Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_029935371.1 N746_RS0107475 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000711195.1:WP_029935371.1 Length = 276 Score = 208 bits (530), Expect = 8e-59 Identities = 112/226 (49%), Positives = 151/226 (66%), Gaps = 5/226 (2%) Query: 10 LVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDY 69 L +NV ++ KL+ DMDSTLI IEC+DEIAD K +V+ ITEAAMRGE++ + Sbjct: 55 LDLNVLPTGFNPAEVKLVISDMDSTLIAIECIDEIADMMDLKPQVSEITEAAMRGELN-F 113 Query: 70 KESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDR 129 +ESL QRV+LLKG+ + ++ +VY RL LN GA + + K +K LVSGGF FFTDR Sbjct: 114 EESLTQRVSLLKGLDIQALQKVYDERLTLNLGAEKCLAGLKQKNIKFALVSGGFDFFTDR 173 Query: 130 IRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIA 189 ++ L +D+ R+N L+ LTG++ G I + K LLE C QL I P Q IA Sbjct: 174 LKQTLNLDFARANKLKIAQDQLTGQID----GSIIGAQAKADFLLELCEQLEIKPNQVIA 229 Query: 190 MGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLELV 235 +GDGANDL MM +AGLS+AYHAKP+V++QA ++N GLD +L+ V Sbjct: 230 VGDGANDLLMMSQAGLSIAYHAKPKVQQQASCSLNYRGLDAILDFV 275 Lambda K H 0.319 0.136 0.385 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: 174 Number of extensions: 4 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: 236 Length of database: 276 Length adjustment: 24 Effective length of query: 212 Effective length of database: 252 Effective search space: 53424 Effective search space used: 53424 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_029935371.1 N746_RS0107475 (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.19608.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-77 245.2 0.8 3.6e-77 244.9 0.8 1.1 1 lcl|NCBI__GCF_000711195.1:WP_029935371.1 N746_RS0107475 phosphoserine pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029935371.1 N746_RS0107475 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 244.9 0.8 3.6e-77 3.6e-77 13 217 .. 68 273 .. 59 275 .. 0.97 Alignments for each domain: == domain 1 score: 244.9 bits; conditional E-value: 3.6e-77 TIGR00338 13 kkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkve 81 + klv+ D+Dstli +E+Ideia ++ + +VseiTe Amrgel+F+esl++Rv+llkgl+++ l+kv+ lcl|NCBI__GCF_000711195.1:WP_029935371.1 68 EVKLVISDMDSTLIAIECIDEIADMMDLKPQVSEITEAAMRGELNFEESLTQRVSLLKGLDIQALQKVY 136 579************************************************************999997 PP TIGR00338 82 .eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivd 149 e+l+l G+e+ Lk+k++k a++SGgFd+++++lk+ L+ld++ aN+L++ +++ltG++ g+i+ lcl|NCBI__GCF_000711195.1:WP_029935371.1 137 dERLTLNLGAEKCLAGLKQKNIKFALVSGGFDFFTDRLKQTLNLDFARANKLKIAQDQLTGQIDGSIIG 205 3689***************************************************************** PP TIGR00338 150 esakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdile 217 ++aka+ ll+l+e+ +i++++++avGDGanDl m+++Agl ia++akp+++++a ++++ + l +il lcl|NCBI__GCF_000711195.1:WP_029935371.1 206 AQAKADFLLELCEQLEIKPNQVIAVGDGANDLLMMSQAGLSIAYHAKPKVQQQASCSLNYRGLDAILD 273 ************************************************************99999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (276 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: 11.76 // [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