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

GapMind for Amino acid biosynthesis

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

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate 3608769 Dshi_2161 serine O-acetyltransferase (RefSeq)

Query= BRENDA::C4IRW0
         (281 letters)



>FitnessBrowser__Dino:3608769
          Length = 269

 Score =  298 bits (764), Expect = 7e-86
 Identities = 143/267 (53%), Positives = 185/267 (69%)

Query: 15  KVNAGLDQVDPIWHSIRAEAEEATRNDPVLGAFLYATILNQPSLEEAVMHRIAERLGHPD 74
           K +  L  VDP+WH I  EA  A  ++ +LG  ++++IL+  + E A+ +RI  +L  P+
Sbjct: 3   KASKSLKAVDPVWHRIGEEARLAVADEQLLGGLVHSSILHHATFEAALAYRITLKLSSPE 62

Query: 75  VSADILRQTFDTMLEANPEWSHVLRVDIQAVYDRDPAYSRFMDPVLYLKGFHAIQTHRLA 134
           +SA  LRQ  D    ++       R D+ AVY+RDPA  R M P+LY KGF A+Q +R+ 
Sbjct: 63  MSAQTLRQLVDDAFASDATLGVAARADLVAVYERDPACHRLMQPLLYFKGFQAVQAYRVG 122

Query: 135 HWLYKQGRKDFAYYLQSRSSSIFQTDIHPAARLGSGLFLDHATGLVVGETAVVEDNVSIL 194
           HWLY QGR D AY++Q R S +F  DIHPAA++G G+ +DHA  +V+GETAVV DNVS+L
Sbjct: 123 HWLYSQGRHDLAYFVQMRVSEVFGVDIHPAAKIGQGIMIDHAHSIVIGETAVVGDNVSML 182

Query: 195 HGVTLGGTGKSSGDRHPKIRQGVLIGAGAKILGNIQVGQCSKIAAGSVVLKSVPHNVTVA 254
           H VTLGGTGK   DRHPKI  GVLIGAGA +LGNI +G CS+IAAGSVVL  VP   TVA
Sbjct: 183 HSVTLGGTGKEDDDRHPKIGDGVLIGAGAHVLGNITIGHCSRIAAGSVVLSDVPPCKTVA 242

Query: 255 GVPARIIGETGCTEPSRVMDQMLGDGI 281
           GVPA+I+GE GC +PS  MDQ+L + I
Sbjct: 243 GVPAKIVGEAGCAQPSVTMDQLLSESI 269


Lambda     K      H
   0.320    0.135    0.403 

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: 295
Number of extensions: 8
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: 281
Length of database: 269
Length adjustment: 25
Effective length of query: 256
Effective length of database: 244
Effective search space:    62464
Effective search space used:    62464
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate 3608769 Dshi_2161 (serine O-acetyltransferase (RefSeq))
to HMM TIGR01172 (cysE: serine O-acetyltransferase (EC 2.3.1.30))

# 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/TIGR01172.hmm
# target sequence database:        /tmp/gapView.7794.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01172  [M=162]
Accession:   TIGR01172
Description: cysE: serine O-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.7e-71  225.5   2.3    1.7e-71  225.5   2.3    1.6  2  lcl|FitnessBrowser__Dino:3608769  Dshi_2161 serine O-acetyltransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608769  Dshi_2161 serine O-acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.13      0.13      21      42 ..      39      60 ..      35      77 .. 0.75
   2 !  225.5   2.3   1.7e-71   1.7e-71       2     162 .]      87     247 ..      86     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.13
                         TIGR01172 21 vlllykglhallayrlahalyk 42
                                       +l ++++ a layr++ +l +
  lcl|FitnessBrowser__Dino:3608769 39 SILHHATFEAALAYRITLKLSS 60
                                      5788899999999999887755 PP

  == domain 2  score: 225.5 bits;  conditional E-value: 1.7e-71
                         TIGR01172   2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliDh 78 
                                       ++dl av+erDPa+++ +++ll++kg++a++ayr+ h+ly+++++ la++++ +v+ ++gvdihPaakig+g++iDh
  lcl|FitnessBrowser__Dino:3608769  87 RADLVAVYERDPACHRLMQPLLYFKGFQAVQAYRVGHWLYSQGRHDLAYFVQMRVSEVFGVDIHPAAKIGQGIMIDH 163
                                       6899************************************************************************* PP

                         TIGR01172  79 atGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpaeat 155
                                       a+ +viGetav+gd+vs++++vtLGgtgke  +RhP++++gv+igaga+vLGni++g+ ++i a+svvl+dvp+  t
  lcl|FitnessBrowser__Dino:3608769 164 AHSIVIGETAVVGDNVSMLHSVTLGGTGKEDDDRHPKIGDGVLIGAGAHVLGNITIGHCSRIAAGSVVLSDVPPCKT 240
                                       ***************************************************************************** PP

                         TIGR01172 156 vvGvpar 162
                                       v+Gvpa+
  lcl|FitnessBrowser__Dino:3608769 241 VAGVPAK 247
                                       *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (162 nodes)
Target sequences:                          1  (269 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.68
//
[ok]

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

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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