Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000018545.1:WP_164924745.1 Length = 355 Score = 333 bits (854), Expect = 5e-96 Identities = 180/365 (49%), Positives = 244/365 (66%), Gaps = 12/365 (3%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 M D+ + + K Y G V+ L I DGEFVVL+GPSGCGKST+LRM+AGLE+ISGG Sbjct: 1 MTDVTIRNVTKRY-GALTVIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGGD 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L +G V+ND PA+ER++A+VFQNYALYPHM+V +N+ F L+ KRP AEID RV + AA Sbjct: 60 LLMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAAA 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L LL+R PRA+SGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLR Q+R +IK L Sbjct: 120 ILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKAL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 HQRL+ TTVYVTHDQ+EAMT+AD++++M +GR+ Q G+P ELY P N+F AGFIG+P+M Sbjct: 180 HQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPSM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300 NFL TV +G L + AL + L V +RP+H+++ Sbjct: 240 NFLPATVAATNGPLL--KTPEGVALPIDGGPTLTGRSEVTYGIRPEHLQL-------GET 290 Query: 301 TCPVSVELVEILGADALLTTRCGDQTLTALVPADRLP-QPGATLTLALDQHELHVFDVES 359 P V +VE G++ L G + + A++ DR+ +PG + L + H+FD + Sbjct: 291 GIPAEVVVVEPTGSETQLYVTVGGREVVAVL-RDRVDVRPGEKIWLTPRKGCAHLFDPNT 349 Query: 360 GENLS 364 G ++ Sbjct: 350 GARIA 354 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: 394 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: 406 Length of database: 355 Length adjustment: 30 Effective length of query: 376 Effective length of database: 325 Effective search space: 122200 Effective search space used: 122200 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