Alignments for a candidate for serB in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Acidovorax sp. GW101-3H11

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate Ac3H11_1039 Phosphoserine phosphatase (EC 3.1.3.3)

Query= SwissProt::Q12A06
         (236 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1039
          Length = 259

 Score =  341 bits (875), Expect = 7e-99
 Identities = 174/233 (74%), Positives = 195/233 (83%)

Query: 4   TEISPGLVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMR 63
           TE +PGLVV   TP L LS +KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAM+
Sbjct: 27  TEFAPGLVVQGITPPLSLSAYKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMQ 86

Query: 64  GEISDYKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGF 123
           G I+DYKESLRQRVALLKGV+V  M++V+  RLR NPGA  L+ A K AGL  LLVSGGF
Sbjct: 87  GVITDYKESLRQRVALLKGVTVQHMEQVFTERLRFNPGAQELITAAKAAGLTTLLVSGGF 146

Query: 124 TFFTDRIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGIS 183
           TFF DR++  LGID+ RSN+LE  DG LTGRMVDQ WGDICDG EKR+ LLE    +GIS
Sbjct: 147 TFFADRVKAGLGIDFARSNMLEVQDGQLTGRMVDQAWGDICDGAEKRRTLLEVASLMGIS 206

Query: 184 PRQAIAMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLELVK 236
           P+QAIA+GDGANDLPMMG AGLSVAYHAKP VR QA VAIN+GGLDRLLE+++
Sbjct: 207 PQQAIAVGDGANDLPMMGAAGLSVAYHAKPTVRAQAKVAINQGGLDRLLEVLR 259


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: 243
Number of extensions: 6
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: 236
Length of database: 259
Length adjustment: 24
Effective length of query: 212
Effective length of database: 235
Effective search space:    49820
Effective search space used:    49820
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: 46 (22.3 bits)

Align candidate Ac3H11_1039 (Phosphoserine phosphatase (EC 3.1.3.3))
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.16505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    3.1e-70  222.2   0.1    3.9e-70  221.9   0.1    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1039  Phosphoserine phosphatase (EC 3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1039  Phosphoserine phosphatase (EC 3.1.3.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.9   0.1   3.9e-70   3.9e-70      12     219 .]      45     258 ..      39     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 3.9e-70
                                        TIGR00338  12 kkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgel.dFkeslreRvkllkgl 72 
                                                      ++ kl+ fD+Dstli++E++deia +aG + eV++iTe Am+g + d+keslr+Rv+llkg+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1039  45 SAYKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMQGVItDYKESLRQRVALLKGV 106
                                                      5679***************************************8659*************** PP

                                        TIGR00338  73 pvellkkv.eeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLe 133
                                                       v+++++v +e+l+  +G++el+ + k +g+ + ++SGgF+++a+++k+ Lg+d++ +N Le
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1039 107 TVQHMEQVfTERLRFNPGAQELITAAKAAGLTTLLVSGGFTFFADRVKAGLGIDFARSNMLE 168
                                                      ***998884689************************************************** PP

                                        TIGR00338 134 vedgkltGkve....geivdesakaktllkllekegislektvavGDGanDlsmikaAglgi 191
                                                      v+dg+ltG++     g+i d  +k +tll+++   gis+++ +avGDGanDl+m+ aAgl +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1039 169 VQDGQLTGRMVdqawGDICDGAEKRRTLLEVASLMGISPQQAIAVGDGANDLPMMGAAGLSV 230
                                                      ********864334499********************************************* PP

                                        TIGR00338 192 afnakpvlkekadiviekkdltdilell 219
                                                      a++akp ++ +a+++i++  l  +le+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1039 231 AYHAKPTVRAQAKVAINQGGLDRLLEVL 258
                                                      *********************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (259 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: 00:00:00.05
# Mc/sec: 1.10
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis