Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_152416156.1 C447_RS11610 ATP-binding cassette domain-containing protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_000336675.1:WP_152416156.1 Length = 233 Score = 148 bits (374), Expect = 1e-40 Identities = 91/213 (42%), Positives = 122/213 (57%), Gaps = 4/213 (1%) Query: 6 DVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVE 65 DV KTY + G + AL L++ G ++G SG+GKSTLL L+ L+ P+ G + V Sbjct: 5 DVRKTYDLGGT-VEALAGVSLSLADGSYTAVMGPSGSGKSTLLNLVGALDTPTDGTVEVA 63 Query: 66 GEDV-TALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSE 124 G D+ A D E +G +FQ FNLL +N+A+PL AG +SR R +E Sbjct: 64 GNDLGAATDDERAAIRGTEIGFVFQTFNLLPRSDAVENVALPLVFAG-WSRERRHERATE 122 Query: 125 LLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLL 184 LL RVGL D P QLSGGQ+QRV IARALA P+++L DE T +D +T A V+ LL Sbjct: 123 LLDRVGLGDRRHHRPTQLSGGQRQRVAIARALAPDPAVVLADEPTGNVDTETGAGVMNLL 182 Query: 185 AEINRELKLTIVLITHEMDVIRRVCDQVAVMDG 217 A N + TI+L+TH ++ V V DG Sbjct: 183 AAAN-DRGTTILLVTHSREIAEHADRIVTVRDG 214 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: 193 Number of extensions: 14 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: 233 Length adjustment: 26 Effective length of query: 309 Effective length of database: 207 Effective search space: 63963 Effective search space used: 63963 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 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