Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_011373283.1 SUDEN_RS08670 phosphoserine phosphatase SerB
Query= SwissProt::Q7M7U5 (206 letters) >NCBI__GCF_000012965.1:WP_011373283.1 Length = 207 Score = 245 bits (626), Expect = 4e-70 Identities = 124/203 (61%), Positives = 155/203 (76%) Query: 1 MKLAVFDFDSTLMDGETIDILAHHYGVGEEVDRITKGAMEGGLDFYESLKRRVALLRGME 60 +KLAVFDFDSTLMDGETID A G+GE+V +IT+ AM G LDF+ESL++RV LL+G+E Sbjct: 2 LKLAVFDFDSTLMDGETIDFFAQELGLGEQVSKITEAAMSGELDFFESLQQRVGLLKGLE 61 Query: 61 LSLVEEICANLTLMEGAKELIQELKRRDYKVVVFSGGFKNATSKARETLGLDADFSNILH 120 S+VE I NL M+GA+E I+ELK R +VV FSGGF++AT A+ LG DADFSN+LH Sbjct: 62 YSVVERISQNLPYMKGAQETIKELKSRGMRVVCFSGGFRSATGYAKSILGYDADFSNVLH 121 Query: 121 HKEGKLTGEVGGEMMFGSSKGEMMQTLQRLLGISPELTMAVGDGANDASMFPFAKQRVAF 180 HK LTG VGG+MMF SKG+M+ LQ LLG+ T+ GDGAND SMF A +RVAF Sbjct: 122 HKNQILTGLVGGDMMFNYSKGDMLVRLQGLLGVKESETLVCGDGANDLSMFAHAGKRVAF 181 Query: 181 CAKPILREKANIIIEKKDLREIL 203 CA+ IL+++ANI+IE KDL +IL Sbjct: 182 CAREILKKEANIVIETKDLTQIL 204 Lambda K H 0.320 0.137 0.382 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: 186 Number of extensions: 6 Number of successful extensions: 1 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: 206 Length of database: 207 Length adjustment: 21 Effective length of query: 185 Effective length of database: 186 Effective search space: 34410 Effective search space used: 34410 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: 45 (21.9 bits)
Align candidate WP_011373283.1 SUDEN_RS08670 (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.5612.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-74 234.5 0.6 5.8e-74 234.4 0.6 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011373283.1 SUDEN_RS08670 phosphoserine phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011373283.1 SUDEN_RS08670 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 234.4 0.6 5.8e-74 5.8e-74 15 217 .. 3 205 .. 1 207 [] 0.99 Alignments for each domain: == domain 1 score: 234.4 bits; conditional E-value: 5.8e-74 TIGR00338 15 klvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkveek 83 kl+vfD+Dstl++ E+Id a++ G +e+Vs+iTe Am geldF esl++Rv llkgl+ ++++++ ++ lcl|NCBI__GCF_000012965.1:WP_011373283.1 3 KLAVFDFDSTLMDGETIDFFAQELGLGEQVSKITEAAMSGELDFFESLQQRVGLLKGLEYSVVERISQN 71 89******************************************************************* PP TIGR00338 84 lelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesa 152 l+ ++G++e++k+Lk +g++v+++SGgF++++++ k+ Lg da f+N L+ ++ ltG v g+++ + + lcl|NCBI__GCF_000012965.1:WP_011373283.1 72 LPYMKGAQETIKELKSRGMRVVCFSGGFRSATGYAKSILGYDADFSNVLHHKNQILTGLVGGDMMFNYS 140 ********************************************************************* PP TIGR00338 153 kaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdile 217 k+++l++l+ g++ +t++ GDGanDlsm+++Ag +af+a+++lk++a+ivie+kdlt+ile lcl|NCBI__GCF_000012965.1:WP_011373283.1 141 KGDMLVRLQGLLGVKESETLVCGDGANDLSMFAHAGKRVAFCAREILKKEANIVIETKDLTQILE 205 ***************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (207 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: 8.33 // [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