Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate YP_425557.1 Rru_A0465 phosphoserine phosphatase
Query= SwissProt::Q5M3B3 (215 letters) >NCBI__GCF_000013085.1:YP_425557.1 Length = 299 Score = 166 bits (419), Expect = 6e-46 Identities = 94/199 (47%), Positives = 122/199 (61%) Query: 5 KGLLVMDVDSTLVQEEVIDLLGEEAGVGREVAEITERAMRGELDFRQALNERVATLKGLP 64 KGLL+ D+DST+V E +D L AG+ ++A IT RAM GE+DF AL ERV L GL Sbjct: 84 KGLLIADMDSTMVIGETLDDLAAHAGLKDKIAAITARAMNGEIDFEAALRERVGMLAGLS 143 Query: 65 DSIFEKVYARIHFNKGAKELVDELHSRGFKVGLVSGGFHETVDRLAKEAGIDYVKANHLE 124 S E+ +A G + LV + + G + LVSGGF ++AK G AN LE Sbjct: 144 ASALEETWAATALTPGGRTLVRTMAANGARCVLVSGGFSVFTAKVAKACGFHDHVANRLE 203 Query: 125 VIDGFLTGKVYGEIVTKDVKVAKLKDWAAENGLKLSQTIAMGDGANDLPMIKTAGIGIAF 184 +IDG L+GKV +V + VK+A LK AA+ GL LS A+GDGANDLPM+ AG+G+AF Sbjct: 204 IIDGALSGKVIDPVVDRAVKLATLKAEAAKLGLPLSACAAVGDGANDLPMVMAAGLGVAF 263 Query: 185 CAKPIVRVQAPYQITEPDL 203 AKP+V Q +I DL Sbjct: 264 HAKPVVAAQTRARIDHGDL 282 Lambda K H 0.317 0.138 0.384 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: 156 Number of extensions: 7 Number of successful extensions: 1 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: 215 Length of database: 299 Length adjustment: 24 Effective length of query: 191 Effective length of database: 275 Effective search space: 52525 Effective search space used: 52525 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
Align candidate YP_425557.1 Rru_A0465 (phosphoserine phosphatase)
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.21338.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-62 195.4 0.2 6.5e-62 195.0 0.2 1.1 1 lcl|NCBI__GCF_000013085.1:YP_425557.1 Rru_A0465 phosphoserine phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013085.1:YP_425557.1 Rru_A0465 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 195.0 0.2 6.5e-62 6.5e-62 9 216 .. 79 286 .. 72 288 .. 0.97 Alignments for each domain: == domain 1 score: 195.0 bits; conditional E-value: 6.5e-62 TIGR00338 9 kllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkv 80 + + k+l++ D+Dst++ E++d++a+ aG ++++++iT rAm+ge+dF+++lreRv +l gl+++ l++ lcl|NCBI__GCF_000013085.1:YP_425557.1 79 EDGRRKGLLIADMDSTMVIGETLDDLAAHAGLKDKIAAITARAMNGEIDFEAALRERVGMLAGLSASALEET 150 5567899***************************************************************** PP TIGR00338 81 eeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesa 152 lt+G + lv+++ +g + +++SGgF++++ k+++ g +aNrLe+ dg+l+Gkv ++vd + lcl|NCBI__GCF_000013085.1:YP_425557.1 151 WAATALTPGGRTLVRTMAANGARCVLVSGGFSVFTAKVAKACGFHDHVANRLEIIDGALSGKVIDPVVDRAV 222 ************************************************************************ PP TIGR00338 153 kaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdil 216 k tl+ + k g++l ++ avGDGanDl+m+ aAglg+af+akpv+ + + i++ dlt++l lcl|NCBI__GCF_000013085.1:YP_425557.1 223 KLATLKAEAAKLGLPLSACAAVGDGANDLPMVMAAGLGVAFHAKPVVAAQTRARIDHGDLTALL 286 *************************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (299 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: 10.03 // [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