Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_068174335.1 HTA01S_RS18550 amino acid ABC transporter permease
Query= TCDB::Q8YPM7 (381 letters) >NCBI__GCF_001592305.1:WP_068174335.1 Length = 355 Score = 232 bits (592), Expect = 1e-65 Identities = 145/394 (36%), Positives = 209/394 (53%), Gaps = 73/394 (18%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGI----IVWATTKAQ-------------WA 46 L WL+ NLFS+ NS+ T+I +AL+LW + G I A A W Sbjct: 9 LAWLKTNLFSSTSNSIKTLIVAALALWAIYGAAGIGIAHAVFSADLEACNSMRGIGACWG 68 Query: 47 VIQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGL 106 VI RL ++GR+P TE+ WR V A ++G+ Sbjct: 69 VIAEKGRLIVMGRYPDTEH----------------------------WRPVIATALMLGV 100 Query: 107 LLILFTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLIGGG-F 165 + I R W WL IWL + L+ GG Sbjct: 101 VGI----SCMPRFW----------------------NRWLGPIWLAMLVVYFVLMRGGVL 134 Query: 166 GLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVP 225 GL V ++ W GL LT+++ +S+ ++FP+ + +ALGR SN+P ++ LY+E++RGVP Sbjct: 135 GLTRVDNDQWGGLPLTVMLTVVSMTMAFPLSIFVALGRRSNMPAIKTLCTLYVELIRGVP 194 Query: 226 LIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAK 285 LI +LF+A MLPLF V++D ++R + + LFSAAYMAE VRGGLQA+ +GQ EAA Sbjct: 195 LITVLFMASFMLPLFMPDGVQIDVLIRVLVAITLFSAAYMAEVVRGGLQALPKGQTEAAA 254 Query: 286 ALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTG-IARSILAQP 344 LGL + IVLPQAL V+P+L+ FIG+FKDTSL+++V L EL G + ++ A Sbjct: 255 TLGLTYWQAQRKIVLPQALSMVVPSLMNTFIGMFKDTSLVTIVSLYELAGAVELALNADA 314 Query: 345 QFIGRYAEVYLFIGLIYWLFCYSMSLASRRLERQ 378 + E Y FI LIY++FC++MS S +E++ Sbjct: 315 DWRPFKLEAYFFIALIYFVFCFAMSRYSLWVEKR 348 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: 442 Number of extensions: 25 Number of successful extensions: 5 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: 355 Length adjustment: 30 Effective length of query: 351 Effective length of database: 325 Effective search space: 114075 Effective search space used: 114075 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