Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 339 bits (870), Expect = 5e-98 Identities = 181/339 (53%), Positives = 239/339 (70%), Gaps = 8/339 (2%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M L+L NV K +G + +K ++L ++ GEF+VFVGPSGCGKSTLLR+I+GLE G++ Sbjct: 1 MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 + G+ +T PP++R +AMVFQSYALYPH++V ENM+ AL+ + I +V A+ Sbjct: 61 ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L+L YL R P LSGGQRQRVAIGR++VR PK+FLFDEPLSNLDAALR NTR+EIA LH Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 R+L A+ +YVTHDQ+EAMTLAD++VVLRDG IEQVGTP+ELY+ P NRFVA FIG P MN Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240 Query: 241 FVPAQRLGGNPGQF--IGIRPEYAR-ISPV-GPLAGEVIHVEKLGGDTNILVDMGE---D 293 PA G P Q +GIRPE+ + +SP G LAG+V+ VE LG +T + V + + Sbjct: 241 VAPASLFGQFPAQVAEVGIRPEHLQMVSPEDGLLAGKVVLVEALGNETLVHVRPDKVQLE 300 Query: 294 LTFTARLFGQHDTNVGETLQFDFDPANCLS-FDEAGQRI 331 RL+G+ +VG+ + +D + + FD G R+ Sbjct: 301 EPLIVRLYGRTTVHVGDRVGLKWDDSKHIHYFDTKGMRL 339 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: 373 Number of extensions: 17 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: 348 Length adjustment: 28 Effective length of query: 303 Effective length of database: 320 Effective search space: 96960 Effective search space used: 96960 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