Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 319 bits (818), Expect = 7e-92 Identities = 162/349 (46%), Positives = 235/349 (67%), Gaps = 3/349 (0%) Query: 19 VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNV 78 V+ L + D EFVVL+GPSGCGKST LRMIAGLE+++ G + IGG VVN +P ++R++ Sbjct: 18 VVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEISIGGRVVNHVPPKDRDI 77 Query: 79 AMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGG 138 AMVFQ+YALYPHM+VY N+AFGL P EIDRRV++ A +L + LL+R+P +SGG Sbjct: 78 AMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEILGISDLLQRRPAQLSGG 137 Query: 139 QQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEA 198 Q+QR A+ RAI++ P FLFDEPLSNLDAKLR Q+R ++ +LH+RL++T VYVTHDQ+EA Sbjct: 138 QRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLHERLQSTIVYVTHDQIEA 197 Query: 199 MTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIET 258 MTLADR+++M+DG+I+Q G P E+Y P N F AGFIG+P+MNFL + + G L+++ Sbjct: 198 MTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMNFLDVRLVEEAGDLWVDG 257 Query: 259 AHQRWALTGERFSRLRHAM--AVKLAVRPDHVR-IAGEREPAASLTCPVSVELVEILGAD 315 R + R R + V +RP+ V+ G+ P V++ E +G++ Sbjct: 258 ESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALPEGVEPLRAEVDVREPIGSE 317 Query: 316 ALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENLS 364 ++T G TA + + + + LA++ +++H+FD ES + L+ Sbjct: 318 VIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHLFDPESEQALN 366 Lambda K H 0.321 0.137 0.403 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: 403 Number of extensions: 16 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: 406 Length of database: 368 Length adjustment: 30 Effective length of query: 376 Effective length of database: 338 Effective search space: 127088 Effective search space used: 127088 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: 50 (23.9 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