Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 248 bits (633), Expect = 2e-70 Identities = 116/232 (50%), Positives = 168/232 (72%) Query: 4 LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63 +++++V K FG L D+ L V+ GEFV +GPSGCGK+TLLR+I+G + A+ GEI I Sbjct: 10 IEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRIS 69 Query: 64 GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123 G+ +T TPP KR + VFQ YAL+PHL+V +N+A LK ++ PK+ I +V A +M+ + Sbjct: 70 GKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGM 129 Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183 DY R LSGGQ+QRVAI RA+V EP++ L DEPL+ LD +R + ++E+ +H+ L Sbjct: 130 TDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSL 189 Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIG 235 + +YVTHDQ EA+TL+D IVV+ +G+I+Q+GTP+++YN P N FVA+FIG Sbjct: 190 GITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIG 241 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: 396 Number of extensions: 16 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: 463 Length adjustment: 31 Effective length of query: 300 Effective length of database: 432 Effective search space: 129600 Effective search space used: 129600 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: 50 (23.9 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