Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_013136651.1 ARNIT_RS14360 phosphoserine phosphatase SerB
Query= SwissProt::Q7M7U5 (206 letters) >NCBI__GCF_000092245.1:WP_013136651.1 Length = 206 Score = 262 bits (669), Expect = 4e-75 Identities = 132/206 (64%), Positives = 163/206 (79%) Query: 1 MKLAVFDFDSTLMDGETIDILAHHYGVGEEVDRITKGAMEGGLDFYESLKRRVALLRGME 60 MKLAVFDFDSTLMDGETID LA G+ E+V +IT+ AM G LDF+ESL RVALL+G+E Sbjct: 1 MKLAVFDFDSTLMDGETIDFLAKPLGLEEKVAKITEEAMAGRLDFFESLIERVALLKGLE 60 Query: 61 LSLVEEICANLTLMEGAKELIQELKRRDYKVVVFSGGFKNATSKARETLGLDADFSNILH 120 SL +IC +L LM GA E + +LK + YKVV FSGGF+ T+ A+E LGLDADFSNILH Sbjct: 61 NSLAVDICKSLPLMPGAMETVAKLKEKGYKVVCFSGGFRIGTTPAKEKLGLDADFSNILH 120 Query: 121 HKEGKLTGEVGGEMMFGSSKGEMMQTLQRLLGISPELTMAVGDGANDASMFPFAKQRVAF 180 HK G LTG VGG+MMFG SKG+M+Q +Q +LG+S E T+ GDGAND SMFP+A +RVAF Sbjct: 121 HKNGILTGLVGGDMMFGFSKGDMIQRVQAMLGVSKENTLVAGDGANDVSMFPYADKRVAF 180 Query: 181 CAKPILREKANIIIEKKDLREILAHL 206 CAK IL+++ANII++ KDL +IL H+ Sbjct: 181 CAKDILKKEANIIVDTKDLTQILEHI 206 Lambda K H 0.320 0.137 0.382 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: 186 Number of extensions: 2 Number of successful extensions: 1 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: 206 Length of database: 206 Length adjustment: 21 Effective length of query: 185 Effective length of database: 185 Effective search space: 34225 Effective search space used: 34225 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: 45 (21.9 bits)
Align candidate WP_013136651.1 ARNIT_RS14360 (phosphoserine phosphatase SerB)
to HMM TIGR00338 (serB: phosphoserine phosphatase SerB (EC 3.1.3.3))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00338.hmm # target sequence database: /tmp/gapView.21792.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00338 [M=219] Accession: TIGR00338 Description: serB: phosphoserine phosphatase SerB Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-75 239.6 1.0 1.6e-75 239.5 1.0 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013136651.1 ARNIT_RS14360 phosphoserine phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013136651.1 ARNIT_RS14360 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 239.5 1.0 1.6e-75 1.6e-75 15 218 .. 2 205 .. 1 206 [] 0.99 Alignments for each domain: == domain 1 score: 239.5 bits; conditional E-value: 1.6e-75 TIGR00338 15 klvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkveek 83 kl+vfD+Dstl++ E+Id +ak G ee+V++iTe+Am g ldF esl eRv+llkgl+ +l+ ++++ lcl|NCBI__GCF_000092245.1:WP_013136651.1 2 KLAVFDFDSTLMDGETIDFLAKPLGLEEKVAKITEEAMAGRLDFFESLIERVALLKGLENSLAVDICKS 70 89******************************************************************* PP TIGR00338 84 lelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesa 152 l+l++G+ e+v kLkekgykv+++SGgF++ + kekLglda f+N L+ ++g ltG v g+++ + lcl|NCBI__GCF_000092245.1:WP_013136651.1 71 LPLMPGAMETVAKLKEKGYKVVCFSGGFRIGTTPAKEKLGLDADFSNILHHKNGILTGLVGGDMMFGFS 139 ********************************************************************* PP TIGR00338 153 kaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 k++++++++ g+s+e+t++ GDGanD+sm++ A+ +af+ak +lk++a+i +++kdlt+ile lcl|NCBI__GCF_000092245.1:WP_013136651.1 140 KGDMIQRVQAMLGVSKENTLVAGDGANDVSMFPYADKRVAFCAKDILKKEANIIVDTKDLTQILEH 205 ***************************************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (206 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.23 // [ok]
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