Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate HSERO_RS22645 HSERO_RS22645 lipase
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__HerbieS:HSERO_RS22645 Length = 362 Score = 197 bits (500), Expect = 5e-55 Identities = 108/277 (38%), Positives = 168/277 (60%), Gaps = 13/277 (4%) Query: 21 LDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLI-VPP 79 L V++ ++ GE +LGPSG+GKTT +R +AGL+ P G + R V + +P Sbjct: 23 LKGVSMELQRGEVVALLGPSGSGKTTLLRAVAGLESPKAGAIDIGKRRVFDGARNFEMPA 82 Query: 80 EDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPR 139 E+R +G+VFQ++AL+P+ T +N+A+ L K EI RV+ V L + H+ +P Sbjct: 83 EERNLGLVFQSYALWPHKTVADNVAYGLKLRKTPSGEIATRVKAVLSQLGLGHLGERYPH 142 Query: 140 ELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSH 199 +LSGGQQQRVA+ARALV +P ++LLDEP SNLDA++R+ ARA ++E+ RLG++ L+V+H Sbjct: 143 QLSGGQQQRVAIARALVYNPQVILLDEPLSNLDAKLREEARAFLRELIVRLGLSALMVTH 202 Query: 200 DPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVTNE----- 254 D + AI+DR+ +L G++ Q G P+ +Y P ++ A +G N+L +V + Sbjct: 203 DQGEAMAISDRILLLNNGRIEQQGTPQSMYQAPNTLFTAEFMGSNNKLAAEVLSREGERV 262 Query: 255 ------GVVIGSLRFPVSVSSDRAIIG-IRPEDVKLS 284 G + +LR V + G IR E V++S Sbjct: 263 TVKLDGGTAVATLRGRSDVRPGEQLTGIIRVEQVRIS 299 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: 289 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 353 Length of database: 362 Length adjustment: 29 Effective length of query: 324 Effective length of database: 333 Effective search space: 107892 Effective search space used: 107892 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