Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_011033056.1 MM_RS05765 phosphoserine phosphatase SerB
Query= SwissProt::Q58989 (211 letters) >NCBI__GCF_000007065.1:WP_011033056.1 Length = 235 Score = 191 bits (486), Expect = 7e-54 Identities = 96/208 (46%), Positives = 143/208 (68%) Query: 4 KKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDL 63 + KLI+FD DSTL++ ETIDE+AR AGV +V++IT AM G L+FEQ+L +RV LL+ L Sbjct: 10 ENKLIVFDMDSTLIDAETIDELARAAGVVSKVEEITNRAMHGDLDFEQALAERVRLLEGL 69 Query: 64 PIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRL 123 P+E A+ +I GA E + +K+RGY A++SGGF IA +I + LG+D+ +N L Sbjct: 70 PVETALDAVNQINLMPGAAELVLYVKSRGYKTAMISGGFTIAAERIGKTLGIDFVVSNEL 129 Query: 124 IVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIA 183 +V+DG L G+V G V + ++K ++ E++A++ + E V VGDGAND +F+ AG IA Sbjct: 130 LVEDGYLLGEVVGPVTQSDSKAKVFEELAQLYNVRPEQCVVVGDGANDACIFEIAGFAIA 189 Query: 184 FCAKPILKEKADICIEKRDLREILKYIK 211 F KPIL+E AD+ I +DLR ++ ++ Sbjct: 190 FNPKPILREYADVVITVKDLRAVIPVLE 217 Lambda K H 0.314 0.136 0.358 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: 135 Number of extensions: 3 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: 211 Length of database: 235 Length adjustment: 22 Effective length of query: 189 Effective length of database: 213 Effective search space: 40257 Effective search space used: 40257 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 45 (21.9 bits)
Align candidate WP_011033056.1 MM_RS05765 (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.3809737.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-80 255.4 0.2 2.7e-80 255.1 0.2 1.0 1 NCBI__GCF_000007065.1:WP_011033056.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000007065.1:WP_011033056.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 255.1 0.2 2.7e-80 2.7e-80 12 219 .] 9 216 .. 4 216 .. 0.98 Alignments for each domain: == domain 1 score: 255.1 bits; conditional E-value: 2.7e-80 TIGR00338 12 kkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkveekl 84 +++kl+vfD+Dstli++E+Ide+a++aGv +V+eiT+rAm+g+ldF+++l eRv+ll glpve++ + +++ NCBI__GCF_000007065.1:WP_011033056.1 9 TENKLIVFDMDSTLIDAETIDELARAAGVVSKVEEITNRAMHGDLDFEQALAERVRLLEGLPVETALDAVNQI 81 6789********************************************************************* PP TIGR00338 85 elteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktl 157 +l++G+ elv k +gyk+a+iSGgF+++ae++ + Lg+d+v++N+L vedg l G+v g+++++++kak+ NCBI__GCF_000007065.1:WP_011033056.1 82 NLMPGAAELVLYVKSRGYKTAMISGGFTIAAERIGKTLGIDFVVSNELLVEDGYLLGEVVGPVTQSDSKAKVF 154 ************************************************************************* PP TIGR00338 158 lkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219 ++l++ +++ +e++v+vGDGanD +++ Ag+ iafn kp+l+e ad+vi kdl++++++l NCBI__GCF_000007065.1:WP_011033056.1 155 EELAQLYNVRPEQCVVVGDGANDACIFEIAGFAIAFNPKPILREYADVVITVKDLRAVIPVL 216 *********************************************************99886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (235 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: 11.00 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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