Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate RR42_RS07660 RR42_RS07660 phosphoserine phosphatase
Query= SwissProt::Q12A06 (236 letters) >FitnessBrowser__Cup4G11:RR42_RS07660 Length = 284 Score = 244 bits (624), Expect = 1e-69 Identities = 126/215 (58%), Positives = 159/215 (73%), Gaps = 4/215 (1%) Query: 20 KLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVAL 79 KLSDFKL+A DMDSTLI IEC+DEIAD G KAEV+AITEAAMRGEI+D+ ESLR+RVAL Sbjct: 71 KLSDFKLVAMDMDSTLITIECIDEIADFCGLKAEVSAITEAAMRGEITDFNESLRRRVAL 130 Query: 80 LKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYT 139 LKG+ + +D VY RLRL+PGA +++ + G++ LLVSGGF FTD+++ L +D T Sbjct: 131 LKGLDASVLDRVYEERLRLSPGAETMLRTVQALGMRTLLVSGGFVHFTDKLKPRLKLDVT 190 Query: 140 RSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPM 199 R+N LE DG LTG+++ G+I + + K + + E C Q+G P QAI MGDG+NDL M Sbjct: 191 RANTLEIVDGKLTGQVL----GEIVNADVKARTVQEVCAQIGADPSQAIVMGDGSNDLKM 246 Query: 200 MGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLEL 234 M AGLSVA+ AKP VR QA VA N GLD LL+L Sbjct: 247 MAVAGLSVAFRAKPVVRAQASVAFNHVGLDGLLQL 281 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: 227 Number of extensions: 8 Number of successful extensions: 2 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: 284 Length adjustment: 24 Effective length of query: 212 Effective length of database: 260 Effective search space: 55120 Effective search space used: 55120 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 RR42_RS07660 RR42_RS07660 (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.28791.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-71 224.7 0.6 6.7e-71 224.4 0.6 1.1 1 lcl|FitnessBrowser__Cup4G11:RR42_RS07660 RR42_RS07660 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS07660 RR42_RS07660 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 224.4 0.6 6.7e-71 6.7e-71 11 218 .. 72 281 .. 64 282 .. 0.96 Alignments for each domain: == domain 1 score: 224.4 bits; conditional E-value: 6.7e-71 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgel.dFkeslreRvkllkglpvellk 78 l+ klv +D+Dstli++E+Ideia +G + eVs+iTe Amrge+ dF+eslr Rv+llkgl++++l+ lcl|FitnessBrowser__Cup4G11:RR42_RS07660 72 LSDFKLVAMDMDSTLITIECIDEIADFCGLKAEVSAITEAAMRGEItDFNESLRRRVALLKGLDASVLD 140 56679****************************************769********************* PP TIGR00338 79 kve.eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvege 146 +v+ e+l+l +G+e + ++ + g+++ ++SGgF +++klk +L+ld+ aN+Le+ dgkltG+v ge lcl|FitnessBrowser__Cup4G11:RR42_RS07660 141 RVYeERLRLSPGAETMLRTVQALGMRTLLVSGGFVHFTDKLKPRLKLDVTRANTLEIVDGKLTGQVLGE 209 997268*************************************************************** PP TIGR00338 147 ivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdi 215 iv++++ka+t+++++ + g ++ + +++GDG+nDl+m++ Agl +af akpv++ +a ++ ++ l ++ lcl|FitnessBrowser__Cup4G11:RR42_RS07660 210 IVNADVKARTVQEVCAQIGADPSQAIVMGDGSNDLKMMAVAGLSVAFRAKPVVRAQASVAFNHVGLDGL 278 ***************************************************************999998 PP TIGR00338 216 lel 218 l+l lcl|FitnessBrowser__Cup4G11:RR42_RS07660 279 LQL 281 876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (284 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: 7.94 // [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