Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AZOBR_RS08665 AZOBR_RS08665 amino acid ABC transporter permease
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__azobra:AZOBR_RS08665 Length = 367 Score = 272 bits (696), Expect = 1e-77 Identities = 156/395 (39%), Positives = 215/395 (54%), Gaps = 75/395 (18%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQ----------------WAV 47 + WLR NLF+TWYN+LLT++ + L + ++ W A W Sbjct: 23 VAWLRNNLFNTWYNALLTILIAWLLFKAIPPLLDWLIFSANSFGTPPQVCRQEGGACWTF 82 Query: 48 IQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLL 107 + LR + G FP E WR L ++ + Sbjct: 83 VSEKLRFVMFGTFPYDEQ----------------------------WRP--LITIVIIIA 112 Query: 108 LILFTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIW---LLSFPIILWLIGGG 164 L+L + D R W PWL+L+W L + +++W GG Sbjct: 113 LVLASCD--RRFW----------------------KPWLALVWIAGLTAVGVLMW--GGV 146 Query: 165 FGLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGV 224 GL V + LW GL LTL+++ + + ++FP VLLALGR S LP +R S+ YIE++RGV Sbjct: 147 LGLTYVENTLWGGLPLTLMLSVVGLSVAFPASVLLALGRRSQLPAIRVISVTYIELIRGV 206 Query: 225 PLIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAA 284 PLI +LF+A VM PLF V D++LRA ++F+AAYMAE +RGGLQA+ +GQ EAA Sbjct: 207 PLISLLFMASVMFPLFLPTGVNFDKLLRAQIAFIMFAAAYMAEAIRGGLQAIPKGQYEAA 266 Query: 285 KALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQP 344 ALGLN + + I+LPQAL IP LV FI FKDTSL+ ++GL +L G A++ L+ P Sbjct: 267 DALGLNYWQAMGKIILPQALAISIPPLVNTFISFFKDTSLVIIIGLYDLLGTAKAALSDP 326 Query: 345 QFIGRYAEVYLFIGLIYWLFCYSMSLASRRLERQL 379 + G Y E YLFIG+IYW+FCYSMS S++LER L Sbjct: 327 AWRGFYREAYLFIGVIYWVFCYSMSKYSQKLERDL 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: 513 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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