Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate SMc01494 SMc01494 phosphoserine phosphatase
Query= SwissProt::Q12A06 (236 letters) >FitnessBrowser__Smeli:SMc01494 Length = 295 Score = 165 bits (418), Expect = 8e-46 Identities = 101/226 (44%), Positives = 136/226 (60%), Gaps = 5/226 (2%) Query: 9 GLVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISD 68 G ++VA D + + + DMDST+I EC+DE+A G K +VAAIT AM GEI+ Sbjct: 65 GAAIDVAVQDAESRRKRFLIADMDSTMIGQECIDELAAEVGLKEKVAAITARAMNGEIA- 123 Query: 69 YKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTD 128 ++ +L +RVALL+G+ V + EV TR+ L PG L+ K G LVSGGFT FT Sbjct: 124 FEPALVERVALLQGLPVTVVAEVIATRITLTPGGRELIATMKAKGHYSALVSGGFTVFTG 183 Query: 129 RIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAI 188 I ++LG D R+N+L +G LTG V +P I + K L++ +LGI+P I Sbjct: 184 PIAEKLGFDENRANILVEENGKLTGD-VARP---ILGKQAKVDALIDISERLGITPADVI 239 Query: 189 AMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLEL 234 A+GDGANDL M+ AG VA HAKP V +QA + I+ G L LL L Sbjct: 240 AVGDGANDLGMLQLAGTGVALHAKPVVADQAKIRIDHGDLTALLYL 285 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: 189 Number of extensions: 9 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: 295 Length adjustment: 25 Effective length of query: 211 Effective length of database: 270 Effective search space: 56970 Effective search space used: 56970 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 SMc01494 SMc01494 (phosphoserine phosphatase)
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.3767.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-69 217.9 0.8 7.5e-69 217.7 0.8 1.1 1 lcl|FitnessBrowser__Smeli:SMc01494 SMc01494 phosphoserine phosphata Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01494 SMc01494 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 217.7 0.8 7.5e-69 7.5e-69 9 218 .. 75 285 .. 67 286 .. 0.96 Alignments for each domain: == domain 1 score: 217.7 bits; conditional E-value: 7.5e-69 TIGR00338 9 kllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve.llkkvee 82 + k+ ++ D+Dst+i +E+Ide+a+++G +e+V++iT rAm+ge+ F+ +l eRv+ll+glpv +++ ++ lcl|FitnessBrowser__Smeli:SMc01494 75 AESRRKRFLIADMDSTMIGQECIDELAAEVGLKEKVAAITARAMNGEIAFEPALVERVALLQGLPVTvVAEVIAT 149 456789999**********************************************************66777889 PP TIGR00338 83 klelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktl 157 +++lt+G +el+ ++k kg a++SGgF+++++ ++ekLg d aN L e+gkltG+v +i+ ++ak + l lcl|FitnessBrowser__Smeli:SMc01494 150 RITLTPGGRELIATMKAKGHYSALVSGGFTVFTGPIAEKLGFDENRANILVEENGKLTGDVARPILGKQAKVDAL 224 *************************************************************************** PP TIGR00338 158 lkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 + e+ gi +++++avGDGanDl m++ Ag g+a +akpv+ ++a+i i++ dlt++l+l lcl|FitnessBrowser__Smeli:SMc01494 225 IDISERLGITPADVIAVGDGANDLGMLQLAGTGVALHAKPVVADQAKIRIDHGDLTALLYL 285 *********************************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (295 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.58 // [ok]
This GapMind analysis is from Apr 09 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