Align Sugar-phosphatase AraL; EC 3.1.3.23; Arabinose operon protein AraL; Phosphoserine phosphatase; EC 3.1.3.3 (uncharacterized)
to candidate WP_020564315.1 A3OW_RS0115245 TIGR01458 family HAD-type hydrolase
Query= curated2:P94526 (272 letters) >NCBI__GCF_000372865.1:WP_020564315.1 Length = 259 Score = 118 bits (295), Expect = 1e-31 Identities = 81/251 (32%), Positives = 123/251 (49%), Gaps = 9/251 (3%) Query: 15 GILIDLDGTVFRGNELIEGAREAIKTLRRMGKKIVFLSNRGNISRAMCRKKLLGAGIETD 74 G L DLDG ++ G +I+GAR AI ++R G + F++N +SRA KL G G + Sbjct: 9 GFLCDLDGVLYVGRNVIDGARAAITEIKRRGYRCRFITNTSTLSRASLHDKLTGLGFDIA 68 Query: 75 VNDIVLSSSVTAAFLKKHYRFSKVWVLGEQGLVDELRLAGVQNASEPKEADWLVI-SLHE 133 ++I+ + L++ WVL E D L + +AD +VI + E Sbjct: 69 GHEIISAPQAALIHLRQLGDPVCHWVLSEDVKQDFRHLRQADD-----KADVVVIGDIGE 123 Query: 134 TLTYDDLNQAFQAAAGGARIIATNKDRSFPNEDGNAIDVAGMIGAIETSAQAKTELVVGK 193 +Y LN+ F GA +IA +K+R + E G +D+ + A+E A K V+GK Sbjct: 124 AWSYSLLNKVFNLLMNGAELIAIHKNRFWQTEHGLQMDIGAFVSALE-YASRKQATVIGK 182 Query: 194 PSWLMAEAACTAMGLSAHECMIIGDSIESDIAMGKLYGMKSALVLTGSAKQG--EQRLYT 251 PS AA + M L IIGD ++SDI G+ G+ LV TG ++ + Sbjct: 183 PSPAFFRAALSEMDLPPENVAIIGDDVDSDIGGGQTAGLTGILVKTGKYRKAYVDDSPIV 242 Query: 252 PDYVLDSIKDV 262 PD + SI D+ Sbjct: 243 PDLTIASIADL 253 Lambda K H 0.317 0.133 0.375 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: 157 Number of extensions: 14 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: 272 Length of database: 259 Length adjustment: 25 Effective length of query: 247 Effective length of database: 234 Effective search space: 57798 Effective search space used: 57798 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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