Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate 200401 SO_1223 phosphoserine phosphatase (RefSeq)
Query= SwissProt::Q5QXU4 (220 letters) >FitnessBrowser__MR1:200401 Length = 330 Score = 181 bits (458), Expect = 2e-50 Identities = 95/198 (47%), Positives = 129/198 (65%) Query: 6 GLIVFDMDSTLIHIECIDEIARLNNRYTKVSAITEAAMRGEIDFAESLTQRVACLEGIKE 65 GL+V DMDST I IECIDE+A + +V+AITE AM+GE+DF +SL QRVA L+G Sbjct: 124 GLLVMDMDSTAIQIECIDELAAMAGVGEQVAAITERAMQGELDFEQSLRQRVAQLKGADA 183 Query: 66 SDLESLFSPIPFNPGAKELIQALQAAGWKTALVSGGFTWFANRVQAALNLDAVVANQLEV 125 + +L +PF PG + ++ L++ W+ + SGGFT F ++ LNLDA AN+L + Sbjct: 184 KIIHTLCESLPFMPGLEAMLAELKSHHWRLVVASGGFTPFVGHLKQLLNLDAAFANELVI 243 Query: 126 ADGCLTGKVLGDIVDAQVKAEQLQQLAGHWNIPPDRTVAVGDGANDGLMLKAAAVGIAFN 185 DG L G V G IVDAQ KA+ + + + W IP + VA+GDGAND M++AA GIAF+ Sbjct: 244 TDGKLAGTVTGKIVDAQFKADVVSRCSQEWQIPAGQRVAIGDGANDIPMVQAADFGIAFH 303 Query: 186 AKPALQAIADYSVNSNNL 203 AKP L A AD + +L Sbjct: 304 AKPKLAAAADARIRGLDL 321 Lambda K H 0.318 0.134 0.384 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: 191 Number of extensions: 8 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: 220 Length of database: 330 Length adjustment: 25 Effective length of query: 195 Effective length of database: 305 Effective search space: 59475 Effective search space used: 59475 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate 200401 SO_1223 (phosphoserine phosphatase (RefSeq))
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.11598.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-82 260.5 0.0 8.2e-82 260.1 0.0 1.1 1 lcl|FitnessBrowser__MR1:200401 SO_1223 phosphoserine phosphatas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200401 SO_1223 phosphoserine phosphatase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.1 0.0 8.2e-82 8.2e-82 11 218 .. 120 327 .. 115 328 .. 0.98 Alignments for each domain: == domain 1 score: 260.1 bits; conditional E-value: 8.2e-82 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkveeklelteG 89 l+k +l+v+D+Dst+i++E+Ide+a++aGv+e+V++iTerAm+geldF++slr+Rv+ lkg+++++++ +e+l+ ++G lcl|FitnessBrowser__MR1:200401 120 LSKPGLLVMDMDSTAIQIECIDELAAMAGVGEQVAAITERAMQGELDFEQSLRQRVAQLKGADAKIIHTLCESLPFMPG 198 56889************************************************************************** PP TIGR00338 90 veelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllkllekegisl 168 +e + +Lk + ++++v+SGgF+ ++++lk+ L+lda+faN+L ++dgkl+G+v+g+ivd++ ka+++ + ++ +i+ lcl|FitnessBrowser__MR1:200401 199 LEAMLAELKSHHWRLVVASGGFTPFVGHLKQLLNLDAAFANELVITDGKLAGTVTGKIVDAQFKADVVSRCSQEWQIPA 277 ******************************************************************************* PP TIGR00338 169 ektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 + va+GDGanD++m++aA++giaf+akp+l +ad+ i+ dl+ + +l lcl|FitnessBrowser__MR1:200401 278 GQRVAIGDGANDIPMVQAADFGIAFHAKPKLAAAADARIRGLDLRVLPYL 327 *****************************************999977665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (330 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.89 // [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