Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate YP_002826538.1 NGR_c20220 phosphoserine phosphatase
Query= SwissProt::Q58989 (211 letters) >NCBI__GCF_000018545.1:YP_002826538.1 Length = 295 Score = 167 bits (422), Expect = 2e-46 Identities = 92/206 (44%), Positives = 131/206 (63%), Gaps = 1/206 (0%) Query: 3 KKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKD 62 ++KK ++ D DST++ E IDE+A E G++E+V IT AM G++ FE +L +RV+LLK Sbjct: 78 RRKKFLIADMDSTMIGQECIDELAAEVGLKEKVAAITARAMNGEIAFEPALIERVALLKG 137 Query: 63 LPIEKVEKAI-KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFAN 121 LP + + I KRIT T G E I +K +G+ A+VSGGF + I EKLG D AN Sbjct: 138 LPTTVIAEVIAKRITLTPGGRELIATMKAKGHYTALVSGGFTVFTGPIAEKLGFDENRAN 197 Query: 122 RLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK 181 L+ ++G LTGDV +L AK + L I++ GI+ D +AVGDGAND+ M + AG Sbjct: 198 ELLEENGALTGDVARPILGRQAKVDALIDISERLGISTADVIAVGDGANDLGMLQLAGSG 257 Query: 182 IAFCAKPILKEKADICIEKRDLREIL 207 +A AKP++ E+A I I+ DL +L Sbjct: 258 VALHAKPVVAEQAKIRIDHGDLSALL 283 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: 171 Number of extensions: 9 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: 211 Length of database: 295 Length adjustment: 24 Effective length of query: 187 Effective length of database: 271 Effective search space: 50677 Effective search space used: 50677 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: 46 (22.3 bits)
Align candidate YP_002826538.1 NGR_c20220 (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.29943.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-69 220.1 1.1 1.6e-69 219.9 1.1 1.1 1 lcl|NCBI__GCF_000018545.1:YP_002826538.1 NGR_c20220 phosphoserine phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000018545.1:YP_002826538.1 NGR_c20220 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 219.9 1.1 1.6e-69 1.6e-69 7 218 .. 73 285 .. 67 286 .. 0.96 Alignments for each domain: == domain 1 score: 219.9 bits; conditional E-value: 1.6e-69 TIGR00338 7 lskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve 75 ++ ++ kk ++ D+Dst+i +E+Ide+a+++G +e+V++iT rAm+ge+ F+ +l eRv+llkglp lcl|NCBI__GCF_000018545.1:YP_002826538.1 73 QEAETRRKKFLIADMDSTMIGQECIDELAAEVGLKEKVAAITARAMNGEIAFEPALIERVALLKGLPTT 141 455678899************************************************************ PP TIGR00338 76 .llkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkv 143 +++ ++++++lt+G +el+ ++k kg +a++SGgF+++++ ++ekLg d aN+L e+g+ltG+v lcl|NCBI__GCF_000018545.1:YP_002826538.1 142 vIAEVIAKRITLTPGGRELIATMKAKGHYTALVSGGFTVFTGPIAEKLGFDENRANELLEENGALTGDV 210 77788899************************************************************* PP TIGR00338 144 egeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdl 212 +i+ +ak + l + e+ gis+++++avGDGanDl m++ Ag g+a +akpv+ e+a+i i++ dl lcl|NCBI__GCF_000018545.1:YP_002826538.1 211 ARPILGRQAKVDALIDISERLGISTADVIAVGDGANDLGMLQLAGSGVALHAKPVVAEQAKIRIDHGDL 279 ********************************************************************* PP TIGR00338 213 tdilel 218 ++l+l lcl|NCBI__GCF_000018545.1:YP_002826538.1 280 SALLYL 285 *99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (295 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: 10.81 // [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