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) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 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.808.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: 8.94 // [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