Alignments for a candidate for cysE in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysE in Xanthobacter autotrophicus Py2

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_041575701.1 XAUT_RS16125 serine O-acetyltransferase

Query= BRENDA::C4IRW0
         (281 letters)



>NCBI__GCF_000017645.1:WP_041575701.1
          Length = 289

 Score =  336 bits (862), Expect = 3e-97
 Identities = 162/261 (62%), Positives = 198/261 (75%)

Query: 21  DQVDPIWHSIRAEAEEATRNDPVLGAFLYATILNQPSLEEAVMHRIAERLGHPDVSADIL 80
           D VDP+W  +R EAEEA   +P+L AFL   +L QPSLE  +  RIA RL H DV A  +
Sbjct: 23  DVVDPVWARLRNEAEEAAEREPLLAAFLIGAVLGQPSLEAVIGERIAARLDHADVPASAI 82

Query: 81  RQTFDTMLEANPEWSHVLRVDIQAVYDRDPAYSRFMDPVLYLKGFHAIQTHRLAHWLYKQ 140
           R  +      +      LR DI AV DRDPA +R ++PVLY KGFHAIQTHRL+H+L+  
Sbjct: 83  RAAWLEAAARDKTIPQALRADIMAVVDRDPAATRTLEPVLYFKGFHAIQTHRLSHFLWAS 142

Query: 141 GRKDFAYYLQSRSSSIFQTDIHPAARLGSGLFLDHATGLVVGETAVVEDNVSILHGVTLG 200
           G++DFA YLQSR+SS+F  DIHP   +G G+FLDHATG+V+G TAV+ED+VSIL GVTLG
Sbjct: 143 GQRDFALYLQSRASSVFAVDIHPQVPMGRGIFLDHATGVVIGATAVIEDDVSILQGVTLG 202

Query: 201 GTGKSSGDRHPKIRQGVLIGAGAKILGNIQVGQCSKIAAGSVVLKSVPHNVTVAGVPARI 260
           GTGK +GDRHPKIR+GVLIGAGAK+LGNI+VG+C++IAAGSVVLK VP N TVAG+PA++
Sbjct: 203 GTGKETGDRHPKIRRGVLIGAGAKVLGNIEVGRCARIAAGSVVLKPVPRNTTVAGIPAKV 262

Query: 261 IGETGCTEPSRVMDQMLGDGI 281
           +GE GC EPSR MDQM  D I
Sbjct: 263 VGEAGCAEPSRSMDQMFEDNI 283


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: 340
Number of extensions: 12
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: 289
Length adjustment: 26
Effective length of query: 255
Effective length of database: 263
Effective search space:    67065
Effective search space used:    67065
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 WP_041575701.1 XAUT_RS16125 (serine O-acetyltransferase)
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.2215778.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.6e-72  228.9   1.0    3.9e-72  227.7   0.9    1.6  2  NCBI__GCF_000017645.1:WP_041575701.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017645.1:WP_041575701.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.11      0.11       7      43 ..      38      75 ..      32      85 .. 0.65
   2 !  227.7   0.9   3.9e-72   3.9e-72       2     162 .]     101     261 ..     100     261 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.11
                             TIGR01172  7 avlerDPaaesa.levlllykglhallayrlahalykr 43
                                          ++ er+P      +  +l  ++l a++  r+a++l + 
  NCBI__GCF_000017645.1:WP_041575701.1 38 EAAEREPLLAAFlIGAVLGQPSLEAVIGERIAARLDHA 75
                                          55666665544314567778888888888888877554 PP

  == domain 2  score: 227.7 bits;  conditional E-value: 3.9e-72
                             TIGR01172   2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgv 74 
                                           ++d+ av++rDPaa+++le++l++kg+ha++++rl+h+l+ ++ + +a +l+++++ ++ vdihP+  +grg+
  NCBI__GCF_000017645.1:WP_041575701.1 101 RADIMAVVDRDPAATRTLEPVLYFKGFHAIQTHRLSHFLWASGQRDFALYLQSRASSVFAVDIHPQVPMGRGI 173
                                           78*********************************************************************** PP

                             TIGR01172  75 liDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvl 147
                                           ++DhatGvviG tavi+ddvsi+qgvtLGgtgke+g+RhP+++ gv+igagakvLGnievg  a+i a+svvl
  NCBI__GCF_000017645.1:WP_041575701.1 174 FLDHATGVVIGATAVIEDDVSILQGVTLGGTGKETGDRHPKIRRGVLIGAGAKVLGNIEVGRCARIAAGSVVL 246
                                           ************************************************************************* PP

                             TIGR01172 148 kdvpaeatvvGvpar 162
                                           k+vp+++tv+G+pa+
  NCBI__GCF_000017645.1:WP_041575701.1 247 KPVPRNTTVAGIPAK 261
                                           *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (162 nodes)
Target sequences:                          1  (289 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: 12.96
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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