Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_034991023.1 DL88_RS02095 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000745425.1:WP_034991023.1 Length = 325 Score = 155 bits (391), Expect = 1e-42 Identities = 97/222 (43%), Positives = 133/222 (59%), Gaps = 6/222 (2%) Query: 12 VNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKE 71 V+V L+ KL DMDST+I EC+DE+A G+K VA ITE AMRGEI+ ++ Sbjct: 70 VDVIVQPLENRRKKLFLADMDSTMIRQECIDELAGEVGKKKHVAEITERAMRGEIA-FEP 128 Query: 72 SLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIR 131 +LR+RVALLKG+ ++ +V R+ ++PGA LVQ + G+ +LVSGGFT FT I Sbjct: 129 ALRERVALLKGLHPDTIRKVIGKRITMSPGARILVQTLRQHGVHTVLVSGGFTAFTSVIG 188 Query: 132 DELGIDYTRSNVLET-TDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAM 190 +++G +NVL DG L G +V +P I + K L+ +L ++ IA+ Sbjct: 189 EQIGFHENHANVLLLGQDGRLAG-LVQEP---ILGKDAKLATLVAKRDELKLAESDTIAV 244 Query: 191 GDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLL 232 GDGANDL M+ AGL +AYHAKP V A I+ G L LL Sbjct: 245 GDGANDLDMIRAAGLGLAYHAKPAVAAAAAACIDHGDLTALL 286 Lambda K H 0.319 0.136 0.385 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: 200 Number of extensions: 13 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: 236 Length of database: 325 Length adjustment: 25 Effective length of query: 211 Effective length of database: 300 Effective search space: 63300 Effective search space used: 63300 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_034991023.1 DL88_RS02095 (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.20008.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-66 208.3 0.2 7.6e-66 207.8 0.2 1.1 1 lcl|NCBI__GCF_000745425.1:WP_034991023.1 DL88_RS02095 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034991023.1 DL88_RS02095 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.8 0.2 7.6e-66 7.6e-66 11 217 .. 79 287 .. 71 288 .. 0.96 Alignments for each domain: == domain 1 score: 207.8 bits; conditional E-value: 7.6e-66 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve.llk 78 ++ kkl++ D+Dst+i++E+Ide+a ++G +++V+eiTerAmrge+ F+ +lreRv+llkgl+ + ++k lcl|NCBI__GCF_000745425.1:WP_034991023.1 79 NRRKKLFLADMDSTMIRQECIDELAGEVGKKKHVAEITERAMRGEIAFEPALRERVALLKGLHPDtIRK 147 5789***********************************************************995666 PP TIGR00338 79 kveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLeve.dgkltGkvege 146 + +++++ +G++ lv++L+++g++++++SGgF+ ++ + e++g aN L + dg+l+G v+ + lcl|NCBI__GCF_000745425.1:WP_034991023.1 148 VIGKRITMSPGARILVQTLRQHGVHTVLVSGGFTAFTSVIGEQIGFHENHANVLLLGqDGRLAGLVQEP 216 77899************************************************99988*********** PP TIGR00338 147 ivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdi 215 i+ ++ak tl+ + + ++ +t+avGDGanDl mi+aAglg+a++akp++ +a ++i++ dlt++ lcl|NCBI__GCF_000745425.1:WP_034991023.1 217 ILGKDAKLATLVAKRDELKLAESDTIAVGDGANDLDMIRAAGLGLAYHAKPAVAAAAAACIDHGDLTAL 285 *******************************************************************99 PP TIGR00338 216 le 217 l+ lcl|NCBI__GCF_000745425.1:WP_034991023.1 286 LY 287 75 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (325 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: 11.98 // [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