Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate 5210367 Shew_2810 phosphoserine phosphatase SerB (RefSeq)
Query= SwissProt::Q5QXU4 (220 letters) >FitnessBrowser__PV4:5210367 Length = 327 Score = 177 bits (449), Expect = 2e-49 Identities = 90/193 (46%), Positives = 129/193 (66%) Query: 6 GLIVFDMDSTLIHIECIDEIARLNNRYTKVSAITEAAMRGEIDFAESLTQRVACLEGIKE 65 GL+V DMDST I IECIDE+A + V+ +TE AM+GE+DF +SL +RVA L G Sbjct: 119 GLLVMDMDSTAIQIECIDELAAMAGVGEAVAEVTERAMQGELDFEQSLRERVAKLAGADA 178 Query: 66 SDLESLFSPIPFNPGAKELIQALQAAGWKTALVSGGFTWFANRVQAALNLDAVVANQLEV 125 +++L + +P PG + ++ LQ GW+ L SGGFT F ++ LNLDA AN+L + Sbjct: 179 GIIDTLCAQLPLMPGLEAMVAELQDYGWRLVLASGGFTPFVGHLKQQLNLDAAYANELVI 238 Query: 126 ADGCLTGKVLGDIVDAQVKAEQLQQLAGHWNIPPDRTVAVGDGANDGLMLKAAAVGIAFN 185 +G L G+V+G +VDAQ KA+ + + A W IP + +A+GDGAND M++AA GIA++ Sbjct: 239 VEGKLKGEVIGTVVDAQFKADTVLRSAESWQIPMGQRLAIGDGANDIPMVQAADFGIAYH 298 Query: 186 AKPALQAIADYSV 198 AKP L+A AD ++ Sbjct: 299 AKPKLKAAADAAI 311 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: 179 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: 327 Length adjustment: 25 Effective length of query: 195 Effective length of database: 302 Effective search space: 58890 Effective search space used: 58890 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 5210367 Shew_2810 (phosphoserine phosphatase SerB (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.21930.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-81 258.3 0.0 3.7e-81 257.9 0.0 1.1 1 lcl|FitnessBrowser__PV4:5210367 Shew_2810 phosphoserine phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5210367 Shew_2810 phosphoserine phosphatase SerB (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.9 0.0 3.7e-81 3.7e-81 10 217 .. 114 321 .. 107 323 .. 0.97 Alignments for each domain: == domain 1 score: 257.9 bits; conditional E-value: 3.7e-81 TIGR00338 10 llkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkveeklelt 87 l +l+v+D+Dst+i++E+Ide+a++aGv+e+V+e+TerAm+geldF++slreRv++l g+++ +++ + +l+l+ lcl|FitnessBrowser__PV4:5210367 114 RLDRPGLLVMDMDSTAIQIECIDELAAMAGVGEAVAEVTERAMQGELDFEQSLRERVAKLAGADAGIIDTLCAQLPLM 191 567789************************************************************************ PP TIGR00338 88 eGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllkllekeg 165 +G+e +v +L+++g++++++SGgF+ ++++lk++L+lda+ aN+L + +gkl G+v g++vd++ ka+t+l+ +e+ + lcl|FitnessBrowser__PV4:5210367 192 PGLEAMVAELQDYGWRLVLASGGFTPFVGHLKQQLNLDAAYANELVIVEGKLKGEVIGTVVDAQFKADTVLRSAESWQ 269 ****************************************************************************** PP TIGR00338 166 islektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdile 217 i++ + +a+GDGanD++m++aA++gia++akp+lk +ad++i k dl+ + + lcl|FitnessBrowser__PV4:5210367 270 IPMGQRLAIGDGANDIPMVQAADFGIAYHAKPKLKAAADAAIAKLDLRVLPY 321 ***********************************************97765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (327 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.77 // [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