Align Phosphoserine phosphatase ThrH; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate WP_086508245.1 BZY95_RS01555 bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH
Query= SwissProt::Q9I2Y2 (205 letters) >NCBI__GCF_002151265.1:WP_086508245.1 Length = 198 Score = 134 bits (338), Expect = 9e-37 Identities = 69/191 (36%), Positives = 106/191 (55%) Query: 1 MEIACLDLEGVLVPEIWIAFAEKTGIDALKATTRDIPDYDVLMKQRLRILDEHGLKLGDI 60 M+IAC+DLEGVL+PE+W A++TGI +L TTR+ P+Y LM+ R+ L + L L + Sbjct: 1 MKIACIDLEGVLIPELWPHIAQETGIASLSLTTREFPNYPELMRTRIETLRRNSLTLATL 60 Query: 61 QEVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSD 120 Q + A + P A EF+ L++ + V I+SD F+E P++ LG P + CH+ ID + Sbjct: 61 QSITANITPFPDAQEFLHRLQKEYDVSIISDCFHELIGPILNTLGSPKIKCHRFNIDPAG 120 Query: 121 RVVGYQLRQKDPKRQSVIAFKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPENVIREFP 180 V + K V + +V+A GD+YND ML AH G L + P Sbjct: 121 YVDHCVYFNRQGKETHVAQALTEGAKVLAVGDAYNDLNMLRLAHHGFLIRPSNSTRAAAP 180 Query: 181 QFPAVHTYEDL 191 + P V++ ++ Sbjct: 181 ELPVVNSLSEV 191 Lambda K H 0.323 0.140 0.408 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: 116 Number of extensions: 3 Number of successful extensions: 2 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: 205 Length of database: 198 Length adjustment: 21 Effective length of query: 184 Effective length of database: 177 Effective search space: 32568 Effective search space used: 32568 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 45 (21.9 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