Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 175 bits (443), Expect = 1e-48 Identities = 106/252 (42%), Positives = 140/252 (55%), Gaps = 14/252 (5%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 ++ F V K Y E+ L L I+ G+ +IG SG+GKSTLLR++ LE G Sbjct: 24 LVRFAGVTKRYG----ELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEG 79 Query: 61 RILVEGEDVTAL-DAEG---------LRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLA 110 I V+GE +T + DA G LRR R +VGM+FQ FNL N+ Sbjct: 80 VIEVDGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQV 139 Query: 111 GGFSRAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATS 170 G S+AE R ELLA VGL D +PAQLSGGQ+QRV IARALA RP ++L DE TS Sbjct: 140 LGLSKAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTS 199 Query: 171 ALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVF 230 ALDP+ VL ++ + LT++++TH+M R D+V G I EQG ++F Sbjct: 200 ALDPELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELF 259 Query: 231 LHPQHPTTRRFV 242 +PQ TR F+ Sbjct: 260 NNPQEERTREFL 271 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: 258 Number of extensions: 13 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: 278 Length adjustment: 27 Effective length of query: 308 Effective length of database: 251 Effective search space: 77308 Effective search space used: 77308 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