Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate CCNA_02182 CCNA_02182 phosphoserine phosphatase
Query= SwissProt::Q12A06 (236 letters) >FitnessBrowser__Caulo:CCNA_02182 Length = 292 Score = 179 bits (453), Expect = 7e-50 Identities = 100/207 (48%), Positives = 132/207 (63%), Gaps = 5/207 (2%) Query: 26 LIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVSV 85 L+ DMDST+IN+EC+DE+AD AG KA+V+ ITE AMRGE++ ++ +LR+RV +LKG+ V Sbjct: 79 LLIADMDSTIINVECLDELADFAGVKAQVSEITERAMRGELA-FEGALRERVGMLKGLGV 137 Query: 86 ASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVLE 145 +++ Y R+RLNPGA LV+ G + LVSGGFTFFT R+ + G R+N L Sbjct: 138 SALQACYDERVRLNPGAETLVRTMAKHGARCALVSGGFTFFTSRVAEAAGFHLNRANTLI 197 Query: 146 TTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAGL 205 DG LTG + D I E K L E LG++P A+A+GDGANDL M+ AGL Sbjct: 198 ELDGALTGAVGD----PILGKEAKLAALREETAALGLTPADALAVGDGANDLAMIEAAGL 253 Query: 206 SVAYHAKPRVREQAMVAINEGGLDRLL 232 VAY AKP V QA ++ L LL Sbjct: 254 GVAYRAKPIVAAQADAKVDHTDLTTLL 280 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: 197 Number of extensions: 9 Number of successful extensions: 3 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: 292 Length adjustment: 25 Effective length of query: 211 Effective length of database: 267 Effective search space: 56337 Effective search space used: 56337 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 CCNA_02182 CCNA_02182 (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.13251.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-66 208.7 0.1 5.7e-66 208.2 0.1 1.1 1 lcl|FitnessBrowser__Caulo:CCNA_02182 CCNA_02182 phosphoserine phospha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02182 CCNA_02182 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.2 0.1 5.7e-66 5.7e-66 10 217 .. 73 281 .. 66 282 .. 0.97 Alignments for each domain: == domain 1 score: 208.2 bits; conditional E-value: 5.7e-66 TIGR00338 10 llkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkve. 81 ++ k+l++ D+Dst+i+ E++de+a aGv+ +VseiTerAmrgel F+ +lreRv +lkgl v+ l+ + lcl|FitnessBrowser__Caulo:CCNA_02182 73 ANRRKGLLIADMDSTIINVECLDELADFAGVKAQVSEITERAMRGELAFEGALRERVGMLKGLGVSALQACYd 145 568899************************************************************8887752 PP TIGR00338 82 eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesaka 154 e+++l +G+e lv+++ ++g + a++SGgF++++ +++e g aN+L+ dg+ltG v +i+ ++ak lcl|FitnessBrowser__Caulo:CCNA_02182 146 ERVRLNPGAETLVRTMAKHGARCALVSGGFTFFTSRVAEAAGFHLNRANTLIELDGALTGAVGDPILGKEAKL 218 789********************************************************************** PP TIGR00338 155 ktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdile 217 l + + g+ +++ +avGDGanDl+mi+aAglg+a+ akp++ +ad++++++dlt +l+ lcl|FitnessBrowser__Caulo:CCNA_02182 219 AALREETAALGLTPADALAVGDGANDLAMIEAAGLGVAYRAKPIVAAQADAKVDHTDLTTLLY 281 ***********************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (292 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: 9.56 // [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