Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_043879333.1 AZC_RS13305 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000010525.1:WP_043879333.1 Length = 299 Score = 186 bits (471), Expect = 6e-52 Identities = 102/208 (49%), Positives = 134/208 (64%), Gaps = 5/208 (2%) Query: 25 KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVS 84 +L DMDST+I EC+DE+AD G KA V+AITE AMRGEIS ++ +LR+RVALLKG++ Sbjct: 84 RLFLADMDSTMIGQECIDELADLVGLKAHVSAITERAMRGEIS-FEPALRERVALLKGLA 142 Query: 85 VASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVL 144 +D+V R R+ L PG LV K G LVSGGFT FT + +G D R+N+L Sbjct: 143 AEVVDDVLRERITLMPGGKALVSTMKANGAYTALVSGGFTLFTSAVAQMIGFDENRANIL 202 Query: 145 ETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAG 204 ET G L+G + + I E K L+E +L +SP + +A+GDGANDL M+GEAG Sbjct: 203 ETDGGKLSGTVTE----PILGKEAKLATLVELRDRLHLSPSETMAVGDGANDLAMLGEAG 258 Query: 205 LSVAYHAKPRVREQAMVAINEGGLDRLL 232 L VAYHAKP+V +A ++ G L LL Sbjct: 259 LGVAYHAKPKVAAEAKARVDHGDLTALL 286 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: 198 Number of extensions: 6 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: 299 Length adjustment: 25 Effective length of query: 211 Effective length of database: 274 Effective search space: 57814 Effective search space used: 57814 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 WP_043879333.1 AZC_RS13305 (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.17691.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-66 209.7 0.3 2.8e-66 209.3 0.3 1.1 1 lcl|NCBI__GCF_000010525.1:WP_043879333.1 AZC_RS13305 phosphoserine phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_043879333.1 AZC_RS13305 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.3 0.3 2.8e-66 2.8e-66 11 217 .. 80 287 .. 71 288 .. 0.96 Alignments for each domain: == domain 1 score: 209.3 bits; conditional E-value: 2.8e-66 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkk 79 + k+l++ D+Dst+i +E+Ide+a l+G + +Vs+iTerAmrge+ F+ +lreRv+llkgl++e+++ lcl|NCBI__GCF_000010525.1:WP_043879333.1 80 GRRKRLFLADMDSTMIGQECIDELADLVGLKAHVSAITERAMRGEISFEPALRERVALLKGLAAEVVDD 148 57899************************************************************7777 PP TIGR00338 80 v.eeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegei 147 v +e+++l++G + lv+++k +g +a++SGgF+l++ +++ +g d aN Le + gkl+G+v+ +i lcl|NCBI__GCF_000010525.1:WP_043879333.1 149 VlRERITLMPGGKALVSTMKANGAYTALVSGGFTLFTSAVAQMIGFDENRANILETDGGKLSGTVTEPI 217 64899**************************************************************** PP TIGR00338 148 vdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdil 216 + ++ak tl++l + ++s+ +t+avGDGanDl+m+ +Aglg+a++akp++ +a++ +++ dlt++l lcl|NCBI__GCF_000010525.1:WP_043879333.1 218 LGKEAKLATLVELRDRLHLSPSETMAVGDGANDLAMLGEAGLGVAYHAKPKVAAEAKARVDHGDLTALL 286 ******************************************************************998 PP TIGR00338 217 e 217 + lcl|NCBI__GCF_000010525.1:WP_043879333.1 287 Y 287 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (299 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 9.46 // [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