Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 210 bits (535), Expect = 4e-59 Identities = 118/244 (48%), Positives = 158/244 (64%), Gaps = 8/244 (3%) Query: 1 MTALQLT--NVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAG 58 MT+++L+ ++ + G +LK ++L V GE V +GPSG GK+TLLR I+GLE + G Sbjct: 1 MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG 60 Query: 59 EISIGGQTVTTTPPA------KRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAA 112 I IG Q V + KR + VFQSYAL+PH +V EN+A LK + P EI Sbjct: 61 SIRIGEQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQ 120 Query: 113 RVAEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNT 172 RV E L L D +R P +LSGGQ+QRVA+ R++V P++ L DEPLSNLDA LR Sbjct: 121 RVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEA 180 Query: 173 RLEIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAE 232 R+ + +L L+ S + VTHDQ EAM +ADK+V+L+DG IEQ GTP E+Y P + FVAE Sbjct: 181 RIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAE 240 Query: 233 FIGA 236 F+GA Sbjct: 241 FMGA 244 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: 318 Number of extensions: 14 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: 353 Length adjustment: 29 Effective length of query: 302 Effective length of database: 324 Effective search space: 97848 Effective search space used: 97848 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 Apr 09 2024. 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