Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate 350360 BT0832 putative phosphoserine phosphatase (NCBI ptt file)
Query= SwissProt::Q12A06 (236 letters) >FitnessBrowser__Btheta:350360 Length = 409 Score = 176 bits (445), Expect = 8e-49 Identities = 101/208 (48%), Positives = 134/208 (64%), Gaps = 6/208 (2%) Query: 25 KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVS 84 +LI FDMDSTLI E +DE+A AG EV AITE+AMRGEI D+ ES +RVALLKG+ Sbjct: 196 RLICFDMDSTLIETEVIDELAIRAGVGDEVKAITESAMRGEI-DFTESFTRRVALLKGLD 254 Query: 85 VASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVL 144 + M E+ + L + G RL+ K G K+ ++SGGFT+F ++ + GIDY +N L Sbjct: 255 ESVMQEIAES-LPITEGVDRLMYVLKKYGYKIAILSGGFTYFGQYLQKKYGIDYVYANEL 313 Query: 145 ETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAG 204 E DG LTGR + GD+ DG+ K ++L + Q IA+GDGANDLPM+G AG Sbjct: 314 EIVDGKLTGRYL----GDVVDGKRKAELLRLIAQVEKVDIAQTIAVGDGANDLPMLGIAG 369 Query: 205 LSVAYHAKPRVREQAMVAINEGGLDRLL 232 L +A+HAKP+V A +IN GLD +L Sbjct: 370 LGIAFHAKPKVVANAKQSINTIGLDGVL 397 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: 244 Number of extensions: 9 Number of successful extensions: 5 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: 409 Length adjustment: 27 Effective length of query: 209 Effective length of database: 382 Effective search space: 79838 Effective search space used: 79838 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: 48 (23.1 bits)
Align candidate 350360 BT0832 (putative phosphoserine phosphatase (NCBI ptt file))
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.29361.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-82 262.1 0.3 2.6e-82 261.7 0.3 1.2 1 lcl|FitnessBrowser__Btheta:350360 BT0832 putative phosphoserine ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350360 BT0832 putative phosphoserine phosphatase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.7 0.3 2.6e-82 2.6e-82 4 218 .. 185 399 .. 182 400 .. 0.98 Alignments for each domain: == domain 1 score: 261.7 bits; conditional E-value: 2.6e-82 TIGR00338 4 kselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkk 79 ++++++++ ++l++fD+Dstlie+EvIde+a aGv++eV++iTe+Amrge+dF+es++ Rv+llkgl+++++++ lcl|FitnessBrowser__Btheta:350360 185 FQQDNMYRRMRRLICFDMDSTLIETEVIDELAIRAGVGDEVKAITESAMRGEIDFTESFTRRVALLKGLDESVMQE 260 678999********************************************************************** PP TIGR00338 80 veeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakak 155 ++e+l++teGv l+ Lk++gyk+a++SGgF+++ ++l++k g+d+v aN+Le+ dgkltG+ g++vd + ka+ lcl|FitnessBrowser__Btheta:350360 261 IAESLPITEGVDRLMYVLKKYGYKIAILSGGFTYFGQYLQKKYGIDYVYANELEIVDGKLTGRYLGDVVDGKRKAE 336 **************************************************************************** PP TIGR00338 156 tllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 l +++ e++++++t+avGDGanDl+m+ Aglgiaf+akp++ +a+++i++ l ++l++ lcl|FitnessBrowser__Btheta:350360 337 LLRLIAQVEKVDIAQTIAVGDGANDLPMLGIAGLGIAFHAKPKVVANAKQSINTIGLDGVLYF 399 ******************************************************999998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (409 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 10.78 // [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