Align Sugar-phosphatase AraL; EC 3.1.3.23; Arabinose operon protein AraL; Phosphoserine phosphatase; EC 3.1.3.3 (uncharacterized)
to candidate WP_013682766.1 ARCVE_RS00230 haloacid dehalogenase
Query= curated2:P94526 (272 letters) >NCBI__GCF_000194625.1:WP_013682766.1 Length = 263 Score = 155 bits (392), Expect = 8e-43 Identities = 85/251 (33%), Positives = 145/251 (57%), Gaps = 7/251 (2%) Query: 15 GILIDLDGTVFRGNELIEGAREAIKTLRRMGKKIVFLSNRGNISRAMCRKKLLGAGIETD 74 G ++D+DG + RG I EA+K LR GKK+VF+SN SR + + G++ Sbjct: 9 GFILDIDGVIGRGETPIPEGVEAVKKLREFGKKLVFVSNNSTRSRTIMIDRFQRFGLDVH 68 Query: 75 VNDIVLSSSVTAAFLKKHYRFSKVWVLGEQGLVDELRLAGVQNASEPKEADWLVISLHET 134 ++++L++ TA +LK+ +K++ GE+GL++EL LAG + ++A++LV+ + Sbjct: 69 EDEMLLATFATARYLKREAGKAKIFTTGEKGLIEELELAG-HEIVDYRDAEYLVVGSNRG 127 Query: 135 LTYDDLNQAFQAAAGGARIIATNKDRSFPNEDGNAIDVAGMIGAIETSAQAKTELVVGKP 194 + ++ + +A + G R IATN DR FP EDG +IG++ ++V+GKP Sbjct: 128 INFEIMTKALRCCLAGTRYIATNPDRIFPAEDGPIPGTGMIIGSLYWMTGRMPDVVIGKP 187 Query: 195 SWLMAEAACTAMGLSAHECMIIGDSIESDIAMGKLYGMKSALVLTG-SAKQGEQRLY--- 250 S ++ E A +GL A E +++GD I+ D+ GK G + LVL+G + K+ +++ Sbjct: 188 SKVIMEEALDILGLKADEVVVVGDQIDIDVKAGKAIGATTLLVLSGVTTKENLEQMIERH 247 Query: 251 --TPDYVLDSI 259 PDYVLD + Sbjct: 248 GEKPDYVLDHL 258 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: 203 Number of extensions: 11 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: 272 Length of database: 263 Length adjustment: 25 Effective length of query: 247 Effective length of database: 238 Effective search space: 58786 Effective search space used: 58786 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