Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q8YPM7 (381 letters) >MicrobesOnline__882:206177 Length = 596 Score = 153 bits (386), Expect = 1e-41 Identities = 87/204 (42%), Positives = 134/204 (65%), Gaps = 4/204 (1%) Query: 177 GLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVM 236 GL +LLMA I+I +SF IG+++ +GRTS+ + R +LYIE++RG PLI ++F Sbjct: 389 GLAYSLLMAVIAISVSFFIGLVVGIGRTSDNRICRIPCLLYIELIRGNPLIIVIFWIYFF 448 Query: 237 LPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVL 296 +P+ F + + A L LF+ AY+AE VR G+Q + GQVEAA + GL + Sbjct: 449 IPVLF--NTFFNVFWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMR 506 Query: 297 LIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLF 356 I+LPQAL+ +IPA+VGQFI +FKDTSL ++G++ELT +A+ I + + E+Y Sbjct: 507 RIILPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQGI--NNRLMVYPMEIYGT 564 Query: 357 IGLIYWLFCYSMSLASRRLERQLN 380 + +Y++ C+SMS+ + RLER+L+ Sbjct: 565 VAFLYFICCWSMSVYAARLERRLS 588 Score = 91.3 bits (225), Expect = 7e-23 Identities = 56/164 (34%), Positives = 90/164 (54%), Gaps = 6/164 (3%) Query: 177 GLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVM 236 GL +T+ ++ IS L+ +G +L + R S +R + +E R PL+ LF Sbjct: 60 GLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWYFA 119 Query: 237 LPLFFAADVRL------DRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLN 290 P ++R A GL ++++A+MAE +R GLQ++ +G +EAA + GLN Sbjct: 120 FPAILPENIRELLFTGNFEFWCATIGLSVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGLN 179 Query: 291 TFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELT 334 V+ I+LP A RA+IP L +F+ K++SL +VG+ ELT Sbjct: 180 YVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELT 223 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: 671 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 381 Length of database: 596 Length adjustment: 33 Effective length of query: 348 Effective length of database: 563 Effective search space: 195924 Effective search space used: 195924 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: 51 (24.3 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