Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 206179 DVU0753 amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >MicrobesOnline__882:206179 Length = 243 Score = 182 bits (463), Expect = 6e-51 Identities = 107/242 (44%), Positives = 139/242 (57%), Gaps = 5/242 (2%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MI F VHK Y + L L+I G++ + G SG+GKSTL+R INRLE G Sbjct: 1 MIHFEHVHKWYPSG---LHVLNDINLDIAQGEVVVICGPSGSGKSTLIRCINRLEAIQKG 57 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 I+V+G D+ A L R VG +FQ FNL TV +NI + L RAE + Sbjct: 58 NIVVDGIDINA-PRTNLTLLRAEVGFVFQQFNLYPHMTVLENITLAPTLVRNIPRAEAER 116 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 ELL +V + D A YP QLSGGQ+QRV IAR LA +P I+L DE TSALDP+ V Sbjct: 117 TAMELLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEV 176 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L ++ ++ RE +T+V +THEM R V D+V MD G +VEQ F +PQH +R Sbjct: 177 LDVMRQLARE-GMTMVCVTHEMGFAREVADRVIFMDQGILVEQNTPDAFFNNPQHERSRE 235 Query: 241 FV 242 F+ Sbjct: 236 FL 237 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: 204 Number of extensions: 9 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: 243 Length adjustment: 26 Effective length of query: 309 Effective length of database: 217 Effective search space: 67053 Effective search space used: 67053 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