Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_084934899.1 HA51_RS12950 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_002095475.1:WP_084934899.1 Length = 367 Score = 265 bits (676), Expect = 2e-75 Identities = 131/248 (52%), Positives = 174/248 (70%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M+ L L ++ K++G L DI+ +G FV +GPSGCGKSTLLR I+GLE A +GEI Sbjct: 1 MSHLSLHHITKAWGEKIALNDISFDAAEGSFVALLGPSGCGKSTLLRTIAGLETADSGEI 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 +T PP++R ++MVFQSYAL+PHL+VREN+ LK + K+ R+ + S++ Sbjct: 61 HFKHSDITHLPPSQRKLSMVFQSYALFPHLNVRENLLFGLKARGEDKQTFTTRLDDVSKL 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 + L+ LDR PS+LSGGQ+QRVA+GRAV+ L L DEPLSNLDA LR + R EI L Sbjct: 121 MELDKLLDRLPSQLSGGQQQRVALGRAVIANNNLCLMDEPLSNLDAKLRQSMRREIRALQ 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 ++L+ +M+YVTHDQ EAM++AD I++L DG IEQ GTP +LYNNPA F A+FIGAP MN Sbjct: 181 KKLALTMLYVTHDQTEAMSMADSIILLNDGHIEQHGTPNDLYNNPATIFAAQFIGAPPMN 240 Query: 241 FVPAQRLG 248 +P G Sbjct: 241 ILPLHAKG 248 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: 271 Number of extensions: 7 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: 367 Length adjustment: 29 Effective length of query: 302 Effective length of database: 338 Effective search space: 102076 Effective search space used: 102076 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