Alignments for a candidate for serB in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Dinoroseobacter shibae DFL-12

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate 3609934 Dshi_3316 phosphoserine phosphatase SerB (RefSeq)

Query= SwissProt::Q12A06
         (236 letters)



>FitnessBrowser__Dino:3609934
          Length = 292

 Score =  165 bits (417), Expect = 1e-45
 Identities = 99/209 (47%), Positives = 123/209 (58%), Gaps = 5/209 (2%)

Query: 26  LIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVSV 85
           ++  DMDST+I  EC+DE+AD AG    VA IT  AM GE+ D++ +LR+RV LL G+  
Sbjct: 78  MLLADMDSTMIRQECIDELADEAGVGPRVAEITARAMNGEL-DFEGALRERVGLLAGLDA 136

Query: 86  ASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVLE 145
           A +D V  TR+ L PG   LV   K  G    LVSGGFT FT R+   LG D  R+N LE
Sbjct: 137 AVIDRVLETRIDLMPGGRALVATMKRDGAYAALVSGGFTAFTARVAALLGFDENRANTLE 196

Query: 146 TTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAGL 205
             DG+LTGR+++     I     K   L E   +LGIS    +A+GDGANDL M+G AG 
Sbjct: 197 IVDGVLTGRVIE----PILGRAAKVAALEEITARLGISEADVMAVGDGANDLGMLGRAGA 252

Query: 206 SVAYHAKPRVREQAMVAINEGGLDRLLEL 234
            VA HAKP V  +    IN G L  LL L
Sbjct: 253 GVALHAKPVVAAECDRRINFGDLSALLFL 281


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: 199
Number of extensions: 12
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: 292
Length adjustment: 25
Effective length of query: 211
Effective length of database: 267
Effective search space:    56337
Effective search space used:    56337
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 3609934 Dshi_3316 (phosphoserine phosphatase SerB (RefSeq))
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.9452.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-64  203.0   0.2      3e-64  202.6   0.2    1.0  1  lcl|FitnessBrowser__Dino:3609934  Dshi_3316 phosphoserine phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609934  Dshi_3316 phosphoserine phosphatase SerB (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.6   0.2     3e-64     3e-64      12     216 ..      74     279 ..      65     281 .. 0.96

  Alignments for each domain:
  == domain 1  score: 202.6 bits;  conditional E-value: 3e-64
                         TIGR00338  12 kkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkv.eeklelt 87 
                                       + k +++ D+Dst+i++E+Ide+a +aGv+  V+eiT rAm+geldF+ +lreRv ll gl++ ++++v e +++l+
  lcl|FitnessBrowser__Dino:3609934  74 RRKAMLLADMDSTMIRQECIDELADEAGVGPRVAEITARAMNGELDFEGALRERVGLLAGLDAAVIDRVlETRIDLM 150
                                       56778999********************************************************999983558**** PP

                         TIGR00338  88 eGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllklleke 164
                                       +G + lv ++k+ g   a++SGgF+ ++ ++++ Lg d   aN+Le+ dg ltG+v  +i+   ak   l++++ + 
  lcl|FitnessBrowser__Dino:3609934 151 PGGRALVATMKRDGAYAALVSGGFTAFTARVAALLGFDENRANTLEIVDGVLTGRVIEPILGRAAKVAALEEITARL 227
                                       ***************************************************************************** PP

                         TIGR00338 165 gislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdil 216
                                       gis ++++avGDGanDl m+ +Ag+g+a +akpv+  + d  i+  dl ++l
  lcl|FitnessBrowser__Dino:3609934 228 GISEADVMAVGDGANDLGMLGRAGAGVALHAKPVVAAECDRRINFGDLSALL 279
                                       ************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (292 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: 11.60
//
[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