Align Sugar-phosphatase AraL; EC 3.1.3.23; Arabinose operon protein AraL; Phosphoserine phosphatase; EC 3.1.3.3 (uncharacterized)
to candidate WP_022947974.1 H035_RS0105375 TIGR01458 family HAD-type hydrolase
Query= curated2:P94526 (272 letters) >NCBI__GCF_000421465.1:WP_022947974.1 Length = 267 Score = 122 bits (305), Expect = 1e-32 Identities = 81/257 (31%), Positives = 135/257 (52%), Gaps = 9/257 (3%) Query: 12 SPAGILIDLDGTVFRGNELIEGAREAIKTLRRMGKKIVFLSNRGNISRAMCRKKLLGAGI 71 S G L DLDG ++ G ++IEGAREA++ +R G F++N +S A + KL G Sbjct: 13 SVRGFLFDLDGVLYVGGQVIEGAREALECIREAGYGCRFITNTSTLSLASLQGKLNALGF 72 Query: 72 ETDVNDIVLSSSVTAAFLKKHYRFSKVWVLGEQGLVDELRLAGVQNASEPKEADWLVI-S 130 + +I+ + +L+ S L L ++++ AD++V+ Sbjct: 73 DIPREEIISAPQAVLLYLQ-----SCDDPLCHLLLAEDVKCDFAAFRQSDTHADYVVVGD 127 Query: 131 LHETLTYDDLNQAFQAAAGGARIIATNKDRSFPNEDGNAIDVAGMIGAIETSAQAKTELV 190 + E Y LN+AF+ GA +IA +K+R + E+G +D+ G + A+E A AK + Sbjct: 128 IGERWNYAVLNRAFRLLIEGAALIAVHKNRFWRTEEGLQMDLGGFVAALE-YAGAKQAQI 186 Query: 191 VGKPSWLMAEAACTAMGLSAHECMIIGDSIESDIAMGKLYGMKSALVLTGSAKQGEQRLY 250 +GKPS E A +GL A + I+GD I++DI G+ G+ LV TG ++ R Sbjct: 187 IGKPSPAFFELALQDLGLPADQVAIVGDDIDADIGGGQASGLSGILVKTGKYREDYVRAV 246 Query: 251 T--PDYVLDSIKDVTKL 265 + PD ++DSI+D+ ++ Sbjct: 247 SVRPDGIIDSIRDLPQV 263 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: 170 Number of extensions: 9 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: 267 Length adjustment: 25 Effective length of query: 247 Effective length of database: 242 Effective search space: 59774 Effective search space used: 59774 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