Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_011426040.1 RHE_RS14290 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000092045.1:WP_011426040.1 Length = 296 Score = 167 bits (424), Expect = 2e-46 Identities = 107/237 (45%), Positives = 139/237 (58%), Gaps = 10/237 (4%) Query: 1 MQPTEISPGLVVNVATPDLKLSDF-----KLIAFDMDSTLINIECVDEIADAAGRKAEVA 55 +Q E + V++ A DL + + KL+ DMDST+I EC+DE+A G K +VA Sbjct: 52 VQAAEANLLAVISSAPIDLVIQEQDSRRKKLLIADMDSTMIGQECIDELAAEVGLKEKVA 111 Query: 56 AITEAAMRGEISDYKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLK 115 IT AM GEI+ ++ +LR+RVALLKG+ ++ +DEV R+ L G L+ K G Sbjct: 112 DITARAMNGEIA-FEPALRERVALLKGLPISVVDEVIAKRITLTSGGPELIATMKAKGHY 170 Query: 116 VLLVSGGFTFFTDRIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLE 175 LVSGGFT FT RI LG D R+N L DG+L+G V +P I + K L E Sbjct: 171 TALVSGGFTVFTSRIAATLGFDENRANTLLDEDGILSG-FVAEP---ILGKQAKVDALNE 226 Query: 176 TCGQLGISPRQAIAMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLL 232 LGISP++AIA+GDGANDL M+ AG VA HAKP V QA + IN L LL Sbjct: 227 ISASLGISPQEAIAVGDGANDLGMLQLAGSGVALHAKPTVAAQAQMRINHADLTALL 283 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: 199 Number of extensions: 6 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: 296 Length adjustment: 25 Effective length of query: 211 Effective length of database: 271 Effective search space: 57181 Effective search space used: 57181 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_011426040.1 RHE_RS14290 (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.9759.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-69 218.7 0.7 5.1e-69 218.2 0.7 1.1 1 lcl|NCBI__GCF_000092045.1:WP_011426040.1 RHE_RS14290 phosphoserine phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092045.1:WP_011426040.1 RHE_RS14290 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 218.2 0.7 5.1e-69 5.1e-69 10 218 .. 76 285 .. 69 286 .. 0.96 Alignments for each domain: == domain 1 score: 218.2 bits; conditional E-value: 5.1e-69 TIGR00338 10 llkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellk 78 + kkl++ D+Dst+i +E+Ide+a+++G +e+V++iT rAm+ge+ F+ +lreRv+llkglp+++++ lcl|NCBI__GCF_000092045.1:WP_011426040.1 76 DSRRKKLLIADMDSTMIGQECIDELAAEVGLKEKVADITARAMNGEIAFEPALRERVALLKGLPISVVD 144 46789*************************************************************777 PP TIGR00338 79 k.veeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvege 146 + ++++++lt+G el+ ++k kg +a++SGgF++++ ++++ Lg d aN+L edg l+G+v + lcl|NCBI__GCF_000092045.1:WP_011426040.1 145 EvIAKRITLTSGGPELIATMKAKGHYTALVSGGFTVFTSRIAATLGFDENRANTLLDEDGILSGFVAEP 213 615789*************************************************************** PP TIGR00338 147 ivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdi 215 i+ ++ak + l ++ + gis+++ +avGDGanDl m++ Ag g+a +akp + +a++ i+++dlt++ lcl|NCBI__GCF_000092045.1:WP_011426040.1 214 ILGKQAKVDALNEISASLGISPQEAIAVGDGANDLGMLQLAGSGVALHAKPTVAAQAQMRINHADLTAL 282 ********************************************************************9 PP TIGR00338 216 lel 218 l++ lcl|NCBI__GCF_000092045.1:WP_011426040.1 283 LYI 285 986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (296 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: 7.68 // [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