Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 174 bits (442), Expect = 2e-48 Identities = 101/223 (45%), Positives = 132/223 (59%), Gaps = 2/223 (0%) Query: 20 ALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRR 79 AL+ L++ G+ + G SG+GKSTL+R IN LE G I + GED D L+R Sbjct: 16 ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRI-GEDEVRPDRRVLQR 74 Query: 80 FRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKYP 139 R RVGM+FQ FNL T+ +N A+ G +R +A ELL RV ++D A KYP Sbjct: 75 IRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADKYP 134 Query: 140 AQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLIT 199 AQLSGGQ+QR IARALA +P I+L DE TSALD + VL ++ + E +T++ +T Sbjct: 135 AQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE-GITMLCVT 193 Query: 200 HEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 HEM R V D++ MD G IVE G D F P H TR F+ Sbjct: 194 HEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 236 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: 215 Number of extensions: 10 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: 335 Length of database: 241 Length adjustment: 26 Effective length of query: 309 Effective length of database: 215 Effective search space: 66435 Effective search space used: 66435 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: 47 (22.7 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