Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Ga0059261_1870 Ga0059261_1870 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Korea:Ga0059261_1870 Length = 273 Score = 154 bits (390), Expect = 2e-42 Identities = 89/218 (40%), Positives = 131/218 (60%), Gaps = 3/218 (1%) Query: 26 LNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRRFRQRVG 85 L+++ G+I G++G SG GKS L+R I L+EP G I V GEDV L+ E R+R G Sbjct: 36 LDVRQGEILGVVGGSGTGKSVLMRSIIGLQEPDAGSIEVFGEDVQHLNTEEAIELRKRWG 95 Query: 86 MIFQHFNLLSSKTVADNIAMPLR-LAGGFSRAEVDARVSELLARVGL-SDHARKYPAQLS 143 ++FQ L S+ TVA+N+ +PL+ F +A +D + + GL SD KYPA+LS Sbjct: 96 VLFQGGALFSTLTVAENVQVPLKEFYPAFDQALLDEIAAYKVVMTGLPSDAGPKYPAELS 155 Query: 144 GGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLITHEMD 203 GG K+R G+AR+LA P +L DE T+ LDP A+ +L + R L LT+ LITH++D Sbjct: 156 GGMKKRAGLARSLALDPELLFLDEPTAGLDPIGAAAFDELTLALQRTLGLTVFLITHDLD 215 Query: 204 VIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRF 241 + +CD+VAV+ ++ G + D L HP + + Sbjct: 216 TLYAICDRVAVLADKHVIAVGTI-DELLALDHPWIQEY 252 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: 218 Number of extensions: 11 Number of successful extensions: 2 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: 273 Length adjustment: 27 Effective length of query: 308 Effective length of database: 246 Effective search space: 75768 Effective search space used: 75768 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 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