Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 17340 b3270 putative transport system permease protein (VIMSS)
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Keio:17340 Length = 367 Score = 256 bits (655), Expect = 5e-73 Identities = 148/381 (38%), Positives = 221/381 (58%), Gaps = 44/381 (11%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVG--RFP 61 + W+RKNLFS+W NSLLT+ C L L+ ++ WA +A W VG R Sbjct: 21 MVWVRKNLFSSWSNSLLTIGCIWLMWELIPPLLNWAFLQANW-----------VGSTRAD 69 Query: 62 QTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLILFTLDLSSRLWL 121 T+ W+ I G G++ + Q+ WR + L L++ + ++ W Sbjct: 70 CTKAGACWVF--IHERFGQFMYGLYPHDQR--WR--------INLALLIGLVSIAPMFWK 117 Query: 122 LLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILW--LIGGGFGLRPVSSNLWNGLL 179 +L R + A W + +P+I+W + GG F L V + W GL Sbjct: 118 ILP-----------HRGRYIAA------WAVIYPLIVWWLMYGGFFALERVETRQWGGLT 160 Query: 180 LTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPL 239 LTL++A++ I + P G+LLALGR S++P+VR S+++IE RGVPLI +LF++ VMLPL Sbjct: 161 LTLIIASVGIAGALPWGILLALGRRSHMPIVRILSVIFIEFWRGVPLITVLFMSSVMLPL 220 Query: 240 FFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIV 299 F A +D+++RA+ G++LF +AY+AE VRGGLQA+ +GQ EAA++L L + L++ Sbjct: 221 FMAEGTSIDKLIRALVGVILFQSAYVAEVVRGGLQALPKGQYEAAESLALGYWKTQGLVI 280 Query: 300 LPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLFIGL 359 LPQAL+ VIP LV I LFKDTSL+ ++GL +L + P ++G E Y+F L Sbjct: 281 LPQALKLVIPGLVNTIIALFKDTSLVIIIGLFDLFSSVQQATVDPAWLGMSTEGYVFAAL 340 Query: 360 IYWLFCYSMSLASRRLERQLN 380 IYW+FC+SMS S+ LE++ N Sbjct: 341 IYWIFCFSMSRYSQYLEKRFN 361 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: 524 Number of extensions: 25 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: 381 Length of database: 367 Length adjustment: 30 Effective length of query: 351 Effective length of database: 337 Effective search space: 118287 Effective search space used: 118287 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 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