Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 249 bits (635), Expect = 1e-70 Identities = 123/268 (45%), Positives = 177/268 (66%), Gaps = 11/268 (4%) Query: 4 LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63 ++L V K+F L I+LT+ +GEF+ +GPSGCGK+T+LR++SG E T+GE+ I Sbjct: 8 IELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRIN 67 Query: 64 GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123 GQ V PP +R + VFQ+YAL+PH++VR+N+A LK + +E A RV +A RM+ L Sbjct: 68 GQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHL 127 Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183 E++ DR+P +LSGGQ+QRVAI RAV+ P + L DEP S LD LR +LEI L RQL Sbjct: 128 ENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQL 187 Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVP 243 + ++VTHDQ EA ++D++VV+ +GRIEQ+G P E+Y PAN +VA F+G Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVG-------- 239 Query: 244 AQRLGGNPGQFIGIRPEYARISPVGPLA 271 + PG+ +R +++ +P PLA Sbjct: 240 --DINALPGRIDAVRLDWS-AAPGTPLA 264 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: 360 Number of extensions: 18 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: 399 Length adjustment: 29 Effective length of query: 302 Effective length of database: 370 Effective search space: 111740 Effective search space used: 111740 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