Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_007693030.1 C447_RS08815 ATP-binding cassette domain-containing protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_000336675.1:WP_007693030.1 Length = 437 Score = 166 bits (419), Expect = 1e-45 Identities = 100/245 (40%), Positives = 141/245 (57%), Gaps = 5/245 (2%) Query: 12 RVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTA 71 R GR + A+ ++ G+ GL+G SG GKST + R EEP+ G I +G D+ A Sbjct: 25 REVGR-VRAVDGIDFDLDRGETLGLVGESGCGKSTAATTLLRFEEPTEGEIEFDGTDLLA 83 Query: 72 LDAEGLRRFRQRVGMIFQHFNLLSSK--TVADNIAMPLRLAGGFSRAEVDARVSELLARV 129 D + L+RFR+R M+FQ N T+ +++A PLR+ G R A V L RV Sbjct: 84 CDKDELKRFRRRAQMVFQDPNSSFDPRMTIGESVAEPLRVHG-LPRERRRAVVRNTLERV 142 Query: 130 GL-SDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEIN 188 GL + A +YP + SGGQKQR+ +ARAL P +++ DE SALD A +L L+ +I Sbjct: 143 GLDATAADRYPHEFSGGQKQRIALARALVLNPDLIVADEPVSALDVSLQAEILTLIDDIQ 202 Query: 189 RELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERV 248 +E L I+ I+H+M VI++VC++VAVM G IVE G VF PQHP T+ + Sbjct: 203 QEFGLGILFISHDMSVIQQVCNRVAVMYLGEIVEIGSTDAVFSDPQHPYTQALLASIPNP 262 Query: 249 DEDER 253 D +R Sbjct: 263 DPRKR 267 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: 359 Number of extensions: 20 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: 437 Length adjustment: 30 Effective length of query: 305 Effective length of database: 407 Effective search space: 124135 Effective search space used: 124135 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: 50 (23.9 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