Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__WCS417:GFF1168 Length = 344 Score = 239 bits (611), Expect = 6e-68 Identities = 130/274 (47%), Positives = 178/274 (64%), Gaps = 4/274 (1%) Query: 3 ALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISI 62 A+Q T+V + FG V+ + +++ ++DGEF +GPSG GK+T LR+I+G E +AG I I Sbjct: 4 AVQFTHVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRI 63 Query: 63 GGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLS 122 G+ PP +R + VFQ YAL+PH++VR+N+A LK + K E R EA M++ Sbjct: 64 HGEEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKTERMNRAEEALGMVA 123 Query: 123 LEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQ 182 L Y DR+P +LSGGQRQRVA+ RA+V P++ L DEPL LD LR + E+ +L RQ Sbjct: 124 LGGYGDRKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQ 183 Query: 183 LSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIG-APAMNF 241 L + I+VTHDQ EA++++D++ V GRIEQV TP LY PA FVAEF+G + + Sbjct: 184 LGITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVGTSNVIRG 243 Query: 242 VPAQRLGGNPGQFIGIRPEYARISPVGPL-AGEV 274 AQRLGG F IRPE+ R + GPL GEV Sbjct: 244 ELAQRLGGTAQPF-SIRPEHVRFAE-GPLGTGEV 275 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: 321 Number of extensions: 15 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: 344 Length adjustment: 28 Effective length of query: 303 Effective length of database: 316 Effective search space: 95748 Effective search space used: 95748 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 17 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