Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_007695653.1 C447_RS15655 ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_000336675.1:WP_007695653.1 Length = 332 Score = 154 bits (390), Expect = 2e-42 Identities = 99/273 (36%), Positives = 143/273 (52%), Gaps = 20/273 (7%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MI F +VHK Y R A+ ++ G L+G SG GK+T +RL+NRLEEP+ G Sbjct: 1 MIRFDNVHKQYPDGTR---AVDGHDFEVEEGTTTVLVGPSGCGKTTTMRLVNRLEEPTEG 57 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 I +G D+ L+A LRR +G + Q L TV +N+A L G + D Sbjct: 58 TIYYDGTDIEELEATDLRR---EIGYVIQDIGLFDHMTVGENVATVPELKGWEAERTAD- 113 Query: 121 RVSELLARVGL--SDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTA 178 RV ELL +GL + YP +LSGGQ+QRVG+ARALA P ++L DE ALDP T Sbjct: 114 RVDELLELMGLPPEEFRDSYPGELSGGQQQRVGVARALAAGPDVMLMDEPFGALDPITRE 173 Query: 179 SVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVE-----------QGDVA 227 + +I +E+ TIV +TH+++ ++ D++AVM+ G +V+ + Sbjct: 174 ELQDEFLDIQKEIDTTIVFVTHDINEALKMGDKIAVMNEGKVVQYDTPTALLDNPKTKFV 233 Query: 228 DVFLHPQHPTTRRFVFEAERVDEDERHDDFAHV 260 + F+ P R V E V + E D+ A V Sbjct: 234 EEFIGPDRTLKRLRVLRVEEVMQAEIPDEHAAV 266 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: 286 Number of extensions: 17 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: 332 Length adjustment: 28 Effective length of query: 307 Effective length of database: 304 Effective search space: 93328 Effective search space used: 93328 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