Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BWI76_RS05955 BWI76_RS05955 ABC transporter
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Koxy:BWI76_RS05955 Length = 272 Score = 203 bits (516), Expect = 5e-57 Identities = 109/241 (45%), Positives = 151/241 (62%), Gaps = 5/241 (2%) Query: 2 IEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGR 61 IEF DV K+Y + L L ++ G++ ++G SG+GKSTL+RLIN+LE SGG Sbjct: 24 IEFRDVAKSYG----DHRVLNGVNLQVEPGEVVAILGPSGSGKSTLIRLINQLESLSGGE 79 Query: 62 ILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDAR 121 IL++G+ L LR+ R RVG +FQ FNL + T +NI + L G+ ++ R Sbjct: 80 ILIDGKPTRQLTGSALRQLRSRVGFVFQQFNLYAHLTAQENITLALERVHGWGKSAARER 139 Query: 122 VSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVL 181 LL++VGL+D A + PAQLSGGQ+QRV IARALA P I+L DE TSALDP+ VL Sbjct: 140 SLALLSQVGLADKAGQMPAQLSGGQQQRVAIARALASSPQIILFDEPTSALDPEMIGEVL 199 Query: 182 QLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRF 241 Q++ + +T+V++THEM R + D+V +DGG I+E A+ F PQH TRRF Sbjct: 200 QVMKTLAHS-GITMVVVTHEMQFAREIADRVVFIDGGDILEVAPPAEFFARPQHARTRRF 258 Query: 242 V 242 + Sbjct: 259 L 259 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: 249 Number of extensions: 13 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: 272 Length adjustment: 27 Effective length of query: 308 Effective length of database: 245 Effective search space: 75460 Effective search space used: 75460 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: 48 (23.1 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