Align Phosphoserine phosphatase RsbU; EC 3.1.3.3; Sigma factor SigB regulation protein RsbU (uncharacterized)
to candidate WP_012974383.1 AZL_RS09335 sigma-B regulation protein
Query= curated2:P40399 (335 letters) >NCBI__GCF_000010725.1:WP_012974383.1 Length = 750 Score = 116 bits (290), Expect = 2e-30 Identities = 72/239 (30%), Positives = 120/239 (50%), Gaps = 3/239 (1%) Query: 97 IKSEIEIAANVQQTLLGTKVPQEEALDIGAISVPAKQMSGDYYHFVKDKES-INIAIADV 155 ++ E+EIA +Q T+L P LDI A +PAK++ GD+Y F +S + + IADV Sbjct: 479 LQQELEIARTMQLTILPQVFPDLPELDIAARMIPAKEVGGDFYDFFPISDSKVALVIADV 538 Query: 156 IGKGIPAALCMSMIKYAMDSLPETGIHPSQVLKNLNRVVEQNVDASMFITMFYANYNMDK 215 GKGIPAA M + + + ++ E+G+ P++ L+ +N ++ + MF+T+FY ++ Sbjct: 539 SGKGIPAAFFMLITRTMLRAIAESGVGPAETLRRVNNLLAAENEQMMFVTVFYGELDLRT 598 Query: 216 HQFTYASAGHEPGFYYSQKDNTFYDLEAKGLVLGISQDYDYKQFDQHLEKGDMIVLFSDG 275 Y++ GH P + G+ L D + + L+ G+M+VLF+DG Sbjct: 599 GVLCYSNGGHNPPLRMTASGAVRELERIPGIALAAMPDMPFGERSVTLDTGEMVVLFTDG 658 Query: 276 VTEC-RTENGFLERPDLQKLIEEHMCSSAQEMVKNIYDSLLKL-QDFQLHDDFTLIVLR 332 VTE E P L + +SA++ + + L + DD T +VLR Sbjct: 659 VTEAFDGEEVMYGDPRLAAAVAGQASASARDGLDGVLADLSRFTAGAPQSDDITCLVLR 717 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: 445 Number of extensions: 24 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: 335 Length of database: 750 Length adjustment: 34 Effective length of query: 301 Effective length of database: 716 Effective search space: 215516 Effective search space used: 215516 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