Alignments for a candidate for cysE in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysE in Caulobacter crescentus NA1000

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate CCNA_02734 CCNA_02734 serine acetyltransferase

Query= BRENDA::Q0ZB96
         (273 letters)



>FitnessBrowser__Caulo:CCNA_02734
          Length = 290

 Score =  276 bits (707), Expect = 3e-79
 Identities = 136/249 (54%), Positives = 175/249 (70%)

Query: 9   VWNNIKAEARALADCEPMLASFYHATLLKHENLGSALSYMLANKLASPIMPAIAIREVVE 68
           VW  ++ +A   A  EP LAS  +A +L H+NL  AL++ LA KL    M A+  RE   
Sbjct: 27  VWVALRNQAEHAAKAEPALASLLNAVILSHDNLADALTFQLARKLGDQEMRAMTAREFAA 86

Query: 69  EAYAADPEMIASAACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWLWTQGRRAL 128
           +A+  D  ++ +A  D++AV  RDPA   Y  P L+ KGF ALQ +R+ HWLW QGR  L
Sbjct: 87  DAFEDDLSIVEAAEADLKAVFERDPACKGYVQPFLFFKGFLALQTHRVSHWLWNQGRETL 146

Query: 129 AIFLQNQVSVSFQVDIHPAAKIGRGIMLDHATGIVVGETAVIEDDVSILQSVTLGGTGKT 188
           A +LQ++ S  FQVDI+PAAKIG+G+ +DH TGIV+GETAV+ DDVS+L  VTLGGTG  
Sbjct: 147 AFYLQSRSSEVFQVDINPAAKIGKGVFIDHGTGIVIGETAVVGDDVSMLHGVTLGGTGAE 206

Query: 189 SGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGVPARIVGKPE 248
            GDRHPKI +GV++GAGAK+LGNI VG  AK+ +GSVVL+PVP H TAAGVPAR+V  P 
Sbjct: 207 RGDRHPKIGKGVLLGAGAKVLGNITVGDYAKVASGSVVLRPVPAHCTAAGVPARLVNCPT 266

Query: 249 SDKPAMDMD 257
            ++PA  MD
Sbjct: 267 CEEPAKTMD 275


Lambda     K      H
   0.319    0.136    0.405 

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: 301
Number of extensions: 13
Number of successful extensions: 2
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: 273
Length of database: 290
Length adjustment: 26
Effective length of query: 247
Effective length of database: 264
Effective search space:    65208
Effective search space used:    65208
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 CCNA_02734 CCNA_02734 (serine 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.8948.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.3e-74  233.1   1.4    1.3e-73  232.5   0.3    1.7  2  lcl|FitnessBrowser__Caulo:CCNA_02734  CCNA_02734 serine acetyltransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02734  CCNA_02734 serine acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0     0.079     0.079       5      48 ..      35      79 ..      31      89 .. 0.76
   2 !  232.5   0.3   1.3e-73   1.3e-73       2     162 .]     100     260 ..      99     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.079
                             TIGR01172  5 lkavlerDPaaesale.vlllykglhallayrlahalykrklkll 48
                                           +++ + +Pa  s l+ v+l +  l   l+++la +l  ++++++
  lcl|FitnessBrowser__Caulo:CCNA_02734 35 AEHAAKAEPALASLLNaVILSHDNLADALTFQLARKLGDQEMRAM 79
                                          566778899998887537788889998999999999888777655 PP

  == domain 2  score: 232.5 bits;  conditional E-value: 1.3e-73
                             TIGR01172   2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgv 74 
                                           ++dlkav+erDPa++ +++++l++kg+ al+++r++h+l+++++++la +l+++++ +++vdi Paakig+gv
  lcl|FitnessBrowser__Caulo:CCNA_02734 100 EADLKAVFERDPACKGYVQPFLFFKGFLALQTHRVSHWLWNQGRETLAFYLQSRSSEVFQVDINPAAKIGKGV 172
                                           689********************************************************************** PP

                             TIGR01172  75 liDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvl 147
                                           +iDh+tG+viGetav+gddvs+++gvtLGgtg e+g+RhP++++gv++gagakvLGni+vg+ ak+ ++svvl
  lcl|FitnessBrowser__Caulo:CCNA_02734 173 FIDHGTGIVIGETAVVGDDVSMLHGVTLGGTGAERGDRHPKIGKGVLLGAGAKVLGNITVGDYAKVASGSVVL 245
                                           ************************************************************************* PP

                             TIGR01172 148 kdvpaeatvvGvpar 162
                                           ++vpa+ t++Gvpar
  lcl|FitnessBrowser__Caulo:CCNA_02734 246 RPVPAHCTAAGVPAR 260
                                           *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (162 nodes)
Target sequences:                          1  (290 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: 7.77
//
[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