Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 176 bits (445), Expect = 1e-48 Identities = 106/295 (35%), Positives = 160/295 (54%), Gaps = 6/295 (2%) Query: 21 DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVAMVYQ 80 DL + G VL+GP+ GK++ +R++AGL+ G+I DVT +P + R++AMV+Q Sbjct: 25 DLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPKDRDIAMVFQ 84 Query: 81 QFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQRT 140 + YP +TV +N+ ++I+G + A I +V +AA++L LT +LDR P LSGGQ+QR Sbjct: 85 NYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKALSGGQRQRV 144 Query: 141 ALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLGG 200 A+ RA+V+ + LMDEPL+NLD KLR R ++ + + G VY T + EA+ +G Sbjct: 145 AMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHDQVEAMTMGD 204 Query: 201 NTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDV-TKSGNVFTRPSGVTI-- 257 A L G + Q +Y RP NL AG P +N ++V G V S V + Sbjct: 205 RVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVKFGESVVQVSR 264 Query: 258 PVPSHLAVVPDGPVTIAFHPHHLGLAPQT---GDAARLQARTLVSEITGSESFVH 309 A D VT+ P HL + T G+ L V E G++ +V+ Sbjct: 265 DAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEELGADGYVY 319 Lambda K H 0.319 0.136 0.392 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: 338 Number of extensions: 15 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: 358 Length of database: 369 Length adjustment: 29 Effective length of query: 329 Effective length of database: 340 Effective search space: 111860 Effective search space used: 111860 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 (21.7 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