Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 152 bits (384), Expect = 2e-41 Identities = 88/204 (43%), Positives = 132/204 (64%), Gaps = 4/204 (1%) Query: 177 GLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVM 236 GL +LLMA I+I +SF IG+ + +GR+S+ V R +LYIE++RG PLI ++F Sbjct: 389 GLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIRGNPLIIVIFWVYFF 448 Query: 237 LPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVL 296 +P+ F + + A L F+ AY+AE VR G+Q + GQVEAA + GL + Sbjct: 449 IPVMFGTTLNV--FWSATWALTAFTGAYIAEIVRTGIQNIPAGQVEAAYSTGLTYLQAMR 506 Query: 297 LIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLF 356 IVLPQAL+ +IPA+VGQFI +FKDTSL ++G++ELT +A+ I + + E+Y Sbjct: 507 RIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQGI--NNRLMIHPMEIYGT 564 Query: 357 IGLIYWLFCYSMSLASRRLERQLN 380 + +Y++ CYSMS+ + RLER+L+ Sbjct: 565 VAFLYFICCYSMSVFAARLERRLS 588 Score = 92.0 bits (227), Expect = 4e-23 Identities = 59/177 (33%), Positives = 95/177 (53%), Gaps = 6/177 (3%) Query: 170 VSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGI 229 + + + GL T+ ++ IS L+ +G +L L R S +R + IE R PL+ Sbjct: 53 MGAEILKGLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQ 112 Query: 230 LFLAQVMLPLFFAADVRLD------RVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEA 283 LF P + R A GL +++A++MAE +R GLQ++ +G +EA Sbjct: 113 LFFWYFAFPAILPDNAREALFSIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEA 172 Query: 284 AKALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSI 340 A + GL+ F V+ I+LP A RA+IP L +F+ K++SL +VG+ ELT A+ + Sbjct: 173 AYSSGLSYFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWHAQQV 229 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: 647 Number of extensions: 33 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