Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_011611622.1 TERY_RS09450 amino acid ABC transporter permease
Query= TCDB::Q8YPM7 (381 letters) >NCBI__GCF_000014265.1:WP_011611622.1 Length = 403 Score = 415 bits (1067), Expect = e-120 Identities = 209/381 (54%), Positives = 288/381 (75%), Gaps = 4/381 (1%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVGRFPQT 63 + WLR+N FSTWYN+LL++I +L LW V I WA T+A+W VI+VNL L +VGR+P+ Sbjct: 20 IKWLRENFFSTWYNTLLSLILFSLILWGVINFISWAKTEAEWQVIKVNLPLLMVGRYPRD 79 Query: 64 EYWRVWIVLAIASTLGAVTAGIFF-NQQKLTWRKVGLFAFIVGLLLILFTLDLSSRLWLL 122 +YWR+W+++ I S+L + G+ N +L V + + +++++ +++ +L LL Sbjct: 80 QYWRIWVIVGIISSLFGFSWGVIARNSAQLFTLPVLIGIAFLPVIILIIPVNVFFKLLLL 139 Query: 123 LTAVLLIPGFLLGSRLT---NLVAPWLSLIWLLSFPIILWLIGGGFGLRPVSSNLWNGLL 179 +L++ G +L+ + + +LS WL++F +I+WLIGGG GL+ VS+N W GL+ Sbjct: 140 GMVILVVATAWSGKKLSIKNSKLGKYLSFYWLIAFILIVWLIGGGLGLKSVSTNDWGGLM 199 Query: 180 LTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPL 239 LT+LMA +SI LSFP+GVLLALGR S LPV+R FSI YIEI+RG+PLI ILF+ Q+++PL Sbjct: 200 LTVLMAVVSIFLSFPLGVLLALGRQSTLPVIRIFSIGYIEIIRGLPLISILFMGQILIPL 259 Query: 240 FFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIV 299 F +R DR+ RAI GL LFSAAY+AENVRGGLQ+V RGQ EAAKALGLNT + LIV Sbjct: 260 FLPDGMRPDRIFRAILGLTLFSAAYLAENVRGGLQSVLRGQSEAAKALGLNTPLSLGLIV 319 Query: 300 LPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLFIGL 359 LPQAL+ IP++VGQFI LF+DT+LLS+VGLVEL GI+RSILAQP+F+G YAEVYLF G+ Sbjct: 320 LPQALKVAIPSIVGQFISLFQDTTLLSIVGLVELLGISRSILAQPEFLGDYAEVYLFDGI 379 Query: 360 IYWLFCYSMSLASRRLERQLN 380 I+W+ CY+MS+ SR+LE++LN Sbjct: 380 IFWIVCYAMSVGSRQLEKKLN 400 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: 629 Number of extensions: 32 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: 403 Length adjustment: 31 Effective length of query: 350 Effective length of database: 372 Effective search space: 130200 Effective search space used: 130200 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: 50 (23.9 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