Align Phosphoserine phosphatase RsbU; EC 3.1.3.3; Sigma factor SigB regulation protein RsbU (uncharacterized)
to candidate WP_012470155.1 GLOV_RS10410 phytochrome sensor protein
Query= curated2:P40399 (335 letters) >NCBI__GCF_000020385.1:WP_012470155.1 Length = 1082 Score = 122 bits (306), Expect = 4e-32 Identities = 74/243 (30%), Positives = 129/243 (53%), Gaps = 10/243 (4%) Query: 97 IKSEIEIAANVQQTLLGTKVPQEEALDIGAISVPAKQMSGDYYHFVK-DKESINIAIADV 155 +K ++EIA +Q +LL P +++ PA + GDYY F K D +I++ IADV Sbjct: 840 VKRDMEIAEQIQLSLLPASPPVLFGIELAGRCYPAAHVGGDYYDFFKRDDHTIDLLIADV 899 Query: 156 IGKGIPAALCMSMIKYAMDSLPETGIHPSQVLKNLN-RVVEQNVDASMFITMFYANYNMD 214 G + AAL M+ ++ + + + PS +L LN ++ E A +FITMFYA Y+ Sbjct: 900 SGHSVGAALIMAEVRTLLRAHSSRAVSPSSILGVLNSQLYEDLTRAELFITMFYARYSAA 959 Query: 215 KHQFTYASAGHEPGFYYSQKDNTFYDLEAKGLVLGISQDYDYKQFDQHLEKGDMIVLFSD 274 + +YA+AGH + Q + + +L+A+GL+LGI +++ +L++GD ++ ++D Sbjct: 960 TGRLSYANAGHNKPLIHRQGEQSCIELDAEGLILGIKPSMIFEERSINLQQGDTLLFYTD 1019 Query: 275 GVTECRTENGFLERPDLQKLIEEHMCSSAQEMVKNIYDSLLKL-----QDFQLHDDFTLI 329 G+ E G L + +H+ + V I DS +L Q L DD +++ Sbjct: 1020 GIPEATNRTGELLGTG---QVCQHLTLQSTLPVDTIADSFFELVKEYSQSTTLQDDVSMV 1076 Query: 330 VLR 332 V++ Sbjct: 1077 VMK 1079 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: 622 Number of extensions: 30 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: 1082 Length adjustment: 37 Effective length of query: 298 Effective length of database: 1045 Effective search space: 311410 Effective search space used: 311410 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: 53 (25.0 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