Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate PfGW456L13_172 Phosphoserine phosphatase (EC 3.1.3.3)
Query= SwissProt::Q9S281 (410 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 Phosphoserine phosphatase (EC 3.1.3.3) Length = 404 Score = 263 bits (673), Expect = 5e-75 Identities = 166/395 (42%), Positives = 231/395 (58%), Gaps = 22/395 (5%) Query: 12 LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALV----TEPPRGLEGD 67 +L+ I G DRPG+TA + LA V+++DI Q V + LV TE + + D Sbjct: 5 VLINITGVDRPGLTAAITGVLAQGGVNILDIGQAVIHDTLSFGILVEIPDTEQGKSVLKD 64 Query: 68 LRATVHSWAESLKL----QAEIISGIGDNRPRGFGRSLVTVLGHPLTAEATAAIAARITE 123 + + + ++ + + +G+ +G R +VT+L +TA A+++ + Sbjct: 65 ILFKGYELDQQVRFTPVSEQDYQQWVGN---QGKKRHIVTLLTRKVTAGQLQAVSSITAK 121 Query: 124 SGSNIDRIFRLA-KYPVTA--------VEFAVSGVETEP--LRTALATEAAALGVDIAVV 172 G NID I RL+ + P+ +EF+V G +P LR + A L VDIA Sbjct: 122 YGLNIDHIDRLSGRMPLDTPADKGKGCIEFSVRGEAADPQALRAEFLSVAQELNVDIAFQ 181 Query: 173 AAGLHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHAR 232 L RR +RL V D+DSTLI+ EVI+ A AG D+V+E+T AM GELDF S R Sbjct: 182 EDSLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGDKVSEITERAMAGELDFRASFKER 241 Query: 233 VALLAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLD 292 +ALL GLD +V+D + A +RLT GA TL LKRLGY+ ++SGGFT LQ +LG+D Sbjct: 242 LALLKGLDVNVLDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFTYFAKQLQAKLGID 301 Query: 293 FAQANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLN 352 + AN LE+VDG++TG IVD KA LL+ A G+ L QT+A+GDGANDL ML Sbjct: 302 YVFANELEVVDGKVTGVAVEPIVDAQRKADLLKELAHKEGLRLEQTIAVGDGANDLPMLA 361 Query: 353 AAGLGVAFNAKPVVREAAHTAVNVPFLDTVLYLLG 387 AGLGVAF AKP+V+++A A++ LD VLYLLG Sbjct: 362 IAGLGVAFRAKPLVKQSAKQAISTLGLDGVLYLLG 396 Lambda K H 0.319 0.135 0.374 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: 387 Number of extensions: 20 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: 410 Length of database: 404 Length adjustment: 31 Effective length of query: 379 Effective length of database: 373 Effective search space: 141367 Effective search space used: 141367 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate PfGW456L13_172 (Phosphoserine phosphatase (EC 3.1.3.3))
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.24855.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-84 268.1 0.9 3.8e-84 267.7 0.9 1.2 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 Phosphoserine phosphatase (EC 3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 Phosphoserine phosphatase (EC 3.1.3.3) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.7 0.9 3.8e-84 3.8e-84 1 219 [] 177 395 .. 177 395 .. 0.99 Alignments for each domain: == domain 1 score: 267.7 bits; conditional E-value: 3.8e-84 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgel 56 dia +e+s ++++++l+vfD+Dstlie+EvIde+ak+aGv+++VseiTerAm gel lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 177 DIAFQEDSLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGDKVSEITERAMAGEL 232 688999999*********************************************** PP TIGR00338 57 dFkeslreRvkllkglpvellkkveeklelteGveelvkkLkekgykvaviSGgFd 112 dF++s++eR++llkgl+v++l+ + +l+lteG+e l +Lk+ gyk+a++SGgF+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 233 DFRASFKERLALLKGLDVNVLDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFT 288 ******************************************************** PP TIGR00338 113 lvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllkllekegisl 168 ++a++l++kLg+d+vfaN+Lev dgk tG +ivd++ ka+ l++l++keg+ l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 289 YFAKQLQAKLGIDYVFANELEVVDGKVTGVAVEPIVDAQRKADLLKELAHKEGLRL 344 ******************************************************** PP TIGR00338 169 ektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219 e+t+avGDGanDl+m++ Aglg+af akp +k+ a+++i++ l ++l+ll lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 345 EQTIAVGDGANDLPMLAIAGLGVAFRAKPLVKQSAKQAISTLGLDGVLYLL 395 ******************************************999999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (404 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.05 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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