Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate HSERO_RS17540 HSERO_RS17540 glutamine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__HerbieS:HSERO_RS17540 Length = 240 Score = 177 bits (450), Expect = 2e-49 Identities = 104/246 (42%), Positives = 147/246 (59%), Gaps = 6/246 (2%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 M+EF V K + G + L L I+ G++ LIG SG+GKSTLLR IN LEE GG Sbjct: 1 MVEFKSVSKRF---GSNV-VLDGINLTIRKGEVVVLIGPSGSGKSTLLRCINALEEIDGG 56 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 +LV+G V + + +R RQ GM+FQ FNL T +N+A R G S E +A Sbjct: 57 DLLVDGISVLS-GSSSVRAIRQEAGMVFQQFNLFPQLTALENVAFGPRHVRGASSEEANA 115 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 SELLA+VGL++ YP +LSGGQ+QRV IARALA RP ++L DE TSALDP+ V Sbjct: 116 LASELLAKVGLAERKHHYPNELSGGQQQRVAIARALAVRPKLMLFDEPTSALDPELRQEV 175 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L+++ + E +T++++THE+ RRV ++ M+ G I G+ ++ + +P R Sbjct: 176 LRVMQSLAEE-GMTMIVVTHEISFARRVGTRLIFMENGHIAIDGNPGELIENSCNPRLRE 234 Query: 241 FVFEAE 246 F+ E Sbjct: 235 FLKHVE 240 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: 196 Number of extensions: 5 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: 240 Length adjustment: 26 Effective length of query: 309 Effective length of database: 214 Effective search space: 66126 Effective search space used: 66126 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: 47 (22.7 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