Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_012503095.1 CPAR_RS09480 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >NCBI__GCF_000020505.1:WP_012503095.1 Length = 407 Score = 269 bits (687), Expect = 1e-76 Identities = 163/397 (41%), Positives = 228/397 (57%), Gaps = 24/397 (6%) Query: 12 LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEG----D 67 LL+ I G D+PG+T+ + + LA Y V V+DI Q V + L L+ P D Sbjct: 5 LLITISGPDKPGLTSKITEVLARYDVPVLDIGQSVIHNHLSLGMLIEVPKASTSAPILKD 64 Query: 68 LRATVHSWAESLKLQA----EIISGIGDNRPRGFGRSLVTVLGHPLTAEATAAIAARITE 123 L T H+ ++ E +G+ +G R L+++LG +++E + +++ Sbjct: 65 LLFTAHTLGLVIEFSPINTREYHKWVGE---QGKPRYLLSLLGRKISSEHLERVTTLVSK 121 Query: 124 SGSNIDRIFRLA-KYPV----------TAVEFAVSGV--ETEPLRTALATEAAALGVDIA 170 G NID I RL+ + P+ +EF++ G + E LR + +LGVDIA Sbjct: 122 HGLNIDTINRLSGRLPLEDERDPGQTKACIEFSLRGALNDEEQLRAEMLDITDSLGVDIA 181 Query: 171 VVAAGLHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLH 230 + RR +RLVV D+DSTLI EVI+ A AG D+VA +T AMRGELDF +SL Sbjct: 182 FQEDNIFRRTRRLVVFDMDSTLITSEVIDELAKEAGSGDQVAAITEQAMRGELDFTESLK 241 Query: 231 ARVALLAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLG 290 RV L GL+ S + KV ++LT GA L L RLG++ ++SGGFT LQ++L Sbjct: 242 MRVGTLKGLEESTLQKVAERLQLTEGAEHLFHNLHRLGFKTAILSGGFTYFGRYLQKKLN 301 Query: 291 LDFAQANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDM 350 +D+ AN LEIVDG++TG V G++VD KA LL A + L QTVA+GDGANDL M Sbjct: 302 IDYVFANELEIVDGKMTGNVIGQVVDGKRKAALLEEIATTENIRLEQTVAVGDGANDLPM 361 Query: 351 LNAAGLGVAFNAKPVVREAAHTAVNVPFLDTVLYLLG 387 L AGLG+AF AKP+VRE A A++ LD +LYL+G Sbjct: 362 LGKAGLGIAFRAKPIVRETAKQAISTLGLDAILYLMG 398 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: 363 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: 407 Length adjustment: 31 Effective length of query: 379 Effective length of database: 376 Effective search space: 142504 Effective search space used: 142504 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_012503095.1 CPAR_RS09480 (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.2678.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-86 275.3 1.6 2.3e-86 274.9 1.6 1.2 1 lcl|NCBI__GCF_000020505.1:WP_012503095.1 CPAR_RS09480 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020505.1:WP_012503095.1 CPAR_RS09480 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 274.9 1.6 2.3e-86 2.3e-86 1 218 [. 179 396 .. 179 397 .. 0.99 Alignments for each domain: == domain 1 score: 274.9 bits; conditional E-value: 2.3e-86 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia +e++ ++++++lvvfD+Dstli++EvIde+ak+aG +++V++iTe+AmrgeldF+esl+ Rv +l lcl|NCBI__GCF_000020505.1:WP_012503095.1 179 DIAFQEDNIFRRTRRLVVFDMDSTLITSEVIDELAKEAGSGDQVAAITEQAMRGELDFTESLKMRVGTL 247 68899999************************************************************* PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 kgl++++l+kv+e+l+lteG+e l ++L++ g+k+a++SGgF+++ +l++kL++d+vfaN+Le+ dgk lcl|NCBI__GCF_000020505.1:WP_012503095.1 248 KGLEESTLQKVAERLQLTEGAEHLFHNLHRLGFKTAILSGGFTYFGRYLQKKLNIDYVFANELEIVDGK 316 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 +tG+v g++vd + ka l++++ +e+i le+tvavGDGanDl+m+ +Aglgiaf akp+++e+a+++i lcl|NCBI__GCF_000020505.1:WP_012503095.1 317 MTGNVIGQVVDGKRKAALLEEIATTENIRLEQTVAVGDGANDLPMLGKAGLGIAFRAKPIVRETAKQAI 385 ********************************************************************* PP TIGR00338 208 ekkdltdilel 218 ++ l +il+l lcl|NCBI__GCF_000020505.1:WP_012503095.1 386 STLGLDAILYL 396 *****999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (407 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.52 // [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