Align Sugar-phosphatase AraL; EC 3.1.3.23; Arabinose operon protein AraL; Phosphoserine phosphatase; EC 3.1.3.3 (uncharacterized)
to candidate WP_026223793.1 A3OW_RS0120950 haloacid dehalogenase
Query= curated2:P94526 (272 letters) >NCBI__GCF_000372865.1:WP_026223793.1 Length = 273 Score = 123 bits (309), Expect = 4e-33 Identities = 80/261 (30%), Positives = 137/261 (52%), Gaps = 13/261 (4%) Query: 16 ILIDLDGTVFRGNELIEGAREAIKTLRRMGKKIVFLSNRGNISRAMCRKKLLGAGIETDV 75 ++ID+DG ++ G+ + G + +TLR G + + +N ++++ KL G G+ D Sbjct: 10 LIIDMDGVLWHGDRPLPGLADFFQTLRNAGIRFLLATNNASLTQEQYVLKLAGMGVTVDR 69 Query: 76 NDIVLSSSVTAAFLKKHYRFSK--VWVLGEQGLVDELR-----LAGVQNASEPKE---AD 125 ++I+ S+ TA +L +H +K V+V+GE GL L L G+ + K AD Sbjct: 70 DEILTSAMATARYLAEHTEPAKTRVFVVGEAGLTQPLLEHGFILTGLYEVGDGKTSRGAD 129 Query: 126 WLVISLHETLTYDDLNQAFQAAAGGARIIATNKDRSFPNEDGNAIDVAGMIGAIETSAQA 185 +V +TLT+D L A GAR I TN D + P E G + ++ A+ET A Sbjct: 130 VVVCGKDKTLTWDKLATATLNLRAGARFIGTNGDTTLPTERGVVLGNGAILAALET-ASG 188 Query: 186 KTELVVGKPSWLMAEAACTAMGLSAHECMIIGDSIESDIAMGKLYGMKSALVLTG--SAK 243 + V+GKP +M A +G S E + IGD +E+DI G++S +VL+G + + Sbjct: 189 VSPTVIGKPEPIMYRQAMNLLGSSPDETVAIGDRLETDILGAVHAGIRSLMVLSGISTLE 248 Query: 244 QGEQRLYTPDYVLDSIKDVTK 264 ++ Y P +++ I+ +T+ Sbjct: 249 DAQKADYQPTWIMPDIRAITE 269 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: 184 Number of extensions: 10 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: 273 Length adjustment: 25 Effective length of query: 247 Effective length of database: 248 Effective search space: 61256 Effective search space used: 61256 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