Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_011840114.1 RSPH17029_RS00095 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000015985.1:WP_011840114.1 Length = 291 Score = 173 bits (439), Expect = 3e-48 Identities = 97/208 (46%), Positives = 128/208 (61%), Gaps = 5/208 (2%) Query: 25 KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVS 84 KL+ DMDST+I EC+DE+AD AG VA IT AM GE++ ++ +LR+RV LLKG+S Sbjct: 77 KLLLADMDSTMIRQECIDELADEAGVGEYVAGITRRAMNGELN-FESALRERVGLLKGLS 135 Query: 85 VASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVL 144 + +D V+ TR++ PG LVQ K G + LVSGGFT FT+++ LG D R+N+L Sbjct: 136 ASVVDRVFETRIQYMPGGRALVQTMKAHGARAALVSGGFTAFTEKVAAGLGFDEHRANIL 195 Query: 145 ETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAG 204 +G LTG + + I E K L E C +LGI A+A+GDGANDL M+ AG Sbjct: 196 HVAEGALTGTVAE----PILGREAKLAALEEICARLGIEVADAMAVGDGANDLGMLKRAG 251 Query: 205 LSVAYHAKPRVREQAMVAINEGGLDRLL 232 VA HAKP V + + IN G L LL Sbjct: 252 AGVALHAKPVVAAECDIRINHGDLTSLL 279 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: 193 Number of extensions: 6 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: 291 Length adjustment: 25 Effective length of query: 211 Effective length of database: 266 Effective search space: 56126 Effective search space used: 56126 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_011840114.1 RSPH17029_RS00095 (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.11573.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-69 218.4 0.3 6.3e-69 217.9 0.3 1.1 1 lcl|NCBI__GCF_000015985.1:WP_011840114.1 RSPH17029_RS00095 phosphoserine Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015985.1:WP_011840114.1 RSPH17029_RS00095 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 217.9 0.3 6.3e-69 6.3e-69 12 216 .. 74 279 .. 66 281 .. 0.97 Alignments for each domain: == domain 1 score: 217.9 bits; conditional E-value: 6.3e-69 TIGR00338 12 kkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkv 80 + kkl++ D+Dst+i++E+Ide+a +aGv+e V+ iT+rAm+gel+F+++lreRv llkgl+++++++v lcl|NCBI__GCF_000015985.1:WP_011840114.1 74 RRKKLLLADMDSTMIRQECIDELADEAGVGEYVAGITRRAMNGELNFESALRERVGLLKGLSASVVDRV 142 679*************************************************************99999 PP TIGR00338 81 ee.klelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeiv 148 e +++ ++G + lv+++k +g + a++SGgF+ ++ek+++ Lg d aN L+v +g+ltG+v +i+ lcl|NCBI__GCF_000015985.1:WP_011840114.1 143 FEtRIQYMPGGRALVQTMKAHGARAALVSGGFTAFTEKVAAGLGFDEHRANILHVAEGALTGTVAEPIL 211 6538***************************************************************** PP TIGR00338 149 desakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdil 216 +ak l++++ + gi++++ +avGDGanDl m+k+Ag+g+a +akpv+ + di i++ dlt++l lcl|NCBI__GCF_000015985.1:WP_011840114.1 212 GREAKLAALEEICARLGIEVADAMAVGDGANDLGMLKRAGAGVALHAKPVVAAECDIRINHGDLTSLL 279 *****************************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (291 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: 8.24 // [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