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) >FitnessBrowser__azobra:AZOBR_RS06540 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.20221.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.56 // [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