Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >MicrobesOnline__882:208681 Length = 349 Score = 196 bits (497), Expect = 1e-54 Identities = 119/355 (33%), Positives = 203/355 (57%), Gaps = 20/355 (5%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M I++ VS+ + G V A+D+V+ +E G+ +LGPSG GK+T +R+IAGL+ ++G Sbjct: 1 MSTIVLDKVSRHW--GDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 + R V + +PP R++ MVFQ++AL+P+LT +NI F L K+ E +KR Sbjct: 59 RILIGGRDVTN-----LPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 ++ +IL + +L P ELSGGQQQRVAL RALV + ++ L+DEP SNLDA++R R Sbjct: 114 LDRAVEILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 ++ +Q LG+T++ V+HD + ++ADR+ ++ G++VQ P ++Y P + S Sbjct: 174 REIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSF 233 Query: 241 IG--EINELEGKVTNEGV-VIGSLRFPVSVSSDR-AIIGIRPEDVKLSKDVIKDDSWILV 296 IG +N + + ++G+ V GS V+ + ++GIRPE ++ I DD W Sbjct: 234 IGTPPMNLVRLQGNDDGIRVAGSRSGRVTCHAGADCMLGIRPEHIR-----IVDDGW--- 285 Query: 297 GKGKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRKDKIKVFE 351 + V+ + Y G ++ E + + G E+ ++ ++ + +F+ Sbjct: 286 -RAVVESVEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFD 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: 277 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: 349 Length adjustment: 29 Effective length of query: 324 Effective length of database: 320 Effective search space: 103680 Effective search space used: 103680 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 17 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