Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Pf6N2E2_1493 ABC-type polar amino acid transport system, ATPase component
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1493 Length = 278 Score = 174 bits (442), Expect = 2e-48 Identities = 101/246 (41%), Positives = 140/246 (56%), Gaps = 6/246 (2%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 ++ D+H ++ P L+ L+++ G+ +IG SG+GKST+LR I L +P G Sbjct: 11 LVSLRDLHLSFG----SNPVLKGIDLDVRRGEAVSIIGPSGSGKSTILRCITGLLQPQRG 66 Query: 61 RILVEGEDVTALDAEGLR-RFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVD 119 I V +V AL E R R+RVG +FQ +NL +V +N+ + R G +RA + Sbjct: 67 SIRVGATEVHALAQEAQRIELRKRVGFVFQQYNLFPHLSVLENLVIAPRKVLGRNRAAAE 126 Query: 120 ARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTAS 179 LLA+V + A YP QLSGGQ+QRV IARALA RP ++L DE TSALDP+T Sbjct: 127 KDARALLAKVRMEHKADAYPGQLSGGQQQRVAIARALAMRPELILFDEVTSALDPETVGE 186 Query: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTR 239 VL ++ E+ E +T VL+THEM + D V + G IVE G A +F HP TR Sbjct: 187 VLTVIRELTEE-GMTCVLVTHEMRFAEEISDVVYFTENGVIVEHGSAARIFQHPTSERTR 245 Query: 240 RFVFEA 245 F+ A Sbjct: 246 EFLHHA 251 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: 226 Number of extensions: 7 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: 278 Length adjustment: 27 Effective length of query: 308 Effective length of database: 251 Effective search space: 77308 Effective search space used: 77308 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