Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 223 bits (567), Expect = 8e-63 Identities = 129/354 (36%), Positives = 191/354 (53%), Gaps = 34/354 (9%) Query: 4 LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63 L+LT + K FG + ++LT+ G F +G SGCGK+T LR+ISGLE TAG I +G Sbjct: 19 LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78 Query: 64 GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123 Q VT P +R + VFQ+YAL+PHL + EN+A L+ R+ + V + ++ L Sbjct: 79 DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLR--RRGIRSVKKPVEDMLDLVEL 136 Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183 R+P++LSGGQ+QR+A+ RA++ +P++ L DEPL LD LR ++E+ R+ ++ Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196 Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVP 243 + ++VTHDQ EAMT+AD I V+ GRIEQ+G+P ELY NP FVA F+G + Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSNLIAGT 256 Query: 244 AQRLGGNPGQ----------------------FIGIRPEYARI--------SPVGPLAGE 273 + + G+ Q +G+RPE RI S L G+ Sbjct: 257 VESVSGDVVQVAAHGRSLALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSGANHLTGK 316 Query: 274 VIHVEKLGGDTNILVDM--GEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFD 325 V +G T LV++ GE+L + GQ G + +DP+ D Sbjct: 317 VTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQGFGLD 370 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: 317 Number of extensions: 24 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: 386 Length adjustment: 29 Effective length of query: 302 Effective length of database: 357 Effective search space: 107814 Effective search space used: 107814 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