Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 198 bits (504), Expect = 2e-55 Identities = 113/289 (39%), Positives = 180/289 (62%), Gaps = 13/289 (4%) Query: 2 VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 ++I +++V K + G+V A+ V+ ++E G+ ILGPSG GKTT +R+IAGL+ ++G Sbjct: 1 MQIEIRDVRKDY--GRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGT 58 Query: 62 LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121 ++ +A +PP R I MVFQ++AL+P+L ENI F L K+ +EI +R+ Sbjct: 59 IH-----IAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRL 113 Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181 + V +L + L+ P ELSGG QQRVAL RA++ + + L+DEP SNLDA++R+S R Sbjct: 114 KRVVDLLGLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRR 173 Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241 + +Q RLG+T++ V+HD + +ADR+ ++ G++VQ PE+ Y+ P + VA I Sbjct: 174 EICSLQRRLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFI 233 Query: 242 G--EINELEGKVTNEGVVI---GSLRFPVSVSSDRAIIGIRPEDVKLSK 285 G +N + T G + G L FP + DR + GIRPE+++L++ Sbjct: 234 GTPPMNIVPLCPTQGGAALEPGGRLLFP-GMDPDRYLFGIRPENLRLAE 281 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: 294 Number of extensions: 12 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: 365 Length adjustment: 29 Effective length of query: 324 Effective length of database: 336 Effective search space: 108864 Effective search space used: 108864 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