Align NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate YP_004143816.1 Mesci_4657 cationic amino acid ABC transporter periplasmic binding protein
Query= TCDB::Q8YPM9 (369 letters) >NCBI__GCF_000185905.1:YP_004143816.1 Length = 342 Score = 318 bits (815), Expect = 1e-91 Identities = 158/316 (50%), Positives = 211/316 (66%), Gaps = 4/316 (1%) Query: 58 NTIKNRGQLICGVSGEVPGFSFVGTDGEYSGIDVDVCRAIAAALFDNPDAVEFRNLSAKE 117 +T+K +G + CGVS + GFS G++ GID D CRA+AAA+F + V+F LSAKE Sbjct: 27 DTVKAKGFIQCGVSTGLAGFSAPDDKGDWQGIDADFCRAVAAAVFGDGSRVKFTPLSAKE 86 Query: 118 RFTALQTGEVDILSRNTTWTLSRATSVGLEFAPVVFYDGQAIMV--RKNSAIKSLADLKD 175 RFTALQ+GE+DILSRNTTWT++R T++GL F V +YDGQ M+ +K + S L Sbjct: 87 RFTALQSGEIDILSRNTTWTINRDTALGLNFIGVTYYDGQGFMINAKKLPGVNSALQLSG 146 Query: 176 KAICVQTGTTTEQNLADQMRKRNITYKPVVFEDVNVTFATYAEGRCDAITADRSALVSRR 235 A+CVQ+GTTTE NLAD + + Y PVVFE + A Y GRCD T D+S L R Sbjct: 147 AAVCVQSGTTTELNLADYFKANKMEYNPVVFEKLEEVNAAYDAGRCDVYTTDQSGLYGIR 206 Query: 236 TTLPTPEDNVVLDEVISSEPLAPAVARGDAKWSNTVNWVVYALIKGEELGINAQNLGQFT 295 TL +P D+VVL E+IS EPL PAV +GD +W + V W +AL++ EELGI N+ + Sbjct: 207 LTLGSPADHVVLPEIISKEPLGPAVRQGDDQWYHIVKWTYFALLQAEELGITKANVDEMK 266 Query: 296 TSNDPDVKRFLGTEGD--LGQGLGLTNDFAARIIKHVGNYAEVYDRNLGPKTKLNLARGQ 353 S P++KR LG E D +G LG++ND+ I+K VGNY E+++RN+G + L +ARG Sbjct: 267 NSASPEIKRVLGQEADTKIGTDLGVSNDWVVNIVKAVGNYGEMFERNVGSGSPLKIARGI 326 Query: 354 NQLWSKGGLLYSPPFR 369 N LW+KGGL Y+PP R Sbjct: 327 NALWTKGGLQYAPPIR 342 Lambda K H 0.317 0.133 0.387 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: 379 Number of extensions: 16 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: 369 Length of database: 342 Length adjustment: 29 Effective length of query: 340 Effective length of database: 313 Effective search space: 106420 Effective search space used: 106420 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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