Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_012465196.1 CLIM_RS01150 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >NCBI__GCF_000020465.1:WP_012465196.1 Length = 405 Score = 264 bits (675), Expect = 3e-75 Identities = 164/402 (40%), Positives = 226/402 (56%), Gaps = 17/402 (4%) Query: 12 LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGDLRAT 71 LL+ I G D+PG+T+ + LA V V+DI Q V + L LV P + Sbjct: 5 LLINITGLDKPGLTSKIAAILADAKVPVLDIGQAVIHNHLSLGMLVEVPKESASSPVLKD 64 Query: 72 VHSWAESLKLQAEIISGIGDNRPRGFG-----RSLVTVLGHPLTAEATAAIAARITESGS 126 + A +L +Q + R G R L+++L ++AE +++ + Sbjct: 65 LLFCAHTLGIQISFTPVADEEYDRWVGEQGKPRYLLSLLSRKISAEQLKRVSSIVAAHHL 124 Query: 127 NIDRIFRLA---------KYPVTAVEFAVSGVETEP--LRTALATEAAALGVDIAVVAAG 175 NID I RL+ + VEF++ G ++ R L +LG+DIA Sbjct: 125 NIDTISRLSGRIPLDNGDNHTRACVEFSLRGTLSDENLFREQLLAITDSLGIDIAFQEDN 184 Query: 176 LHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVAL 235 + RR +R+VV D+DSTLI EVI+ A AG +EV+ +T AMRGELDF +SL RVA Sbjct: 185 IFRRNRRMVVFDMDSTLITSEVIDELAKEAGVGEEVSAITEQAMRGELDFNESLQRRVAQ 244 Query: 236 LAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQ 295 L GLD V++ + A ++LT GA L LKRLGY+ ++SGGFT LQ++L +D+ Sbjct: 245 LRGLDEHVMESIAARLQLTEGAERLFGNLKRLGYKTAILSGGFTYFGHYLQKKLSIDYVY 304 Query: 296 ANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAG 355 ANTLEI +G LTGRV G +VD A KA LL A + L QTVA+GDGANDL ML AG Sbjct: 305 ANTLEIENGCLTGRVLGRVVDGARKAELLELLAEKENISLEQTVAVGDGANDLPMLGKAG 364 Query: 356 LGVAFNAKPVVREAAHTAVNVPFLDTVLYLLGITREEVEAAD 397 LG+AF AKP+VRE A A++ LD +LYL+G R+ E A+ Sbjct: 365 LGIAFRAKPIVRERAKQAISTLGLDAILYLMGF-RDRDELAE 405 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: 347 Number of extensions: 14 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: 410 Length of database: 405 Length adjustment: 31 Effective length of query: 379 Effective length of database: 374 Effective search space: 141746 Effective search space used: 141746 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_012465196.1 CLIM_RS01150 (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.422.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-86 273.2 0.3 1e-85 272.8 0.3 1.2 1 lcl|NCBI__GCF_000020465.1:WP_012465196.1 CLIM_RS01150 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020465.1:WP_012465196.1 CLIM_RS01150 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 272.8 0.3 1e-85 1e-85 1 218 [. 177 394 .. 177 395 .. 0.99 Alignments for each domain: == domain 1 score: 272.8 bits; conditional E-value: 1e-85 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia +e++ +++++++vvfD+Dstli++EvIde+ak+aGv+eeVs+iTe+AmrgeldF+esl+ Rv+ l lcl|NCBI__GCF_000020465.1:WP_012465196.1 177 DIAFQEDNIFRRNRRMVVFDMDSTLITSEVIDELAKEAGVGEEVSAITEQAMRGELDFNESLQRRVAQL 245 68899999************************************************************* PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 +gl++++++ ++ +l+lteG+e l +Lk+ gyk+a++SGgF+++ +l++kL +d+v aN+Le+e+g lcl|NCBI__GCF_000020465.1:WP_012465196.1 246 RGLDEHVMESIAARLQLTEGAERLFGNLKRLGYKTAILSGGFTYFGHYLQKKLSIDYVYANTLEIENGC 314 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 ltG+v g++vd ka+ l+ l+eke+isle+tvavGDGanDl+m+ +Aglgiaf akp+++e+a+++i lcl|NCBI__GCF_000020465.1:WP_012465196.1 315 LTGRVLGRVVDGARKAELLELLAEKENISLEQTVAVGDGANDLPMLGKAGLGIAFRAKPIVRERAKQAI 383 ********************************************************************* PP TIGR00338 208 ekkdltdilel 218 ++ l +il+l lcl|NCBI__GCF_000020465.1:WP_012465196.1 384 STLGLDAILYL 394 *****999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (405 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: 11.09 // [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