Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_013645645.1 METBO_RS10255 phosphoserine phosphatase SerB
Query= SwissProt::Q58989 (211 letters) >NCBI__GCF_000191585.1:WP_013645645.1 Length = 600 Score = 219 bits (558), Expect = 8e-62 Identities = 109/203 (53%), Positives = 153/203 (75%), Gaps = 1/203 (0%) Query: 6 KLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPI 65 KLI FD D+ L++ E IDEI + GVE ++ +ITK+AMEG L+FE SL KRV+LLK + Sbjct: 3 KLIAFDLDNVLIDGEAIDEIGKLMGVESKISEITKKAMEGDLDFETSLNKRVALLKGASV 62 Query: 66 EKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIV 125 E + + + ++ EGAEETI ELK RGY +A ++G F+I ++K+ LGLDYAF+N L Sbjct: 63 EDIREVVFKMPFMEGAEETIAELKKRGYKIATITGSFEIVAERMKDTLGLDYAFSNILHE 122 Query: 126 KDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFC 185 ++GKLTG V G ++K +K E+L++I ++E I E+T AVGDGAND+SM ++AGL IAF Sbjct: 123 EEGKLTGQVSGPLVK-GSKAEVLKEIMEMENIIAEETAAVGDGANDVSMLEEAGLGIAFN 181 Query: 186 AKPILKEKADICIEKRDLREILK 208 AKP+LKEKAD+ +EKRDL+E+L+ Sbjct: 182 AKPVLKEKADVIVEKRDLKELLE 204 Lambda K H 0.314 0.136 0.358 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: 489 Number of extensions: 31 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: 211 Length of database: 600 Length adjustment: 29 Effective length of query: 182 Effective length of database: 571 Effective search space: 103922 Effective search space used: 103922 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_013645645.1 METBO_RS10255 (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.26125.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-81 256.7 8.1 8.9e-81 256.7 8.1 1.7 2 lcl|NCBI__GCF_000191585.1:WP_013645645.1 METBO_RS10255 phosphoserine phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000191585.1:WP_013645645.1 METBO_RS10255 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.7 8.1 8.9e-81 8.9e-81 14 218 .. 2 205 .. 1 206 [. 0.99 2 ? -3.8 0.5 0.42 0.42 69 98 .. 429 458 .. 421 468 .. 0.57 Alignments for each domain: == domain 1 score: 256.7 bits; conditional E-value: 8.9e-81 TIGR00338 14 kklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkvee 82 kl+ fDlD++li+ E+Idei+kl+Gve ++seiT++Am+g+ldF+ sl++Rv+llkg++ve++++v lcl|NCBI__GCF_000191585.1:WP_013645645.1 2 IKLIAFDLDNVLIDGEAIDEIGKLMGVESKISEITKKAMEGDLDFETSLNKRVALLKGASVEDIREVVF 70 589****************************************************************** PP TIGR00338 83 klelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdes 151 k++ +eG+ee++ +Lk++gyk+a i G+F++vae++k+ Lgld++f+N L+ e+gkltG+v+g++v+ s lcl|NCBI__GCF_000191585.1:WP_013645645.1 71 KMPFMEGAEETIAELKKRGYKIATITGSFEIVAERMKDTLGLDYAFSNILHEEEGKLTGQVSGPLVKGS 139 ********************************************************************* PP TIGR00338 152 akaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 ka++l++++e e+i e+t avGDGanD+sm+++Aglgiafnakpvlkekad+ +ek+dl+++le+ lcl|NCBI__GCF_000191585.1:WP_013645645.1 140 -KAEVLKEIMEMENIIAEETAAVGDGANDVSMLEEAGLGIAFNAKPVLKEKADVIVEKRDLKELLEI 205 .***************************************************************987 PP == domain 2 score: -3.8 bits; conditional E-value: 0.42 TIGR00338 69 lkglpvellkkveeklelteGveelvkkLk 98 + ++ + ++ ++++ el++ v++l k+L lcl|NCBI__GCF_000191585.1:WP_013645645.1 429 IEKTIETKVLDMRKENELVKKVQDLSKTLS 458 444444455555555555555555555554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (600 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: 15.82 // [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