Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_337833398.1 BUB04_RS10875 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_900129305.1:WP_337833398.1 Length = 257 Score = 174 bits (440), Expect = 3e-48 Identities = 102/248 (41%), Positives = 149/248 (60%), Gaps = 11/248 (4%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 M+E ++HK + G ++ L+ L ++ G++ ++G SG+GKSTLLR IN LEEP+ G Sbjct: 7 MVEVSNLHKVF---GEDLHVLRGIDLEVKKGEVVVILGPSGSGKSTLLRCINFLEEPTAG 63 Query: 61 RILV------EGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFS 114 I V G+ +A+ L R+RVGM FQ FNL T +NI G S Sbjct: 64 TIRVGDITIGAGKKTKEHNAKILE-IRRRVGMCFQSFNLFPHMTALENIIEGPVTVLGQS 122 Query: 115 RAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDP 174 + E ELLA VGL+D +YP++LSGGQ+QRV IAR+LA +P ++L DE TSALDP Sbjct: 123 KKEAIPYAEELLAWVGLTDKRDEYPSRLSGGQQQRVAIARSLAMKPDVMLFDEPTSALDP 182 Query: 175 QTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQ 234 + V+ ++ + E +TI+ +THEM R V D+V +MDGG VE G ++F +P+ Sbjct: 183 ELVKEVVDVMERLAAE-GMTIIAVTHEMHFARDVADRVLIMDGGVWVESGPPEEIFTNPK 241 Query: 235 HPTTRRFV 242 +R+F+ Sbjct: 242 EARSRQFL 249 Lambda K H 0.322 0.138 0.393 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: 201 Number of extensions: 7 Number of successful extensions: 4 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: 335 Length of database: 257 Length adjustment: 26 Effective length of query: 309 Effective length of database: 231 Effective search space: 71379 Effective search space used: 71379 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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