Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_089136416.1 CES79_RS04320 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_002217945.1:WP_089136416.1 Length = 314 Score = 179 bits (455), Expect = 6e-50 Identities = 98/234 (41%), Positives = 144/234 (61%), Gaps = 4/234 (1%) Query: 4 LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63 ++L NV K + L ++LT+ DGE V VGPSG GK+TLL+ I+ L T+G++ I Sbjct: 2 IELLNVNKEYQEQHALDHLSLTINDGELFVLVGPSGSGKTTLLKTINRLVVPTSGQVKID 61 Query: 64 GQTVTTTP--PAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRML 121 G+ V +R I V Q+ AL+P+++V EN ++ L + P E+ R+AE + Sbjct: 62 GKDVADVDLQQLRRRIGYVLQTGALFPNMTVAENASVQLDNLKWPAEKKHERIAELMTEV 121 Query: 122 SLED--YLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARL 179 L+ +LDR PSELSGG+ QRV I RA+ +P L L DE S LD R + + L Sbjct: 122 GLDPDHFLDRMPSELSGGEAQRVGIVRALAAKPGLVLMDESFSALDPVSRRQLQQIVINL 181 Query: 180 HRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEF 233 HR L +++++VTHD EA+ LAD+I V+ +G+++QVGTP E+ PAN FV+ F Sbjct: 182 HRDLDSTIVFVTHDMHEALRLADRIAVVYNGKLQQVGTPTEILTEPANAFVSSF 235 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: 252 Number of extensions: 9 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: 331 Length of database: 314 Length adjustment: 28 Effective length of query: 303 Effective length of database: 286 Effective search space: 86658 Effective search space used: 86658 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