Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_086509734.1 BZY95_RS09705 ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_002151265.1:WP_086509734.1 Length = 313 Score = 161 bits (408), Expect = 2e-44 Identities = 102/238 (42%), Positives = 138/238 (57%), Gaps = 10/238 (4%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MIE DV K + G E A+ L ++ G++ L+G SG GKST LR+INRL E GG Sbjct: 1 MIELFDVTKRF---GDET-AVDGISLRVEKGELCALVGTSGCGKSTTLRMINRLIEHDGG 56 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 I ++G+ V + D LRR R+G + Q L TVA NI + RL + + +V Sbjct: 57 EIHLDGQPVRSFDEVALRR---RIGYVIQSTGLFPHWTVARNIGLVPRLLK-WPKGKVRD 112 Query: 121 RVSELLARVGL--SDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTA 178 RV EL+ +GL ++ A KYP QLSGGQ QRVG+ARALA P ILL DE ALDP T A Sbjct: 113 RVEELMQLLGLPVAEFADKYPRQLSGGQAQRVGVARALAADPDILLMDEPFGALDPITRA 172 Query: 179 SVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHP 236 ++ L + L T+V +TH+MD + D++ VM G IV+QG ++ P +P Sbjct: 173 TLQDELRVLQARLHKTVVFVTHDMDEALALADRLVVMHQGRIVQQGSPVELLREPANP 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: 278 Number of extensions: 13 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: 313 Length adjustment: 28 Effective length of query: 307 Effective length of database: 285 Effective search space: 87495 Effective search space used: 87495 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 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