Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_041471445.1 CPHAMN1_RS01745 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >NCBI__GCF_000020545.1:WP_041471445.1 Length = 409 Score = 268 bits (686), Expect = 2e-76 Identities = 167/401 (41%), Positives = 228/401 (56%), Gaps = 23/401 (5%) Query: 12 LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEG----D 67 LL+ I G D+ G+TA L LA Y+V ++DI Q V ++ L LV P D Sbjct: 5 LLLNISGPDKSGLTAQLSSILARYNVRILDIGQEVIHDQLSLGMLVEVPSEFQSAPVLKD 64 Query: 68 LRATVHSWAESLKLQAEIISG----IGDNRPRGFGRSLVTVLGHPLTAEATAAIAARITE 123 L TVH+ S+ +G+ +G R L+T+L + AE A + + I E Sbjct: 65 LLFTVHTLGLSISFTPITDEAYEHWVGE---QGKPRHLLTLLAREIKAEQIARVTSTIAE 121 Query: 124 SGSNIDRIFRL----------AKYPVTAVEFAVSG--VETEPLRTALATEAAALGVDIAV 171 NID I RL A+ +EF++ G V + R + LG+DIA Sbjct: 122 HNLNIDTINRLSGRIPLGKRLAENTKACIEFSLRGAIVNEDRFREQMLAITDDLGIDIAF 181 Query: 172 VAAGLHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHA 231 ++RR +RLVV D+DSTLI EVI+ A AG ++VAE+T AMRGE+DF +SL Sbjct: 182 QEDNIYRRNRRLVVFDMDSTLITSEVIDELAIEAGSGEKVAEITEQAMRGEIDFTESLQM 241 Query: 232 RVALLAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGL 291 RV+ L GLD SV+ KV ++LT GA TL L LG++ ++SGGFT LQ++L + Sbjct: 242 RVSTLKGLDESVLQKVAKRLQLTEGAETLFYNLHNLGFKTAIISGGFTYFGHYLQKKLTI 301 Query: 292 DFAQANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDML 351 D+ ANTLEI G+LTG+V GE+VD KA LL A + L QT+A+GDGANDL ML Sbjct: 302 DYVYANTLEIEGGKLTGKVLGEVVDGKRKAALLEHIAREEKISLDQTIAVGDGANDLPML 361 Query: 352 NAAGLGVAFNAKPVVREAAHTAVNVPFLDTVLYLLGITREE 392 AGLG+AF AKP+V+E+A A++ LD +LYL+G E Sbjct: 362 GKAGLGIAFRAKPIVKESAKQAISTLGLDAILYLMGFRDRE 402 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: 336 Number of extensions: 16 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: 409 Length adjustment: 31 Effective length of query: 379 Effective length of database: 378 Effective search space: 143262 Effective search space used: 143262 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_041471445.1 CPHAMN1_RS01745 (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.20882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-85 271.7 1.4 3.1e-85 271.2 1.4 1.2 1 lcl|NCBI__GCF_000020545.1:WP_041471445.1 CPHAMN1_RS01745 phosphoserine ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_041471445.1 CPHAMN1_RS01745 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 271.2 1.4 3.1e-85 3.1e-85 1 218 [. 178 395 .. 178 396 .. 0.99 Alignments for each domain: == domain 1 score: 271.2 bits; conditional E-value: 3.1e-85 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia +e++ ++++++lvvfD+Dstli++EvIde+a +aG +e+V+eiTe+Amrge+dF+esl+ Rv++l lcl|NCBI__GCF_000020545.1:WP_041471445.1 178 DIAFQEDNIYRRNRRLVVFDMDSTLITSEVIDELAIEAGSGEKVAEITEQAMRGEIDFTESLQMRVSTL 246 6889999************************************************************** PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 kgl++++l+kv+++l+lteG+e l +L++ g+k+a+iSGgF+++ +l++kL +d+v aN+Le+e gk lcl|NCBI__GCF_000020545.1:WP_041471445.1 247 KGLDESVLQKVAKRLQLTEGAETLFYNLHNLGFKTAIISGGFTYFGHYLQKKLTIDYVYANTLEIEGGK 315 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 ltGkv ge+vd + ka l++++++e+isl +t+avGDGanDl+m+ +Aglgiaf akp++ke a+++i lcl|NCBI__GCF_000020545.1:WP_041471445.1 316 LTGKVLGEVVDGKRKAALLEHIAREEKISLDQTIAVGDGANDLPMLGKAGLGIAFRAKPIVKESAKQAI 384 ********************************************************************* PP TIGR00338 208 ekkdltdilel 218 ++ l +il+l lcl|NCBI__GCF_000020545.1:WP_041471445.1 385 STLGLDAILYL 395 *****999987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 16.53 // [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