Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_028310576.1 H566_RS0105020 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_000482785.1:WP_028310576.1 Length = 402 Score = 185 bits (470), Expect = 1e-51 Identities = 96/215 (44%), Positives = 146/215 (67%), Gaps = 2/215 (0%) Query: 28 IQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRRFRQR-VGM 86 ++ G+IF L+G SG+GKSTL+RLINRL EP+ GR+L++G+DV L A+ LR R+R + M Sbjct: 52 VREGEIFVLMGLSGSGKSTLIRLINRLVEPTAGRVLIDGQDVVTLPADKLRDLRRRDMSM 111 Query: 87 IFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKYPAQLSGGQ 146 +FQ F LL ++TV DN A L +AG R E + E+L +VGL ARK+P +LSGG Sbjct: 112 VFQSFALLPNRTVLDNAAFGLEVAG-VGRKERERAAMEVLEQVGLKPFARKHPHELSGGM 170 Query: 147 KQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIR 206 +QRVG+ARALA PS+++ DEA SALDP + +L ++ E K TIV ++H+++ Sbjct: 171 RQRVGLARALAVNPSLMIMDEAFSALDPLKRREMQDVLLQLQAEHKRTIVFVSHDIEEAF 230 Query: 207 RVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRF 241 R+ +++A+M+GG +++ G+ + +P + R F Sbjct: 231 RIGNRIAIMEGGRLIQLGEPRQIIENPANDYVRAF 265 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: 347 Number of extensions: 18 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: 402 Length adjustment: 30 Effective length of query: 305 Effective length of database: 372 Effective search space: 113460 Effective search space used: 113460 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: 49 (23.5 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