Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_008504345.1 BIBO1_RS07175 amino acid ABC transporter permease
Query= TCDB::Q8YPM7 (381 letters) >NCBI__GCF_000182725.1:WP_008504345.1 Length = 385 Score = 248 bits (633), Expect = 2e-70 Identities = 153/405 (37%), Positives = 221/405 (54%), Gaps = 83/405 (20%) Query: 6 WLRKNLFSTWYNSLLTVICSALSLWLVQGIIVW--------------ATTKAQ------- 44 WLR NLF+T ++ LT+ L +W V II W T AQ Sbjct: 29 WLRVNLFATPVDAALTIFGLVLVVWFVLPIIEWLFINAAWTGTSRTACLTAAQGGAQPDG 88 Query: 45 -----WAVIQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGL 99 WA + FL GR+P +E WRV Sbjct: 89 WSGACWAFVNAKYEQFLYGRYPISERWRV------------------------------- 117 Query: 100 FAFIVGLLLILFTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILW 159 DL++ ++ L LLIP + + N ++++ L FP++ + Sbjct: 118 --------------DLTALIFAALLVPLLIPK--VPKKGLN------AILFFLVFPVVAF 155 Query: 160 --LIGGGFGLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILY 217 L+GG FGL V + LW GLL+TL+++ + I +S P+G++LALGR S LPV++ SI++ Sbjct: 156 FLLVGGWFGLPYVETPLWGGLLVTLVLSFVGIAVSLPLGIVLALGRRSKLPVIKTLSIIF 215 Query: 218 IEIVRGVPLIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVS 277 IE+VRGVPL+ +LF+A VMLPLF V D++LRA+ G+ LF++AYMAE VRGGLQA+ Sbjct: 216 IEMVRGVPLVTVLFMASVMLPLFLPPGVTFDKLLRALIGVALFASAYMAEVVRGGLQAIP 275 Query: 278 RGQVEAAKALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIA 337 RGQ E A ALGL+ + L+VLPQAL+ VIP +V FIGLFKDTSL+ ++G+ +L GI Sbjct: 276 RGQYEGADALGLSYWQKTGLVVLPQALKLVIPGIVNTFIGLFKDTSLVYIIGMFDLLGIV 335 Query: 338 RSILAQPQFIGRY--AEVYLFIGLIYWLFCYSMSLASRRLERQLN 380 R + + A +F G ++W+FC++MS S +ER+L+ Sbjct: 336 RQNFSDANWASPQTPATGLIFAGFVFWIFCFAMSRYSIFMERRLD 380 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: 523 Number of extensions: 28 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: 385 Length adjustment: 30 Effective length of query: 351 Effective length of database: 355 Effective search space: 124605 Effective search space used: 124605 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 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