Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_009493201.1 MICLODRAFT_RS27670 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_000262405.1:WP_009493201.1 Length = 363 Score = 329 bits (843), Expect = 7e-95 Identities = 183/358 (51%), Positives = 225/358 (62%), Gaps = 27/358 (7%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M + L V KSFG E+L+DI+L+V+DGEFVVFVGPSGCGKSTLLR+I+GLE + GEI Sbjct: 1 MADVSLHGVAKSFGATEILRDIDLSVDDGEFVVFVGPSGCGKSTLLRIIAGLETVSGGEI 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 I + V PPA R IAMVFQSYALYPH++V +NMA LK + K E+ RV +A+ + Sbjct: 61 RIDSRRVNELPPADRKIAMVFQSYALYPHMNVYKNMAFGLKFAKTDKAEVDRRVRQAAEI 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L L LDR+P ELSGGQRQRVAIGRA+VR P +FLFDEPLSNLDAALR+NTRLEIA+LH Sbjct: 121 LKLTPLLDRKPRELSGGQRQRVAIGRAIVRNPSVFLFDEPLSNLDAALRVNTRLEIAKLH 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 R L A+MIYVTHDQ+EAMTLA KIVV+ GRIEQVG P+ELY P N FVA FIG+P MN Sbjct: 181 RDLGATMIYVTHDQVEAMTLASKIVVMNHGRIEQVGAPLELYRFPRNLFVAGFIGSPRMN 240 Query: 241 FVPAQ-------------------------RLGGNPGQFIGIRPEYARI--SPVGPLAGE 273 F+ Q L IGIRPE+ + + L G Sbjct: 241 FIKGQVLRVEGSSATIGFAGTEALVDVRTGSLSAGDSVTIGIRPEHMEVGGADATSLRGT 300 Query: 274 VIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQRI 331 + VE+LG + + + + R G+ D G + FD +G + Sbjct: 301 IDAVEQLGESSYVYMRLASGDDVIVRAPGETDAAPGGSYTAHVPRRALHVFDASGMSV 358 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: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 363 Length adjustment: 29 Effective length of query: 302 Effective length of database: 334 Effective search space: 100868 Effective search space used: 100868 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