Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate Dsui_2379 Dsui_2379 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >FitnessBrowser__PS:Dsui_2379 Length = 280 Score = 232 bits (592), Expect = 5e-66 Identities = 124/217 (57%), Positives = 158/217 (72%), Gaps = 5/217 (2%) Query: 18 DLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRV 77 D KL+D+ LI FDMDSTLI IEC+DE+AD AG+KAEV+A+TE+AMRGEI DY+ESLR+R+ Sbjct: 66 DRKLADYGLICFDMDSTLITIECIDELADFAGKKAEVSAVTESAMRGEI-DYRESLRRRL 124 Query: 78 ALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGID 137 ALL G+ + VY RL L+ GA L++A + AGL+ ++SGGFT+FT+R+R ELG D Sbjct: 125 ALLAGLDARVLARVYGERLLLSEGARELLEAAQTAGLRTAILSGGFTYFTERLRIELGFD 184 Query: 138 YTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDL 197 + SN LE + G LTG++V GDI D + K L +LG+ Q IA+GDGANDL Sbjct: 185 FATSNELEISGGKLTGKVV----GDIVDAQAKAHHLNRLRDELGLEREQVIAVGDGANDL 240 Query: 198 PMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLEL 234 MM EAGLSVA+HAKP R +A VAI+ GGLD LL L Sbjct: 241 LMMAEAGLSVAFHAKPATRAKASVAISHGGLDSLLNL 277 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: 201 Number of extensions: 11 Number of successful extensions: 3 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: 280 Length adjustment: 24 Effective length of query: 212 Effective length of database: 256 Effective search space: 54272 Effective search space used: 54272 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 Dsui_2379 Dsui_2379 (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.17620.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-73 233.1 0.1 1.8e-73 232.8 0.1 1.1 1 lcl|FitnessBrowser__PS:Dsui_2379 Dsui_2379 phosphoserine phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_2379 Dsui_2379 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.8 0.1 1.8e-73 1.8e-73 11 218 .. 69 277 .. 61 278 .. 0.96 Alignments for each domain: == domain 1 score: 232.8 bits; conditional E-value: 1.8e-73 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkve.eklel 86 l +l++fD+Dstli++E+Ide+a aG + eVs++Te+Amrge+d++eslr R++ll gl++ +l +v+ e+l l lcl|FitnessBrowser__PS:Dsui_2379 69 LADYGLICFDMDSTLITIECIDELADFAGKKAEVSAVTESAMRGEIDYRESLRRRLALLAGLDARVLARVYgERLLL 145 55678************************************************************99999758999* PP TIGR00338 87 teGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllkllek 163 eG++el ++ +++g+++a++SGgF++++e+l+ +Lg d++ +N+Le++ gkltGkv g+ivd++aka+ l +l + lcl|FitnessBrowser__PS:Dsui_2379 146 SEGARELLEAAQTAGLRTAILSGGFTYFTERLRIELGFDFATSNELEISGGKLTGKVVGDIVDAQAKAHHLNRLRDE 222 ***************************************************************************** PP TIGR00338 164 egislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 g++ e+++avGDGanDl m+++Agl +af+akp+ + ka ++i++ l ++l+l lcl|FitnessBrowser__PS:Dsui_2379 223 LGLEREQVIAVGDGANDLLMMAEAGLSVAFHAKPATRAKASVAISHGGLDSLLNL 277 **********************************************999988875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (280 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: 10.39 // [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