Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate H281DRAFT_00860 H281DRAFT_00860 phosphoserine phosphatase
Query= SwissProt::Q12A06 (236 letters) >FitnessBrowser__Burk376:H281DRAFT_00860 Length = 279 Score = 253 bits (647), Expect = 2e-72 Identities = 129/215 (60%), Positives = 164/215 (76%), Gaps = 4/215 (1%) Query: 20 KLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVAL 79 +L DF L+A DMDSTLI IEC+DEIAD G KAEVAAITEA+MRGEI D+ ESL +RVAL Sbjct: 68 QLRDFGLVAMDMDSTLITIECIDEIADFCGLKAEVAAITEASMRGEIKDFNESLTRRVAL 127 Query: 80 LKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYT 139 LKG+ ++++ VY RL+L+PGA +++ K+AGLK LLVSGGF FFT++++ LG+D+T Sbjct: 128 LKGLDASALERVYEERLQLSPGAEQMLAGAKEAGLKTLLVSGGFNFFTEKLKARLGLDFT 187 Query: 140 RSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPM 199 R+N L+ DG LTG+++ G+I + + K + L ETC QLGI P +AIAMGDG+NDL M Sbjct: 188 RANTLDIVDGKLTGKVI----GEIVNADVKARTLRETCAQLGIEPSRAIAMGDGSNDLKM 243 Query: 200 MGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLEL 234 M EAGLSVA+ AKP VRE A VA N GLD LL L Sbjct: 244 MAEAGLSVAFRAKPVVREAASVAFNYVGLDGLLRL 278 Lambda K H 0.319 0.136 0.385 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: 223 Number of extensions: 11 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: 236 Length of database: 279 Length adjustment: 24 Effective length of query: 212 Effective length of database: 255 Effective search space: 54060 Effective search space used: 54060 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate H281DRAFT_00860 H281DRAFT_00860 (phosphoserine phosphatase)
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.24254.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-71 226.1 0.6 2.5e-71 225.7 0.6 1.1 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00860 H281DRAFT_00860 phosphoserine ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00860 H281DRAFT_00860 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.7 0.6 2.5e-71 2.5e-71 11 217 .. 69 277 .. 61 279 .] 0.95 Alignments for each domain: == domain 1 score: 225.7 bits; conditional E-value: 2.5e-71 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgel.dFkeslreRvkllkglpve 75 l+ +lv +D+Dstli++E+Ideia +G + eV++iTe mrge+ dF+esl+ Rv+llkgl+++ lcl|FitnessBrowser__Burk376:H281DRAFT_00860 69 LRDFGLVAMDMDSTLITIECIDEIADFCGLKAEVAAITEASMRGEIkDFNESLTRRVALLKGLDAS 134 566789***************************************978****************** PP TIGR00338 76 llkkve.eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgklt 140 l++v+ e+l+l +G+e++ ke+g+k+ ++SGgF++++eklk++Lgld+ aN+L++ dgklt lcl|FitnessBrowser__Burk376:H281DRAFT_00860 135 ALERVYeERLQLSPGAEQMLAGAKEAGLKTLLVSGGFNFFTEKLKARLGLDFTRANTLDIVDGKLT 200 999996268********************************************************* PP TIGR00338 141 GkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiv 206 Gkv geiv++++ka+tl + + + gi++ + +a+GDG+nDl+m+++Agl +af akpv++e+a ++ lcl|FitnessBrowser__Burk376:H281DRAFT_00860 201 GKVIGEIVNADVKARTLRETCAQLGIEPSRAIAMGDGSNDLKMMAEAGLSVAFRAKPVVREAASVA 266 *****************************************************************9 PP TIGR00338 207 iekkdltdile 217 + l ++l lcl|FitnessBrowser__Burk376:H281DRAFT_00860 267 FNYVGLDGLLR 277 99888877765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (279 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: 8.56 // [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