Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_092058844.1 BQ4888_RS16930 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >NCBI__GCF_900111775.1:WP_092058844.1 Length = 398 Score = 282 bits (722), Expect = 1e-80 Identities = 173/394 (43%), Positives = 233/394 (59%), Gaps = 10/394 (2%) Query: 8 DVPTLLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGD 67 D +L+ + G DR GI A + +A + DIEQ VT + L L+ P E D Sbjct: 2 DNKMVLLTLTGPDRTGIIAAVTGHIAEAGARIRDIEQSVTHTLLSLSVLIDFPTG--ESD 59 Query: 68 LRATVHSWAE-----SLKLQAEIISGIGDNRPRGFGRSLVTVLGHPLTAEATAAIAARIT 122 + V L L +++S R +VT+LG + A A A ++ + Sbjct: 60 QKPLVKELLFLAKELGLDLDFQVLSEAEYRRKTTRNAYVVTILGGEVNALALARVSRILA 119 Query: 123 ESGSNIDRIFRLAKYPVTAVEFAVS---GVETEPLRTALATEAAALGVDIAVVAAGLHRR 179 E NI+RI +L + + VEF ++ ++ + + L A++GVDIAV L+RR Sbjct: 120 EHAVNIERISKLTQGQLRCVEFLITTTPDLDVKVMTRKLLHTGASVGVDIAVQKESLYRR 179 Query: 180 AQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVALLAGL 239 A+RLVVMD+DSTLIQ EVI+ A AG ++VAE+T AM GELDF +L RVALL GL Sbjct: 180 AKRLVVMDMDSTLIQVEVIDELARVAGVGEQVAEITERAMNGELDFSGALRERVALLKGL 239 Query: 240 DASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQANTL 299 A +++V + LTPGAR L+ LKRLG++ V+SGGF TD L+ LGLD+A AN L Sbjct: 240 KAEALEQVYRNIPLTPGARNLVTILKRLGFKTAVISGGFQFFTDRLKSDLGLDYAYANGL 299 Query: 300 EIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAGLGVA 359 EIVDG +TG V G IVD A KA+LL A G+ L Q +AIGDGANDL ML AGLG+A Sbjct: 300 EIVDGIVTGEVAGTIVDGARKAQLLEEIAGKEGITLDQAIAIGDGANDLPMLGRAGLGIA 359 Query: 360 FNAKPVVREAAHTAVNVPFLDTVLYLLGITREEV 393 FNAK VRE A +N LD++LYL+G++ E+ Sbjct: 360 FNAKARVREQADFHINQQNLDSILYLIGLSEREM 393 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: 383 Number of extensions: 12 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: 398 Length adjustment: 31 Effective length of query: 379 Effective length of database: 367 Effective search space: 139093 Effective search space used: 139093 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 WP_092058844.1 BQ4888_RS16930 (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.16348.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-88 282.0 1.0 2.2e-88 281.6 1.0 1.2 1 lcl|NCBI__GCF_900111775.1:WP_092058844.1 BQ4888_RS16930 phosphoserine pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900111775.1:WP_092058844.1 BQ4888_RS16930 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.6 1.0 2.2e-88 2.2e-88 1 219 [] 168 386 .. 168 386 .. 0.99 Alignments for each domain: == domain 1 score: 281.6 bits; conditional E-value: 2.2e-88 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia++++s ++++k+lvv+D+Dstli+ EvIde+a++aGv+e+V+eiTerAm+geldF +lreRv+ll lcl|NCBI__GCF_900111775.1:WP_092058844.1 168 DIAVQKESLYRRAKRLVVMDMDSTLIQVEVIDELARVAGVGEQVAEITERAMNGELDFSGALRERVALL 236 6899999************************************************************** PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 kgl++e l++v+ +++lt+G+++lv Lk+ g+k+aviSGgF++++++lk+ Lgld++ aN Le+ dg lcl|NCBI__GCF_900111775.1:WP_092058844.1 237 KGLKAEALEQVYRNIPLTPGARNLVTILKRLGFKTAVISGGFQFFTDRLKSDLGLDYAYANGLEIVDGI 305 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 tG+v g+ivd ka+ l++++ kegi l + +a+GDGanDl+m+ +Aglgiafnak ++e+ad i lcl|NCBI__GCF_900111775.1:WP_092058844.1 306 VTGEVAGTIVDGARKAQLLEEIAGKEGITLDQAIAIGDGANDLPMLGRAGLGIAFNAKARVREQADFHI 374 ********************************************************************* PP TIGR00338 208 ekkdltdilell 219 ++++l +il+l+ lcl|NCBI__GCF_900111775.1:WP_092058844.1 375 NQQNLDSILYLI 386 ********9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (398 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: 12.14 // [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