Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate AZOBR_RS06540 AZOBR_RS06540 phosphoserine phosphatase
Query= SwissProt::Q12A06 (236 letters) >lcl|FitnessBrowser__azobra:AZOBR_RS06540 AZOBR_RS06540 phosphoserine phosphatase Length = 303 Score = 170 bits (431), Expect = 3e-47 Identities = 100/224 (44%), Positives = 138/224 (61%), Gaps = 6/224 (2%) Query: 9 GLVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISD 68 GL V+V +L+ DM+ST+I E +DE+ D G K +AAIT AM GEI D Sbjct: 73 GLAVDVIAQKPGSRKKRLLVADMESTIIEQEMLDELGDYVGLKDHIAAITARAMNGEI-D 131 Query: 69 YKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTD 128 +K ++R+RVALLKG++ + +DEV++ R L PGA LV + G +LVSGGF FT+ Sbjct: 132 FKGAVRERVALLKGLNESVVDEVWQ-RATLMPGARTLVSTMRANGATCVLVSGGFRCFTE 190 Query: 129 RIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAI 188 R+R +G D R NVLE DG++TG +V+ I D + K + LL G+ + + + Sbjct: 191 RVRQWVGFDDDRGNVLEVVDGVMTGAVVEP----ILDKDSKLEALLAYAGERHVPTVETM 246 Query: 189 AMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLL 232 A+GDGANDLPM+ AGL VA+HAKP V QA ++ G L LL Sbjct: 247 AVGDGANDLPMLLAAGLGVAFHAKPTVAAQARARVDHGDLTALL 290 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: 192 Number of extensions: 9 Number of successful extensions: 4 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: 303 Length adjustment: 25 Effective length of query: 211 Effective length of database: 278 Effective search space: 58658 Effective search space used: 58658 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 AZOBR_RS06540 AZOBR_RS06540 (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.17796.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-66 208.4 0.1 6.9e-66 208.0 0.1 1.1 1 lcl|FitnessBrowser__azobra:AZOBR_RS06540 AZOBR_RS06540 phosphoserine phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS06540 AZOBR_RS06540 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.0 0.1 6.9e-66 6.9e-66 8 216 .. 82 290 .. 76 292 .. 0.98 Alignments for each domain: == domain 1 score: 208.0 bits; conditional E-value: 6.9e-66 TIGR00338 8 skllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvel 76 ++ +kk+l+v D++st+ie+E++de++ ++G ++++++iT rAm+ge+dFk ++reRv+llkgl++++ lcl|FitnessBrowser__azobra:AZOBR_RS06540 82 KPGSRKKRLLVADMESTIIEQEMLDELGDYVGLKDHIAAITARAMNGEIDFKGAVRERVALLKGLNESV 150 566789*************************************************************** PP TIGR00338 77 lkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkveg 145 +++v ++ +l++G++ lv++++ +g +++SGgF+ ++e++++ g d +N Lev dg +tG v lcl|FitnessBrowser__azobra:AZOBR_RS06540 151 VDEVWQRATLMPGARTLVSTMRANGATCVLVSGGFRCFTERVRQWVGFDDDRGNVLEVVDGVMTGAVVE 219 ********************************************************************* PP TIGR00338 146 eivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltd 214 +i+d+++k + ll + + ++++ +t+avGDGanDl+m+ aAglg+af+akp + +a + +++ dlt+ lcl|FitnessBrowser__azobra:AZOBR_RS06540 220 PILDKDSKLEALLAYAGERHVPTVETMAVGDGANDLPMLLAAGLGVAFHAKPTVAAQARARVDHGDLTA 288 *******************************************************************99 PP TIGR00338 215 il 216 +l lcl|FitnessBrowser__azobra:AZOBR_RS06540 289 LL 290 86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (303 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: 9.41 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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