Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 150 bits (380), Expect = 4e-41 Identities = 88/213 (41%), Positives = 123/213 (57%), Gaps = 8/213 (3%) Query: 29 GEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTVTTTP------PAKRGIAMVFQ 82 GEF+ VGPSG GK+TLLR+I+GL G I G + + P R I V Q Sbjct: 28 GEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRHIGFVPQ 87 Query: 83 SYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDRRPSELSGGQRQRV 142 + L+P LS N+ AL + P +E R A ++L DR PS+LSGGQ+QRV Sbjct: 88 HFGLFPKLSALGNIMAAL--DHLPSQERRPRALAALEKVNLHGLTDRLPSQLSGGQKQRV 145 Query: 143 AIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIYVTHDQIEAMTLAD 202 A+ RA+ REP++ L DEP S +D R LE+ARL +L+ +I VTHD EA+ LAD Sbjct: 146 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLNEALLLAD 205 Query: 203 KIVVLRDGRIEQVGTPMELYNNPANRFVAEFIG 235 ++++ G + Q GTP ++++ P N VA +G Sbjct: 206 SMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 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: 258 Number of extensions: 13 Number of successful extensions: 2 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: 370 Length adjustment: 29 Effective length of query: 302 Effective length of database: 341 Effective search space: 102982 Effective search space used: 102982 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