Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 278 bits (712), Expect = 1e-79 Identities = 157/343 (45%), Positives = 213/343 (62%), Gaps = 20/343 (5%) Query: 4 LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63 +++ +V K +G V+ ++ ++ +VE+G+ +V +GPSGCGK+TLLR+I+GLE T+G I I Sbjct: 3 IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62 Query: 64 GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123 G VT PP KR I+MVFQSYAL+PHL+VREN+ LK + P +EI R+ +L L Sbjct: 63 GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122 Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183 LD +P ELSGG +QRVA+GRA++ E + L DEPLSNLDA LR + R EI L R+L Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182 Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVP 243 +MIYVTHDQ+EAMT+AD+IV++RDG+I Q +P Y PAN FVA FIG P MN VP Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVP 242 Query: 244 --------AQRLGGN---PGQ-----FIGIRPEYARISPVGPLAGEVIHVEKLGGDTNIL 287 A GG PG GIRPE R++ G A V E LG DT + Sbjct: 243 LCPTQGGAALEPGGRLLFPGMDPDRYLFGIRPENLRLAESGQPA-MVTGREYLGSDTFVS 301 Query: 288 VDM-GEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQ 329 ++ G+++ R G+ + G + +DP + FD Q Sbjct: 302 CEIHGQEVIVRTR--GRRNIREGTVVHLTWDPGDVNLFDARTQ 342 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: 339 Number of extensions: 12 Number of successful extensions: 1 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: 365 Length adjustment: 29 Effective length of query: 302 Effective length of database: 336 Effective search space: 101472 Effective search space used: 101472 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