Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_010529737.1 ON01_RS04145 HAD family hydrolase
Query= SwissProt::P94512 (260 letters) >NCBI__GCF_000224785.1:WP_010529737.1 Length = 261 Score = 278 bits (710), Expect = 1e-79 Identities = 136/260 (52%), Positives = 178/260 (68%), Gaps = 2/260 (0%) Query: 1 MKAVFFDLDDTLLWDEKSVRTTFAETCLQAEKKYGLAPEEFEAAVREAARELYMSYETYP 60 +K + FDLDDTL+WDEKS+ F C A +K P E +RE A+ L+ SY+TY Sbjct: 2 LKTIMFDLDDTLIWDEKSIDEAFKAACRLAAQKSDADPNLLETKIREHAQSLFASYDTYE 61 Query: 61 YTVMIGINPFEGLWSNFSEPISEGFQKLNKIVPEYRRNAWTNGLKALGIDDPAYGEYLGE 120 +T MIGI+PFEGLW F + E F++LN+I P YR+ +W LK G+DDP G L E Sbjct: 62 FTEMIGISPFEGLWGEFDDE-GESFRQLNEIAPIYRKESWAKALKEAGVDDPQLGLELAE 120 Query: 121 FFAAERRKRPFVYDETFAVLDQLKGKYELLLLTNGDPSLQKEKLAGVPELAPYFNEIVIS 180 F ERRK +V++ETF VL++L+G Y+LL+LTNG P LQ+ KL PE+ PYF+ IVIS Sbjct: 121 AFQEERRKNQYVFEETFDVLNKLRGDYQLLMLTNGSPDLQQTKLNITPEIKPYFDHIVIS 180 Query: 181 GAFGKGKPDVSIFEHCLKLMNIEKDDAIMVGDNLNTDILGASRAGIKTVWINRTDKKNET 240 GAFGKGKPD SIF+H L L++ EKD+ +MVGDN N+DILGASRAG+++VWIN K Sbjct: 181 GAFGKGKPDPSIFDHALSLLSAEKDEVLMVGDNPNSDILGASRAGVQSVWINH-QKYEIG 239 Query: 241 DVKPDYIISSLHDLFPILEK 260 D P + I+ L +L +L K Sbjct: 240 DNNPTFEITRLEELLEVLAK 259 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: 262 Number of extensions: 8 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: 260 Length of database: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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: 47 (22.7 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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