Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_026606695.1 METAC_RS0108500 phosphoserine phosphatase SerB
Query= SwissProt::Q21YU0 (237 letters) >NCBI__GCF_000427445.1:WP_026606695.1 Length = 326 Score = 159 bits (401), Expect = 8e-44 Identities = 91/209 (43%), Positives = 130/209 (62%), Gaps = 6/209 (2%) Query: 25 KLIAFDMDSTLINIECVDEIADAVGRKREVAAITEAAMRGEITDYKESLRQRVALLQGVT 84 KL+ DMDST+I ECVDE+A +G+K +VAAITE AMRGEI ++ +LR+RVAL +G+ Sbjct: 84 KLLLADMDSTIIRQECVDELAAEIGKKPQVAAITERAMRGEIA-FEPALRERVALFKGLH 142 Query: 85 EVQMNQIYQERMQFNPGAAELVAACKAAGLKVLLVSGGFTHFTDRVAQRLGIDYTRSNVL 144 + ++ +++ PGA LV +A G LVSGGFT F VA+++G D+ ++N L Sbjct: 143 PHTIPRVLSKKISLTPGARVLVQTMRAHGAHTALVSGGFTLFAAPVAEKVGFDHVQANEL 202 Query: 145 QI-ENGVLTGRMVDQPWGDICDGAEKRKMLLETCALLGIAPKQAIAVGDGANDLPMMREA 203 + E+G +G + + G+ K + LL G+ P + +AVGDGAND+PM+REA Sbjct: 203 LLGEDGRFSGLLAEPVLGE----RAKLETLLALREGRGLGPSETLAVGDGANDIPMLREA 258 Query: 204 GLSVAFHAKSAVRELANVSIESGGLDRLL 232 GL +AF K AV E A I+ L LL Sbjct: 259 GLGIAFRGKPAVAEAAQARIDHADLTALL 287 Lambda K H 0.321 0.137 0.390 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: 188 Number of extensions: 11 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: 237 Length of database: 326 Length adjustment: 25 Effective length of query: 212 Effective length of database: 301 Effective search space: 63812 Effective search space used: 63812 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_026606695.1 METAC_RS0108500 (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.2840.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-65 207.1 0.0 1.7e-65 206.7 0.0 1.1 1 lcl|NCBI__GCF_000427445.1:WP_026606695.1 METAC_RS0108500 phosphoserine ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026606695.1 METAC_RS0108500 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.7 0.0 1.7e-65 1.7e-65 12 217 .. 81 288 .. 74 289 .. 0.96 Alignments for each domain: == domain 1 score: 206.7 bits; conditional E-value: 1.7e-65 TIGR00338 12 kkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkv 80 + kkl++ D+Dst+i++E++de+a+++G + +V++iTerAmrge+ F+ +lreRv+l kgl+ +++ +v lcl|NCBI__GCF_000427445.1:WP_026606695.1 81 RRKKLLLADMDSTIIRQECVDELAAEIGKKPQVAAITERAMRGEIAFEPALRERVALFKGLHPHTIPRV 149 5799*********************************************************99977666 PP TIGR00338 81 .eeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLeve.dgkltGkvegei 147 +k+ lt+G++ lv++++ +g ++a++SGgF+l+a ++ek g d v aN+L + dg+++G ++ lcl|NCBI__GCF_000427445.1:WP_026606695.1 150 lSKKISLTPGARVLVQTMRAHGAHTALVSGGFTLFAAPVAEKVGFDHVQANELLLGeDGRFSGLLAEPV 218 2789************************************************99977************ PP TIGR00338 148 vdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdil 216 + e+ak +tll l e g+ + +t+avGDGanD++m+++Aglgiaf +kp++ e+a++ i+++dlt++l lcl|NCBI__GCF_000427445.1:WP_026606695.1 219 LGERAKLETLLALREGRGLGPSETLAVGDGANDIPMLREAGLGIAFRGKPAVAEAAQARIDHADLTALL 287 ******************************************************************997 PP TIGR00338 217 e 217 + lcl|NCBI__GCF_000427445.1:WP_026606695.1 288 Y 288 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (326 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: 9.08 // [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