Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_010875848.1 MTH_RS00945 haloacid dehalogenase
Query= SwissProt::P94512 (260 letters) >NCBI__GCF_000008645.1:WP_010875848.1 Length = 226 Score = 66.6 bits (161), Expect = 4e-16 Identities = 73/244 (29%), Positives = 105/244 (43%), Gaps = 44/244 (18%) Query: 1 MKAVFFDLDDTLLWDEKSVRTTFAETCLQAEKKYGL--APEEFEAAVREAARELYMSYET 58 +KAVFFD+DDTL +D + L GL EE +RE E +Y+ Sbjct: 2 LKAVFFDIDDTL-YDTSGFAKLARKAALNVMIDAGLPLTQEEAYKLLREIISEKGSNYDR 60 Query: 59 YPYTVMIGINPFEGLWSNFSEPISEGFQKLNKIVPEYRRNAWTNGLKALGIDDPAYGEYL 118 + F L K V + L ALG+ Y Sbjct: 61 H-------------------------FNVLTKTVFGEEKPL----LIALGMIT-----YH 86 Query: 119 GEFFAAERRKRPFVYDETFAVLDQLKGK-YELLLLTNGDPSLQKEKLAGVPELAPYFNEI 177 FA RPF T + L LK K Y L +++NG Q EKL + + +F+E+ Sbjct: 87 NVKFAL---LRPF--PNTTSTLIDLKSKGYRLGVISNGITIKQWEKLIRLG-IHHFFDEV 140 Query: 178 VISGAFGKGKPDVSIFEHCLKLMNIEKDDAIMVGDNLNTDILGASRAGIKTVWINRTDKK 237 V S G KP++ IFE L+ M + + ++MVG+ N DILGA+ AG+ + +N + Sbjct: 141 VTSDEVGFEKPNIRIFEEALRRMGCKPERSVMVGNKFNEDILGATNAGMSAILVNSELTE 200 Query: 238 NETD 241 E D Sbjct: 201 AERD 204 Lambda K H 0.318 0.138 0.409 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: 157 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 226 Length adjustment: 23 Effective length of query: 237 Effective length of database: 203 Effective search space: 48111 Effective search space used: 48111 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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