Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_069332842.1 C8J29_RS18660 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_003046325.1:WP_069332842.1 Length = 352 Score = 202 bits (513), Expect = 1e-56 Identities = 129/346 (37%), Positives = 199/346 (57%), Gaps = 36/346 (10%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M + V+NV K + + +++++ +I +GE +GPSG GK+T +R+IAGL+ G Sbjct: 1 MSTVHVRNVKKSYSD--LTVIEDLSFDIHDGEFMVFVGPSGCGKSTLLRMIAGLESFQGG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 E+ +R+V NG VP DR I MVFQ +ALYP++T +N++F L K EI +R Sbjct: 59 EVAIGERVV--NG---VPARDRNIAMVFQDYALYPHMTIRDNMSFGLKMRKTPTAEIERR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V A+IL I H+L+ PR LSGGQ+QRVA+ RA+V++P + L DEP SNLDA++R R Sbjct: 114 VAAAAEILQIGHLLDRKPRALSGGQRQRVAMGRAIVREPDVFLFDEPLSNLDAKLRVEVR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 +K + +RLG T++ V+HD + +ADR+ VL G + Q+G P++LY P + VA Sbjct: 174 TEIKRLHARLGATMIYVTHDQVEAMTMADRIVVLKGGAVEQIGTPQELYREPRTRFVAGF 233 Query: 241 IGE--INELEGKVTNE-GVVIGSLRFPVS--VSSDRAI---IGIRPEDVKLSK------- 285 IG +N ++ + ++ R PV S RA+ IGIRPE V+L+ Sbjct: 234 IGSPGMNFAPARIEGDVATLVTGDRVPVRRLSSGTRAVQGEIGIRPEHVQLADPHGPGVE 293 Query: 286 ---DVIKD---DSWILVGKGKV--------KVIGYQGGLFRITITP 317 DV++ D+ + V G+ ++I +G R++ TP Sbjct: 294 TLVDVVEPLGADTLVAVRLGEAQLMVRLPGEIIPAEGDRLRLSFTP 339 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: 265 Number of extensions: 13 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: 353 Length of database: 352 Length adjustment: 29 Effective length of query: 324 Effective length of database: 323 Effective search space: 104652 Effective search space used: 104652 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 Sep 24 2021. 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