Align NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_245299991.1 B1812_RS19680 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q8YPM9 (369 letters) >NCBI__GCF_002117405.1:WP_245299991.1 Length = 350 Score = 255 bits (652), Expect = 1e-72 Identities = 134/356 (37%), Positives = 196/356 (55%), Gaps = 11/356 (3%) Query: 18 KLAVILGASLIFTTTACGGDSAPTTDTSTNSGSTLVANRWNTIKNRGQLICGVSGEVPGF 77 K A++L + F A G + + STL I+ RG ++CG + PGF Sbjct: 2 KFAILLFLLMAFGLVA--GAPRLAAQPESKASSTL-----QEIRRRGVVVCGATAPAPGF 54 Query: 78 SFVGTDGEYSGIDVDVCRAIAAALFDNPDAVEFRNLSAKERFTALQTGEVDILSRNTTWT 137 + + G +SG D+D CRA+A A D+P + L K+R AL +G+VD+L WT Sbjct: 55 AVMDEAGSWSGFDIDFCRALAVAALDDPQKIRIETLQQKQRLPALHSGDVDVLLSGAPWT 114 Query: 138 LSRATSVGLEFAPVVFYDGQAIMVRKNSAIKSL----ADLKDKAICVQTGTTTEQNLADQ 193 +R L + + FY GQ + R+ A +CVQ G ++E NLA Sbjct: 115 EAREAGHQLLYGAISFYGGQGFLGRRAWGPTGEPWRGAGGTPPRVCVQQGGSSELNLAQF 174 Query: 194 MRKRNITYKPVVFEDVNVTFATYAEGRCDAITADRSALVSRRTTLPTPEDNVVLDEVISS 253 R+ + Y+PV F + Y G CD +AD L R+ L P+D+VV +IS Sbjct: 175 YREHGVAYRPVAFGSLEEAARAYDAGDCDLFSADLVELHQWRSRLQKPDDHVVAPALISK 234 Query: 254 EPLAPAVARGDAKWSNTVNWVVYALIKGEELGINAQNLGQFTTSNDPDVKRFLGTEGDLG 313 PL P V +GD +W N V W ++A++ EELG++A+ + +S+ PD++R +G++GD G Sbjct: 235 SPLGPIVRQGDDQWFNVVRWTLFAMVDAEELGVDAKTVDAALSSDIPDLRRLVGSDGDFG 294 Query: 314 QGLGLTNDFAARIIKHVGNYAEVYDRNLGPKTKLNLARGQNQLWSKGGLLYSPPFR 369 +GLGL D+A R+I VGNYAEV+DRNLG + + R QN LWSKGGL+Y+PP R Sbjct: 295 EGLGLRPDWAYRVIHEVGNYAEVFDRNLGKSSPFAMERRQNALWSKGGLMYAPPVR 350 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: 340 Number of extensions: 16 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: 369 Length of database: 350 Length adjustment: 29 Effective length of query: 340 Effective length of database: 321 Effective search space: 109140 Effective search space used: 109140 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 Apr 09 2024. 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