Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate GFF3562 PGA1_c36160 phosphoserine phosphatase SerB
Query= SwissProt::Q58989 (211 letters) >FitnessBrowser__Phaeo:GFF3562 Length = 309 Score = 165 bits (418), Expect = 7e-46 Identities = 92/206 (44%), Positives = 130/206 (63%), Gaps = 1/206 (0%) Query: 3 KKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKD 62 ++KK++L D DST++ E IDE+A EAGV VK+IT AM G+LNF+ +LR+RV+LLK Sbjct: 92 RRKKMLLADMDSTMIQQECIDELAEEAGVGARVKEITARAMNGELNFDGALRERVALLKG 151 Query: 63 LPIEKVEKAI-KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFAN 121 LP+E + + + +RIT G + +K G A+VSGGF +++ E+LG D AN Sbjct: 152 LPVEVIAQVLDRRITLMPGGAALLATMKADGAYAALVSGGFTAFTSRVAEQLGFDENRAN 211 Query: 122 RLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK 181 L+V DG LTG+V +L AK E LE+I G++ D +AVGDGAND+ M +AG Sbjct: 212 TLLVADGLLTGEVGMPILGRAAKVEALEQITARLGLSEADVMAVGDGANDLGMLGRAGAG 271 Query: 182 IAFCAKPILKEKADICIEKRDLREIL 207 +A AKP + + DI I DL +L Sbjct: 272 VALHAKPSVAAECDIRINHGDLTALL 297 Lambda K H 0.314 0.136 0.358 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: 148 Number of extensions: 5 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: 211 Length of database: 309 Length adjustment: 24 Effective length of query: 187 Effective length of database: 285 Effective search space: 53295 Effective search space used: 53295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate GFF3562 PGA1_c36160 (phosphoserine phosphatase SerB)
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.29738.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-67 212.7 0.4 3.1e-67 212.4 0.4 1.1 1 lcl|FitnessBrowser__Phaeo:GFF3562 PGA1_c36160 phosphoserine phosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3562 PGA1_c36160 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 212.4 0.4 3.1e-67 3.1e-67 11 218 .. 91 299 .. 84 300 .. 0.96 Alignments for each domain: == domain 1 score: 212.4 bits; conditional E-value: 3.1e-67 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkv.eekle 85 + kk+++ D+Dst+i++E+Ide+a +aGv+ V+eiT rAm+gel+F+ +lreRv+llkglpve++ +v +++ lcl|FitnessBrowser__Phaeo:GFF3562 91 GRRKKMLLADMDSTMIQQECIDELAEEAGVGARVKEITARAMNGELNFDGALRERVALLKGLPVEVIAQVlDRRIT 166 578999***********************************************************666661568** PP TIGR00338 86 lteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllkll 161 l++G l ++k g a++SGgF+ ++ +++e+Lg d aN+L v dg ltG+v +i+ ak + l++++ lcl|FitnessBrowser__Phaeo:GFF3562 167 LMPGGAALLATMKADGAYAALVSGGFTAFTSRVAEQLGFDENRANTLLVADGLLTGEVGMPILGRAAKVEALEQIT 242 **************************************************************************** PP TIGR00338 162 ekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 + g+s ++++avGDGanDl m+ +Ag+g+a +akp + + di i++ dlt++l+l lcl|FitnessBrowser__Phaeo:GFF3562 243 ARLGLSEADVMAVGDGANDLGMLGRAGAGVALHAKPSVAAECDIRINHGDLTALLYL 299 *****************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (309 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: 7.00 // [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