Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate YP_004141765.1 Mesci_2579 binding-protein-dependent transport system inner membrane protein
Query= TCDB::Q8YPM7 (381 letters) >NCBI__GCF_000185905.1:YP_004141765.1 Length = 359 Score = 175 bits (444), Expect = 2e-48 Identities = 121/395 (30%), Positives = 186/395 (47%), Gaps = 69/395 (17%) Query: 3 KLTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWA-----------------TTKAQW 45 +L LR+ F+T +++++ C + ++LV ++ WA T A W Sbjct: 13 RLEDLRRRFFATPLQAVVSLACLTIMVFLVWKLLNWAVFSAVFTTSGGPEACQATAGACW 72 Query: 46 AVIQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVG 105 +VI R+ G +P E WR S L V Sbjct: 73 SVIAARWRIIFFGLYPYEEQWR--------SALACVAV---------------------- 102 Query: 106 LLLILFTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLIGGGF 165 +++T + IP F G R+ + L ++L + GG Sbjct: 103 ---------------VVMTVLSCIPAFWTGRRIALVWGAGTGLFYVL-------MKGGVL 140 Query: 166 GLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVP 225 GL V W GL LTL + + ++ FP+ + LAL R S LP + + L I+ VR +P Sbjct: 141 GLAHVGEEAWGGLALTLFIFVTTCLIGFPLAICLALLRRSELPWISRTTGLIIDGVRSLP 200 Query: 226 LIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAK 285 LI ILF V+LP ++ D++ R I G LF +AY AE VRGG+Q V+ GQ EAA Sbjct: 201 LISILFTFAVVLPFALPQWLQGDKLYRVILGSALFFSAYQAEIVRGGMQGVATGQEEAAM 260 Query: 286 ALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQ 345 ALG+ + + I+LPQA+R +PA + QF+ FK+TSL+ +VG E+ + + Sbjct: 261 ALGMRYWQRISRILLPQAMRNAMPATINQFVISFKETSLVVIVGFFEILASGNAAYGTGE 320 Query: 346 FIGRYAEVYLFIGLIYWLFCYSMSLASRRLERQLN 380 + Y EVY FI IY++F +S+S LER+++ Sbjct: 321 WRFAYVEVYAFIAFIYFIFVFSLSRYGAFLERRMS 355 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: 430 Number of extensions: 29 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: 359 Length adjustment: 30 Effective length of query: 351 Effective length of database: 329 Effective search space: 115479 Effective search space used: 115479 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: 49 (23.5 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