Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate GFF2574 HP15_2518 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >FitnessBrowser__Marino:GFF2574 Length = 410 Score = 265 bits (677), Expect = 2e-75 Identities = 161/405 (39%), Positives = 229/405 (56%), Gaps = 19/405 (4%) Query: 12 LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGDLRAT 71 +L+ + G+D+PG+T+ + + Y V ++DI Q V + L+ P + Sbjct: 5 VLINVSGRDKPGLTSEITGIMGRYDVRILDIGQAVIHDHLTWGILIEIPDESKSSPVIRD 64 Query: 72 VHSWAESLKLQAEIISGIGDN-----RPRGFGRSLVTVLGHPLTAEATAAIAARITESGS 126 + +L LQ + R +VT+L + AE A ++A G Sbjct: 65 LLFRLHALDLQVRFAPITVEEYQSWAAARNRACYIVTLLARDIKAEQIARVSAITARHGL 124 Query: 127 NIDRIFRLAKYP--------VTAVEFAVSGV--ETEPLRTALATEAAALGVDIAVVAAGL 176 NID I RL+ P + VEF+V G + E LR A + VDIA + Sbjct: 125 NIDNISRLSARPSLNAADNRIACVEFSVRGTPSDLEKLRADFLHIAGEMNVDIAFQEDSI 184 Query: 177 HRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVALL 236 RR +RLVV D+DSTLI+ EVI+ AA AG ++VAE+T AM+GELDF QS R+ALL Sbjct: 185 FRRNRRLVVFDMDSTLIEAEVIDELAAEAGVGEQVAEITERAMQGELDFSQSFAERLALL 244 Query: 237 AGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQA 296 GLD SV++ + + +R+T GA LI +LK LGY+ ++SGGFT LQ +LG+D+ A Sbjct: 245 KGLDESVLEGIASRLRMTEGAEHLILSLKALGYRTAILSGGFTYFARHLQRKLGIDYIYA 304 Query: 297 NTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAGL 356 N LEI G++TG+V+G+IVD KA LL A + Q +A+GDGANDL ML+ AGL Sbjct: 305 NELEIEGGKVTGKVSGQIVDGKRKAELLLEIAEKEHISREQVIAVGDGANDLPMLSQAGL 364 Query: 357 GVAFNAKPVVREAAHTAVNVPFLDTVLYLLGI----TREEVEAAD 397 GVAF AKP+V+E+A A++ LD +LYL+G T + +E AD Sbjct: 365 GVAFRAKPLVKESARHAISTLGLDAILYLIGFRESETNQSLENAD 409 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: 376 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: 410 Length adjustment: 31 Effective length of query: 379 Effective length of database: 379 Effective search space: 143641 Effective search space used: 143641 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 GFF2574 HP15_2518 (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.31380.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-86 275.7 0.4 1.7e-86 275.4 0.4 1.1 1 lcl|FitnessBrowser__Marino:GFF2574 HP15_2518 phosphoserine phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2574 HP15_2518 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.4 0.4 1.7e-86 1.7e-86 1 219 [] 176 394 .. 176 394 .. 0.99 Alignments for each domain: == domain 1 score: 275.4 bits; conditional E-value: 1.7e-86 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve 75 dia +e+s ++++++lvvfD+Dstlie+EvIde+a++aGv+e+V+eiTerAm+geldF +s+ eR++llkgl+++ lcl|FitnessBrowser__Marino:GFF2574 176 DIAFQEDSIFRRNRRLVVFDMDSTLIEAEVIDELAAEAGVGEQVAEITERAMQGELDFSQSFAERLALLKGLDES 250 688999999****************************************************************** PP TIGR00338 76 llkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivde 150 +l+ ++++l++teG+e l+ +Lk gy++a++SGgF+++a +l+ kLg+d++ aN+Le+e gk tGkv+g+ivd lcl|FitnessBrowser__Marino:GFF2574 251 VLEGIASRLRMTEGAEHLILSLKALGYRTAILSGGFTYFARHLQRKLGIDYIYANELEIEGGKVTGKVSGQIVDG 325 *************************************************************************** PP TIGR00338 151 sakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219 + ka+ ll+++eke+is e+++avGDGanDl+m+++Aglg+af akp +ke a ++i++ l +il+l+ lcl|FitnessBrowser__Marino:GFF2574 326 KRKAELLLEIAEKEHISREQVIAVGDGANDLPMLSQAGLGVAFRAKPLVKESARHAISTLGLDAILYLI 394 ****************************************************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (410 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: 15.57 // [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