Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_011384921.1 AMB_RS12790 ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_000009985.1:WP_011384921.1 Length = 232 Score = 138 bits (347), Expect = 2e-37 Identities = 87/227 (38%), Positives = 127/227 (55%), Gaps = 6/227 (2%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 + E + K + + AL+ L++ G++ GL+G SG+GKSTLL +I + EP+ G Sbjct: 7 LAELTGIAKHFGEGASRVDALRGVDLSLHPGEVVGLLGPSGSGKSTLLNIIGCVVEPNAG 66 Query: 61 RILVEGEDVT--ALDAEGLRRFR-QRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAE 117 R++++G V A LRR R ++G IFQ NLL DN+A+ L LAG A Sbjct: 67 RMVLDGVVVYDGAWTGGDLRRLRLDKIGFIFQFHNLLPFLNSRDNVAVVLELAGQ-DPAA 125 Query: 118 VDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTT 177 R ELL + + A P QLSGG+ QRV IARALA P ++L DE T+ALD Q Sbjct: 126 ARRRAGELLDYLEVGARAEASPGQLSGGEAQRVAIARALANNPRLILADEPTAALDSQRA 185 Query: 178 ASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQG 224 A V+ LL ++ RE +++++H+ + R V V DG ++E G Sbjct: 186 AIVMDLLIKVAREQNAAVLVVSHDEKIYDRFDRMVRVRDG--VLESG 230 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: 212 Number of extensions: 8 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: 232 Length adjustment: 25 Effective length of query: 310 Effective length of database: 207 Effective search space: 64170 Effective search space used: 64170 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 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