Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_026128224.1 D471_RS0129830 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >NCBI__GCF_000341125.1:WP_026128224.1 Length = 403 Score = 434 bits (1117), Expect = e-126 Identities = 232/399 (58%), Positives = 290/399 (72%), Gaps = 8/399 (2%) Query: 7 SDVPTLLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEG 66 +D TL V + G+DRPGI+A L TL+ + V +VD+EQVV GR+VL A++ R G Sbjct: 2 NDETTLSVTVTGRDRPGISARLLSTLSVFPVAIVDLEQVVLGGRLVLGAILEVDERVAPG 61 Query: 67 --------DLRATVHSWAESLKLQAEIISGIGDNRPRGFGRSLVTVLGHPLTAEATAAIA 118 ++R + A L ++ E G G R VTVL PL A AAI Sbjct: 62 VTRHRVFEEVRGALDKTAIDLDMETEYGDGNGRVNAYDPNRLHVTVLADPLRPGALAAIT 121 Query: 119 ARITESGSNIDRIFRLAKYPVTAVEFAVSGVETEPLRTALATEAAALGVDIAVVAAGLHR 178 + + +G+NIDRI RL+ YPVT+VE +SG + LR LA EA+ VD+AV ++GLHR Sbjct: 122 SCVARAGANIDRIERLSSYPVTSVEMDISGGSADQLRAELAMEASTQAVDVAVQSSGLHR 181 Query: 179 RAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVALLAG 238 R + L++MDVDSTLIQ EVIEL AAHAGCE E+A+VT AMRGELDFE+SL ARVALL G Sbjct: 182 RGKHLIIMDVDSTLIQGEVIELLAAHAGCEAEIAKVTEQAMRGELDFEESLRARVALLRG 241 Query: 239 LDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQANT 298 LDAS +D+VR E+ LTPGARTL+RTLKRLGY+ G+VSGGFTQ+TD+L E L LD++ ANT Sbjct: 242 LDASAIDRVREEIVLTPGARTLVRTLKRLGYECGIVSGGFTQITDSLVELLDLDYSAANT 301 Query: 299 LEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAGLGV 358 LE+V+G+LTG + G I+DR GKA L++FA AGVPL+QTVAIGDGANDLDML AGLGV Sbjct: 302 LEVVNGKLTGELVGPIIDRKGKATTLQQFADEAGVPLTQTVAIGDGANDLDMLQTAGLGV 361 Query: 359 AFNAKPVVREAAHTAVNVPFLDTVLYLLGITREEVEAAD 397 AFNAKPVVRE A T+V VP+LD + ++LGITREE+EAAD Sbjct: 362 AFNAKPVVREQADTSVTVPYLDAIAFILGITREEIEAAD 400 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: 444 Number of extensions: 13 Number of successful extensions: 2 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: 403 Length adjustment: 31 Effective length of query: 379 Effective length of database: 372 Effective search space: 140988 Effective search space used: 140988 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_026128224.1 D471_RS0129830 (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.28413.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-79 252.4 0.2 2.5e-79 251.9 0.2 1.2 1 lcl|NCBI__GCF_000341125.1:WP_026128224.1 D471_RS0129830 phosphoserine pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_026128224.1 D471_RS0129830 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.9 0.2 2.5e-79 2.5e-79 2 219 .] 172 389 .. 171 389 .. 0.98 Alignments for each domain: == domain 1 score: 251.9 bits; conditional E-value: 2.5e-79 TIGR00338 2 iakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllk 70 +a+++ +++ k+l+++D+Dstli+ EvI+ +a+ aG e e++++Te+AmrgeldF+eslr Rv+ll+ lcl|NCBI__GCF_000341125.1:WP_026128224.1 172 VAVQSSGLHRRGKHLIIMDVDSTLIQGEVIELLAAHAGCEAEIAKVTEQAMRGELDFEESLRARVALLR 240 677777788999********************************************************* PP TIGR00338 71 glpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkl 139 gl+++ +++v+e++ lt+G++ lv++Lk+ gy+ ++SGgF+++++ l e L+ld+ +aN+Lev +gkl lcl|NCBI__GCF_000341125.1:WP_026128224.1 241 GLDASAIDRVREEIVLTPGARTLVRTLKRLGYECGIVSGGFTQITDSLVELLDLDYSAANTLEVVNGKL 309 ********************************************************************* PP TIGR00338 140 tGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivie 208 tG+ g+i+d + ka tl++ + + g++l++tva+GDGanDl m+++Aglg+afnakpv++e+ad+++ lcl|NCBI__GCF_000341125.1:WP_026128224.1 310 TGELVGPIIDRKGKATTLQQFADEAGVPLTQTVAIGDGANDLDMLQTAGLGVAFNAKPVVREQADTSVT 378 ********************************************************************* PP TIGR00338 209 kkdltdilell 219 +l +i+ +l lcl|NCBI__GCF_000341125.1:WP_026128224.1 379 VPYLDAIAFIL 389 ****9998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (403 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: 12.62 // [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