Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 181 bits (459), Expect = 3e-50 Identities = 108/290 (37%), Positives = 157/290 (54%), Gaps = 14/290 (4%) Query: 31 VLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVAMVYQQFINYPALTV 90 VL+GP+ GK++ +R++AGL+ T G I G V +P + R++AMV+Q + YP + V Sbjct: 33 VLVGPSGCGKSTTLRMIAGLEEVTSGEISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNV 92 Query: 91 YNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQRTALARALVKNA 150 Y N+A + G IDR V++AAE+L ++ L R P LSGGQ+QR A+ RA+V++ Sbjct: 93 YKNMAFGLMNRGVPRDEIDRRVKQAAEILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDP 152 Query: 151 SLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLGGNTATLNQGRV 210 L DEPL+NLD KLR ++R EL K+ + + VY T + EA+ L + G++ Sbjct: 153 QAFLFDEPLSNLDAKLRVQMRAELAKLHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKI 212 Query: 211 TQFGPTIEVYRRPVNLATAGIFADPPLNTLD---VTKSGNVFTRPSGVTIPVPSHLAVVP 267 Q GP +EVY RP N AG P +N LD V ++G+++ + VP H A Sbjct: 213 MQVGPPLEVYERPANRFVAGFIGSPSMNFLDVRLVEEAGDLWVDGESFRLKVPRHRAPAF 272 Query: 268 DG----PVTIAFHPHHLGLAPQTGDA-----ARLQARTLVSEITGSESFV 308 G PV P + P GDA L+A V E GSE + Sbjct: 273 RGHVNRPVIFGIRPEDVKERP--GDALPEGVEPLRAEVDVREPIGSEVII 320 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: 312 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: 368 Length adjustment: 29 Effective length of query: 329 Effective length of database: 339 Effective search space: 111531 Effective search space used: 111531 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