Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Korea:Ga0059261_0562 Length = 232 Score = 144 bits (362), Expect = 3e-39 Identities = 88/215 (40%), Positives = 125/215 (58%), Gaps = 7/215 (3%) Query: 10 TYRVAGREIPA--LQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGE 67 T + RE P L+ ++I G ++G SG+GKS+L+ +++ LE SGG + V G Sbjct: 17 TLTLGTREAPTEILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGI 76 Query: 68 DVTALDAEGLRRFRQ-RVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELL 126 LD +GL R R+ RVG++ Q F+LL + T +N+A+PL LAG + AR L Sbjct: 77 AYGTLDEDGLARARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGA---PDAFARAGAEL 133 Query: 127 ARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAE 186 VGL YP QLSGG++QRV IARA+A RP IL DE T LD T+ +++ LL + Sbjct: 134 DAVGLGHRLTHYPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIVDLLFD 193 Query: 187 INRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIV 221 R T+++ITH+ + R CD+V M G IV Sbjct: 194 RQRAADATLLIITHDPALAER-CDRVLTMRDGLIV 227 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: 217 Number of extensions: 14 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