GLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFI 347 GLN + ++LPQA + V+P L GQFI L KDTSL+S++ + ELT R + Sbjct: 228 GLNAGQSMRHVILPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELTKSGREAITTS--- 284 Query: 348 GRYAEVYLFIGLIYWLFCYSMSLASRRLERQL 379 E++ + +Y L +S + RLER+L Sbjct: 285 FSTFEIWFCVAGLYLLINLPLSHIASRLERRL 316 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: 314 Number of extensions: 18 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: 320 Length adjustment: 29 Effective length of query: 352 Effective length of database: 291 Effective search space: 102432 Effective search space used: 102432 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