Align Phosphoserine phosphatase RsbU; EC 3.1.3.3; Sigma factor SigB regulation protein RsbU (uncharacterized)
to candidate WP_027720854.1 H589_RS0104085 HAMP domain-containing protein
Query= curated2:P40399 (335 letters) >NCBI__GCF_000425265.1:WP_027720854.1 Length = 710 Score = 123 bits (309), Expect = 1e-32 Identities = 78/249 (31%), Positives = 133/249 (53%), Gaps = 13/249 (5%) Query: 96 EIKSEIEIAANVQQTLLGTKVPQEEALDIGAISVPAKQMSGDYYHFVK---DKESINIAI 152 EIKS +++A VQ LL P DI S ++ GDY+ +++ D E++ IAI Sbjct: 458 EIKSALDVAMEVQTNLLPQHSPHIRGYDIYGESRYCDELGGDYFDYIRPDRDGENMRIAI 517 Query: 153 ADVIGKGIPAALCMSMIKYAMDSLPETGIHPSQVLKNLNRVVEQNV-DASMFITMFYANY 211 DV G G+PAA+ M ++ + + +G +++ ++N +V Q+ F+TM Sbjct: 518 GDVSGHGVPAAMLMGSVRGYLRARTLSGGQLDEIISDVNSLVAQDTYKTGQFMTMLMVEL 577 Query: 212 NMDKHQFTYASAGHEPGFYYSQKDNTFYDLEAKGLVLGISQDYDYKQ-FDQHLEKGDMIV 270 + K + + AGHEPG + + F LE +G+VLG +D +Y + LE+G ++V Sbjct: 578 DPAKSELRWVRAGHEPGLIFDPAEKDFIRLEGEGIVLGAFEDVEYSENCCADLEEGQILV 637 Query: 271 LFSDGVTECRTENG-FLERPDLQKLIEEHMCSSAQEMVKNIYDSLLKLQDF----QLHDD 325 L +DG+ E +NG F + L LI SSA+ +V I+ + +QDF + DD Sbjct: 638 LGTDGIWEASNKNGEFFGKQRLWDLINLKKNSSAESIVSGIFAA---VQDFTGRSKQEDD 694 Query: 326 FTLIVLRRK 334 T++V++++ Sbjct: 695 LTVVVIKKE 703 Lambda K H 0.320 0.136 0.385 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: 472 Number of extensions: 27 Number of successful extensions: 4 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: 335 Length of database: 710 Length adjustment: 34 Effective length of query: 301 Effective length of database: 676 Effective search space: 203476 Effective search space used: 203476 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 (21.8 bits) S2: 52 (24.6 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