Align NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate SMc00676 SMc00676 amino acid-binding periplasmic signal peptide protein
Query= TCDB::Q8YPM9 (369 letters) >FitnessBrowser__Smeli:SMc00676 Length = 331 Score = 317 bits (812), Expect = 3e-91 Identities = 157/326 (48%), Positives = 213/326 (65%) Query: 44 TSTNSGSTLVANRWNTIKNRGQLICGVSGEVPGFSFVGTDGEYSGIDVDVCRAIAAALFD 103 T+ +G+T A + +K RG+L CGVS V GFS GE+SG D+D CRA+AAA Sbjct: 6 TAFLAGTTAQAATLDVVKQRGELRCGVSQGVLGFSAPDDKGEWSGFDIDFCRAVAAATLG 65 Query: 104 NPDAVEFRNLSAKERFTALQTGEVDILSRNTTWTLSRATSVGLEFAPVVFYDGQAIMVRK 163 +PD V++ LS KERFTALQ+GEVD+LSR TTWTLSR T +G+ F V +YDGQA MVR Sbjct: 66 SPDKVKYVPLSTKERFTALQSGEVDLLSRQTTWTLSRDTDLGMSFVGVNYYDGQAFMVRG 125 Query: 164 NSAIKSLADLKDKAICVQTGTTTEQNLADQMRKRNITYKPVVFEDVNVTFATYAEGRCDA 223 + +KS+ +L ++C +TGTTTEQN+AD I Y+ + FE + T + GRCD Sbjct: 126 DIGVKSVKELSGASVCTETGTTTEQNMADYFSANKIEYQVIAFEKADQTIQAFNSGRCDV 185 Query: 224 ITADRSALVSRRTTLPTPEDNVVLDEVISSEPLAPAVARGDAKWSNTVNWVVYALIKGEE 283 + D SAL S+R TL P+ VVL EVIS EPL PAV +GD +W V W ++A+I+ EE Sbjct: 186 YSTDASALYSQRLTLNDPDRFVVLPEVISKEPLGPAVRQGDDQWFKVVRWTLFAMIEAEE 245 Query: 284 LGINAQNLGQFTTSNDPDVKRFLGTEGDLGQGLGLTNDFAARIIKHVGNYAEVYDRNLGP 343 LGI +N S KRFLG + + G+ LGL +A + + VGNY E+++R+LG Sbjct: 246 LGITRENAASLLESGTAAQKRFLGIDNEAGKALGLDPKWAYQTVAAVGNYGEIFERHLGK 305 Query: 344 KTKLNLARGQNQLWSKGGLLYSPPFR 369 ++ L + RG N+LW+ GGL+Y+PP R Sbjct: 306 ESALRIDRGLNKLWNNGGLIYAPPVR 331 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: 366 Number of extensions: 13 Number of successful extensions: 1 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: 331 Length adjustment: 29 Effective length of query: 340 Effective length of database: 302 Effective search space: 102680 Effective search space used: 102680 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 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