Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 343 bits (881), Expect = 3e-99 Identities = 185/346 (53%), Positives = 236/346 (68%), Gaps = 22/346 (6%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 + + L+++ K +G +V+ G+DLDV+DGEF +FVGPSGCGKSTLLR +AGLE+ T G++ Sbjct: 1 MSGVTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTI 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 +I G +V + P+ RG++MVFQ+YALYPH+TV++NMG GLK G +I+EKVA+A+ + Sbjct: 61 RIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L L+ YL R+P LSGGQRQRVAIGRAIVR P++FLFDEPLSNLDA LRV R+EIARLH Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 + + ATMIYVTHDQVEAMTLADKIVVL AGRIEQVG+PMELY P N FVAGFIGSP MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMN 240 Query: 257 FI-------------------EAAKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHL 297 FI + A +G+ IG+RPEH+ L S +V E L Sbjct: 241 FIRGRVQGGEVVSDGLVHSVSKTASAQEGQEVLIGLRPEHLELRPGSSH---RVDLTESL 297 Query: 298 GADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDA 343 G + ++ + V G+HR + D+V M FDA Sbjct: 298 GGVSYAHLIGPDGEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFDA 343 Lambda K H 0.320 0.137 0.393 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: 381 Number of extensions: 15 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: 352 Length of database: 350 Length adjustment: 29 Effective length of query: 323 Effective length of database: 321 Effective search space: 103683 Effective search space used: 103683 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 24 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