Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_041590033.1 TERTU_RS02885 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >NCBI__GCF_000023025.1:WP_041590033.1 Length = 417 Score = 280 bits (716), Expect = 6e-80 Identities = 170/398 (42%), Positives = 235/398 (59%), Gaps = 15/398 (3%) Query: 12 LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEG----D 67 +L+ I G+DRPG+T+ + LA + +++DI Q V + L LV P D Sbjct: 20 ILINISGEDRPGVTSSVTAILARNNANILDIGQAVIHDHLSLGMLVELPSEEASALAVKD 79 Query: 68 LRATVHSWAESLKLQAEIISGIGD-NRPRGFGRSLVTVLGHPLTAEATAAIAARITESGS 126 + +H ++ Q D +G R +VT+L +TA +A+A + E G Sbjct: 80 ILYRMHDSGMQVRFQPISEQSYSDWVGQQGKQRHIVTLLARHITASHISALAEILAEHGL 139 Query: 127 NIDRIFRLA-KYPVTA-------VEFAVSG--VETEPLRTALATEAAALGVDIAVVAAGL 176 NID I RL + P+ A VEF+ G + LR ALA A+ + VDIA + Sbjct: 140 NIDNISRLTGRVPLDAENKGQACVEFSARGRVADITVLRAALADIASDMDVDIAFQEDNM 199 Query: 177 HRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVALL 236 RR +R+V D+DSTLI+ EVI+ A AG D+VA +T AAMRGELDF +S AR+ALL Sbjct: 200 FRRTRRMVCFDMDSTLIEAEVIDELAKAAGVGDQVAAITEAAMRGELDFNESFRARMALL 259 Query: 237 AGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQA 296 GLD SV+D + + LT GA L+ TL +LGY+ ++SGGF +Q++LG+D+ A Sbjct: 260 KGLDESVLDGIAQRLPLTEGAARLVSTLNKLGYKTAILSGGFNYFGRYIQQKLGIDYVFA 319 Query: 297 NTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAGL 356 N LEIVDG++TG VTG+IV+ KA LLR A G+ L Q VA+GDGANDL ML+ AGL Sbjct: 320 NELEIVDGKVTGNVTGQIVNGQRKAELLRSLAEQEGISLEQVVAVGDGANDLPMLSIAGL 379 Query: 357 GVAFNAKPVVREAAHTAVNVPFLDTVLYLLGITREEVE 394 G+AF AKP+VR A A++ LD +LYL+G E+E Sbjct: 380 GIAFRAKPLVRAEAKQAISTLGLDAILYLMGFRDREME 417 Lambda K H 0.319 0.135 0.374 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: 366 Number of extensions: 15 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: 410 Length of database: 417 Length adjustment: 31 Effective length of query: 379 Effective length of database: 386 Effective search space: 146294 Effective search space used: 146294 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_041590033.1 TERTU_RS02885 (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.25572.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-87 278.8 0.5 2.1e-87 278.3 0.5 1.2 1 lcl|NCBI__GCF_000023025.1:WP_041590033.1 TERTU_RS02885 phosphoserine phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_041590033.1 TERTU_RS02885 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.3 0.5 2.1e-87 2.1e-87 1 218 [. 191 408 .. 191 409 .. 0.99 Alignments for each domain: == domain 1 score: 278.3 bits; conditional E-value: 2.1e-87 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia +e++++++++++v+fD+Dstlie+EvIde+ak+aGv+++V++iTe AmrgeldF+es+r R++ll lcl|NCBI__GCF_000023025.1:WP_041590033.1 191 DIAFQEDNMFRRTRRMVCFDMDSTLIEAEVIDELAKAAGVGDQVAAITEAAMRGELDFNESFRARMALL 259 68999**************************************************************** PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 kgl++++l+ ++++l+lteG+ lv++L++ gyk+a++SGgF+++ ++++kLg+d+vfaN+Le+ dgk lcl|NCBI__GCF_000023025.1:WP_041590033.1 260 KGLDESVLDGIAQRLPLTEGAARLVSTLNKLGYKTAILSGGFNYFGRYIQQKLGIDYVFANELEIVDGK 328 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 tG+v+g+iv+ + ka+ l +l+e+egisle++vavGDGanDl+m++ Aglgiaf akp ++ +a+++i lcl|NCBI__GCF_000023025.1:WP_041590033.1 329 VTGNVTGQIVNGQRKAELLRSLAEQEGISLEQVVAVGDGANDLPMLSIAGLGIAFRAKPLVRAEAKQAI 397 ********************************************************************* PP TIGR00338 208 ekkdltdilel 218 ++ l +il+l lcl|NCBI__GCF_000023025.1:WP_041590033.1 398 STLGLDAILYL 408 ****9999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (417 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: 13.77 // [ok]
This GapMind analysis is from Apr 10 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