Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_028999131.1 H537_RS0119320 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000430725.1:WP_028999131.1 Length = 239 Score = 343 bits (881), Expect = 1e-99 Identities = 172/234 (73%), Positives = 196/234 (83%) Query: 3 PTEISPGLVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAM 62 P +PGL V TP L+L DF LIAFDMDSTLINIEC+DE+ADAAGRKAEVAAITEA+M Sbjct: 5 PLAFAPGLTVRGFTPPLQLRDFGLIAFDMDSTLINIECIDEVADAAGRKAEVAAITEASM 64 Query: 63 RGEISDYKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGG 122 RGEI+D+KESLR+RVA+L+GV + EV+ RL+ NPGA L+ AC+ AGLK LLVSGG Sbjct: 65 RGEITDFKESLRRRVAMLQGVPAQFLHEVFEQRLKPNPGAKELIDACRAAGLKTLLVSGG 124 Query: 123 FTFFTDRIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGI 182 FTFF +R+ LGIDY RSNVLE DG LTGR+VDQ WGDICDG EKR+MLL TC QLGI Sbjct: 125 FTFFAERVCSLLGIDYARSNVLEIVDGHLTGRLVDQDWGDICDGAEKRRMLLATCEQLGI 184 Query: 183 SPRQAIAMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLELVK 236 +P +AIAMGDGANDLPMMG AGLSVAYHAKP+VREQAMV+I EGGLDRLLELV+ Sbjct: 185 APSRAIAMGDGANDLPMMGAAGLSVAYHAKPKVREQAMVSIEEGGLDRLLELVR 238 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: 236 Number of extensions: 3 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: 236 Length of database: 239 Length adjustment: 23 Effective length of query: 213 Effective length of database: 216 Effective search space: 46008 Effective search space used: 46008 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: 46 (22.3 bits)
Align candidate WP_028999131.1 H537_RS0119320 (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.23181.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-68 215.8 0.0 3.4e-68 215.5 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_028999131.1 H537_RS0119320 phosphoserine pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_028999131.1 H537_RS0119320 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.5 0.0 3.4e-68 3.4e-68 14 218 .. 26 236 .. 20 237 .. 0.94 Alignments for each domain: == domain 1 score: 215.5 bits; conditional E-value: 3.4e-68 TIGR00338 14 kklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgel.dFkeslreRvkllkglpvellkkv. 80 +l+ fD+Dstli++E+Ide+a +aG + eV++iTe mrge+ dFkeslr Rv++l+g+p++ l++v lcl|NCBI__GCF_000430725.1:WP_028999131.1 26 FGLIAFDMDSTLINIECIDEVADAAGRKAEVAAITEASMRGEItDFKESLRRRVAMLQGVPAQFLHEVf 94 579***************************************769******************666653 PP TIGR00338 81 eeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGk....veg 145 e++l+ +G++el+ + + +g+k+ ++SGgF+++ae++ + Lg+d++ +N Le+ dg+ltG+ + g lcl|NCBI__GCF_000430725.1:WP_028999131.1 95 EQRLKPNPGAKELIDACRAAGLKTLLVSGGFTFFAERVCSLLGIDYARSNVLEIVDGHLTGRlvdqDWG 163 789**********************************************************73222569 PP TIGR00338 146 eivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltd 214 +i d +k ++ll +e+ gi + + +a+GDGanDl+m+ aAgl +a++akp+++e+a ++ie+ l lcl|NCBI__GCF_000430725.1:WP_028999131.1 164 DICDGAEKRRMLLATCEQLGIAPSRAIAMGDGANDLPMMGAAGLSVAYHAKPKVREQAMVSIEEGGLDR 232 ****************************************************************99999 PP TIGR00338 215 ilel 218 +lel lcl|NCBI__GCF_000430725.1:WP_028999131.1 233 LLEL 236 9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (239 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.61 // [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