Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_059150771.1 V474_RS04385 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_001046635.1:WP_059150771.1 Length = 293 Score = 156 bits (395), Expect = 4e-43 Identities = 89/211 (42%), Positives = 126/211 (59%), Gaps = 6/211 (2%) Query: 25 KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVS 84 +L DMDST+I EC+DE+ D AG K +AAITE AM+GE+ D++++L +RV LL+G+S Sbjct: 80 RLFISDMDSTMIGQECIDELGDFAGLKERIAAITERAMQGEL-DFEQALYERVGLLEGLS 138 Query: 85 VASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVL 144 +++DE R+R GA LV+ K G + +LV+GGF F D + LG ++ N L Sbjct: 139 TSAIDECLAARIRPMAGAKTLVETLKKLGCRTVLVTGGFHHFADPVAARLGFEHVVGNRL 198 Query: 145 ETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAG 204 E +G LTG + G I D K+ LL ++G +A GDGAND+PM+ A Sbjct: 199 EVANGKLTGGLE----GGIVDSAVKKATLLAEMAKMG-EGATCLATGDGANDIPMLEAAT 253 Query: 205 LSVAYHAKPRVREQAMVAINEGGLDRLLELV 235 +AYHAKP+ R A IN G L +L L+ Sbjct: 254 YGIAYHAKPKARIAANGWINRGDLTSVLRLL 284 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: 203 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: 293 Length adjustment: 25 Effective length of query: 211 Effective length of database: 268 Effective search space: 56548 Effective search space used: 56548 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_059150771.1 V474_RS04385 (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.1814663.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-65 206.3 0.0 3e-65 205.9 0.0 1.1 1 NCBI__GCF_001046635.1:WP_059150771.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_059150771.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 205.9 0.0 3e-65 3e-65 14 219 .] 79 284 .. 71 284 .. 0.95 Alignments for each domain: == domain 1 score: 205.9 bits; conditional E-value: 3e-65 TIGR00338 14 kklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve.llkkveekle 85 +l++ D+Dst+i +E+Ide++ aG +e +++iTerAm+geldF+++l eRv ll gl+ + + + + +++ NCBI__GCF_001046635.1:WP_059150771.1 79 PRLFISDMDSTMIGQECIDELGDFAGLKERIAAITERAMQGELDFEQALYERVGLLEGLSTSaIDECLAARIR 151 6899**********************************************************44555789*** PP TIGR00338 86 lteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktll 158 + G++ lv++Lk+ g++++++ GgF+ +a+ ++++Lg + v++NrLev +gkltG eg ivd+ +k tll NCBI__GCF_001046635.1:WP_059150771.1 152 PMAGAKTLVETLKKLGCRTVLVTGGFHHFADPVAARLGFEHVVGNRLEVANGKLTGGLEGGIVDSAVKKATLL 224 *******************************************************************999999 PP TIGR00338 159 kllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219 + k g + + ++a GDGanD++m++aA gia++akp+ + +a+ i++ dlt++l ll NCBI__GCF_001046635.1:WP_059150771.1 225 AEMAKMG-EGATCLATGDGANDIPMLEAATYGIAYHAKPKARIAANGWINRGDLTSVLRLL 284 8888887.67889********************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (293 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: 13.29 // [ok]
This GapMind analysis is from Jul 26 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