Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_035130044.1 Q763_RS00890 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_000769915.1:WP_035130044.1 Length = 319 Score = 136 bits (343), Expect = 6e-37 Identities = 81/265 (30%), Positives = 138/265 (52%), Gaps = 8/265 (3%) Query: 12 SFGPVE--VLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTVTT 69 SFG E +L +++ TV+ G+ + +G SGCGKSTLL++I GL D GEI+ G+ V Sbjct: 8 SFGYTEKTILHNLSFTVKTGQNIAVIGESGCGKSTLLKLIYGLYDIEEGEITYKGEPVLG 67 Query: 70 TP----PAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLED 125 P + + Q + L P+++ EN+ L EE R+ E ++ + + Sbjct: 68 PKFNLIPGMSYMKYLAQDFDLMPYITAAENVGAFLSNFYP--EEKQRRIMELLDIVEMRE 125 Query: 126 YLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSA 185 + D + LSGGQ+QR+A+ + + EP++ L DEP S++D + R + +Q Sbjct: 126 FADVKAQFLSGGQQQRIALAKVLALEPEVLLLDEPFSHIDNFRKNALRRNLFAYLKQKGV 185 Query: 186 SMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVPAQ 245 + I THD +A++ AD+ +V++ GR+ ++Y NPA+++ A G + Sbjct: 186 TCIVATHDSTDALSFADETIVIKGGRMLSKAKSKDIYYNPADKYTASLFGEVNEIKLELL 245 Query: 246 RLGGNPGQFIGIRPEYARISPVGPL 270 L NP + + I P ++ GPL Sbjct: 246 TLTQNPEETVLIYPHQLKVVEEGPL 270 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: 233 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 319 Length adjustment: 28 Effective length of query: 303 Effective length of database: 291 Effective search space: 88173 Effective search space used: 88173 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: 48 (23.1 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