Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 140 bits (353), Expect = 4e-38 Identities = 76/226 (33%), Positives = 132/226 (58%), Gaps = 9/226 (3%) Query: 16 VEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTVTTTPPA-- 73 + L+ ++LT+++GE +G SG GKSTL+R+I+ LED + G + I G+ VT A Sbjct: 18 ISALQPLDLTIQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGGRLLIAGEDVTALETAGL 77 Query: 74 ---KRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDRR 130 +R I M+FQ + L +V N+A L+ P+ +I ARVAE + + L+ + D+ Sbjct: 78 RTLRRRIGMIFQHFNLLSSRTVASNVAFPLELAGTPRAQIDARVAELLQTVGLQAHADKY 137 Query: 131 PSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIYV 190 P++LSGGQ+QRV I RA+ P++ L DE S LD + +++++R+L +++ + Sbjct: 138 PAQLSGGQKQRVGIARALATGPQILLCDEATSALDPQTTASVLALLSKINRELGLTIVLI 197 Query: 191 THDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNP----ANRFVAE 232 TH+ + D++ VL G + ++G +++ +P RFV+E Sbjct: 198 THEMDVIRRVCDRVAVLDAGEMVEMGPVTDVFLHPQHPTTRRFVSE 243 Lambda K H 0.320 0.137 0.391 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: 268 Number of extensions: 11 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: 331 Length of database: 335 Length adjustment: 28 Effective length of query: 303 Effective length of database: 307 Effective search space: 93021 Effective search space used: 93021 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 (21.8 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