Align Phosphoserine phosphatase RsbU; EC 3.1.3.3; Sigma factor SigB regulation protein RsbU (uncharacterized)
to candidate WP_012411420.1 NPUN_RS25970 fused response regulator/phosphatase
Query= curated2:P40399 (335 letters) >NCBI__GCF_000020025.1:WP_012411420.1 Length = 557 Score = 103 bits (256), Expect = 1e-26 Identities = 66/205 (32%), Positives = 111/205 (54%), Gaps = 9/205 (4%) Query: 87 HQTLRGIQQEIKSEIEIAANVQQTLLGTKVPQEEALDIGAISVPAKQMSGDYYH-FVKDK 145 +Q L+ QQ+I +E+E+A +Q LL +P + + + A PA+++ GD++ FV K Sbjct: 290 YQRLQEKQQQIHNELEVARQIQYNLLRQSLPDIKGVKVQACCYPAREVGGDFFEVFVHPK 349 Query: 146 ESINIAIADVIGKGIPAALCMSMIKYAM--DSLPETGIHPSQVLKNLNRVVEQN-VDASM 202 + +A+ DV GKG+PAAL M+ I + + ET P+ V++NLN + ++ + + Sbjct: 350 GDLWLAVGDVSGKGVPAALFMASIISVLRRELSQETPAEPNVVMQNLNHALSEDLISNNY 409 Query: 203 FITMFYANYNMDKHQFTYASAGHEPGFYYSQK----DNTFYDLEAKGLVLGISQDYDYKQ 258 FIT+ A Y + Y +AGH +S++ DN Y L+ + + LGI + + Sbjct: 410 FITLVLACYTPSTKELVYTNAGHIYPLLWSRQDALGDNPNY-LKVRSVPLGILPKWQAQS 468 Query: 259 FDQHLEKGDMIVLFSDGVTECRTEN 283 L GD ++L SDG+TE N Sbjct: 469 GRLVLATGDTLLLASDGITEATISN 493 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: 404 Number of extensions: 23 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: 557 Length adjustment: 32 Effective length of query: 303 Effective length of database: 525 Effective search space: 159075 Effective search space used: 159075 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: 51 (24.3 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