Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 202 bits (515), Expect = 9e-57 Identities = 119/297 (40%), Positives = 181/297 (60%), Gaps = 22/297 (7%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M I + V+K FKK VV + + + + E ++GPSG GK+T +R+IAGL+ ++G Sbjct: 1 MAEIKLDQVNKRFKKNWVVR--DFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 E+ R+V VPP+DR I MVFQ++ALYP++ ++N+AF L N + ++EI +R Sbjct: 59 EISIGGRVVNH-----VPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V++ A+IL I +L P +LSGGQ+QRVA+ RA+V+DP L DEP SNLDA++R R Sbjct: 114 VKQAAEILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 A + ++ RL T++ V+HD + +ADR+ V+ GK++QVG P ++Y+ P + VA Sbjct: 174 AELAKLHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGF 233 Query: 241 IG--EINELEGKVTNEG--VVIGSLRFPVSVSSDRA-----------IIGIRPEDVK 282 IG +N L+ ++ E + + F + V RA I GIRPEDVK Sbjct: 234 IGSPSMNFLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVK 290 Lambda K H 0.319 0.139 0.390 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: 310 Number of extensions: 13 Number of successful extensions: 3 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: 353 Length of database: 368 Length adjustment: 29 Effective length of query: 324 Effective length of database: 339 Effective search space: 109836 Effective search space used: 109836 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