Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate 6936796 Sama_0978 phosphoserine phosphatase (RefSeq)
Query= SwissProt::Q5QXU4 (220 letters) >FitnessBrowser__SB2B:6936796 Length = 316 Score = 170 bits (431), Expect = 2e-47 Identities = 90/198 (45%), Positives = 127/198 (64%) Query: 6 GLIVFDMDSTLIHIECIDEIARLNNRYTKVSAITEAAMRGEIDFAESLTQRVACLEGIKE 65 GL+V DMDST I IECIDE+A + V+ +TE AM+GE+DF +SL QRVA L G Sbjct: 110 GLLVMDMDSTAIKIECIDELAAMAGVGEAVAEVTERAMQGELDFKQSLRQRVAKLAGADA 169 Query: 66 SDLESLFSPIPFNPGAKELIQALQAAGWKTALVSGGFTWFANRVQAALNLDAVVANQLEV 125 +++L + +P G E++ L+ GWK + SGGFT F ++A L LDA AN+L + Sbjct: 170 GIIDTLCARLPLMDGLTEMLAELKGHGWKLVVASGGFTPFVGHLKATLGLDAAFANELVI 229 Query: 126 ADGCLTGKVLGDIVDAQVKAEQLQQLAGHWNIPPDRTVAVGDGANDGLMLKAAAVGIAFN 185 ADG L G+V G +VDA KA+ + +L + I + +A+GDGAND M++ A GIAF+ Sbjct: 230 ADGKLVGEVTGTVVDANFKADVVSRLGDEYGIKDGQRLAIGDGANDIPMVQRADFGIAFH 289 Query: 186 AKPALQAIADYSVNSNNL 203 AKP L A AD +++ +L Sbjct: 290 AKPKLAAAADARIHTLDL 307 Lambda K H 0.318 0.134 0.384 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: 187 Number of extensions: 7 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: 220 Length of database: 316 Length adjustment: 25 Effective length of query: 195 Effective length of database: 291 Effective search space: 56745 Effective search space used: 56745 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)
Align candidate 6936796 Sama_0978 (phosphoserine phosphatase (RefSeq))
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.29599.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-81 259.1 0.0 2.1e-81 258.7 0.0 1.1 1 lcl|FitnessBrowser__SB2B:6936796 Sama_0978 phosphoserine phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936796 Sama_0978 phosphoserine phosphatase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.7 0.0 2.1e-81 2.1e-81 9 215 .. 104 310 .. 97 314 .. 0.97 Alignments for each domain: == domain 1 score: 258.7 bits; conditional E-value: 2.1e-81 TIGR00338 9 kllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkveekle 85 + l++ +l+v+D+Dst+i++E+Ide+a++aGv+e+V+e+TerAm+geldFk+slr+Rv++l g+++ +++ + +l+ lcl|FitnessBrowser__SB2B:6936796 104 PSLRHPGLLVMDMDSTAIKIECIDELAAMAGVGEAVAEVTERAMQGELDFKQSLRQRVAKLAGADAGIIDTLCARLP 180 5678899********************************************************************** PP TIGR00338 86 lteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllklle 162 l++G++e+ +Lk +g+k++v+SGgF+ ++++lk+ Lglda+faN+L + dgkl G+v+g++vd++ ka+++ +l lcl|FitnessBrowser__SB2B:6936796 181 LMDGLTEMLAELKGHGWKLVVASGGFTPFVGHLKATLGLDAAFANELVIADGKLVGEVTGTVVDANFKADVVSRLGD 257 ***************************************************************************** PP TIGR00338 163 kegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdi 215 ++gi+ + +a+GDGanD++m+++A++giaf+akp+l +ad+ i++ dl+ + lcl|FitnessBrowser__SB2B:6936796 258 EYGIKDGQRLAIGDGANDIPMVQRADFGIAFHAKPKLAAAADARIHTLDLRVL 310 ************************************************99866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (316 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: 12.35 // [ok]
This GapMind analysis is from Apr 09 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