Alignments for a candidate for cysE in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysE in Azospirillum brasilense Sp245

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate AZOBR_RS25375 AZOBR_RS25375 serine acetyltransferase

Query= BRENDA::Q0ZB96
         (273 letters)



>FitnessBrowser__azobra:AZOBR_RS25375
          Length = 260

 Score =  303 bits (776), Expect = 2e-87
 Identities = 146/250 (58%), Positives = 186/250 (74%), Gaps = 1/250 (0%)

Query: 9   VWNNIKAEARALADCEPMLASFYHATLLKHENLGSALSYMLANKLASPIMPAIAIREVVE 68
           +W  ++ EA A+AD +P+L  F H  +L H+   SAL   LA KL    +PA  + ++ E
Sbjct: 1   LWARLRTEAEAVADGDPLLRGFIHIVVLSHDGFASALGGHLARKLGDWYIPAERLADITE 60

Query: 69  EAYAADPEMIASAACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWLWTQGRRAL 128
           +A+A DP ++A+A  D+ A+ TRDPA D   TP LY KGFHALQ +R+ HWLW QGRR L
Sbjct: 61  QAHAGDPGIVAAAVADLTAIVTRDPAADGLLTPFLYFKGFHALQWHRVAHWLWAQGRRDL 120

Query: 129 AIFLQNQVSVSFQVDIHPAAKIGRGIMLDHATGIVVGETAVIEDDVSILQSVTLGGTGKT 188
             FLQ++VS  F VDIHPA  IGRG+++DH TG+V+GETAV+ DDVSILQ VTLGGTGK 
Sbjct: 121 PHFLQSRVSEVFAVDIHPAVSIGRGVLIDHGTGVVIGETAVVGDDVSILQGVTLGGTGKE 180

Query: 189 SGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGVPARIVGKPE 248
            GDRHPK+R+GV++ AGAK+LGNIEVGR AK+GAGSVVL+PVPP  T AGVPAR+VG   
Sbjct: 181 HGDRHPKVRDGVLLAAGAKVLGNIEVGRHAKVGAGSVVLKPVPPGATVAGVPARVVGWLT 240

Query: 249 SDK-PAMDMD 257
           S + PA++MD
Sbjct: 241 SGQAPAVEMD 250


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: 297
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: 273
Length of database: 260
Length adjustment: 25
Effective length of query: 248
Effective length of database: 235
Effective search space:    58280
Effective search space used:    58280
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 AZOBR_RS25375 AZOBR_RS25375 (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.18995.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.2e-74  235.8   2.5    1.8e-74  235.3   2.5    1.2  1  lcl|FitnessBrowser__azobra:AZOBR_RS25375  AZOBR_RS25375 serine acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS25375  AZOBR_RS25375 serine acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.3   2.5   1.8e-74   1.8e-74       3     162 .]      75     234 ..      73     234 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.3 bits;  conditional E-value: 1.8e-74
                                 TIGR01172   3 edlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakig 71 
                                               +dl+a+++rDPaa+  l+++l++kg+hal+++r+ah+l+ ++++ l ++l+++v+ ++ vdihPa +ig
  lcl|FitnessBrowser__azobra:AZOBR_RS25375  75 ADLTAIVTRDPAADGLLTPFLYFKGFHALQWHRVAHWLWAQGRRDLPHFLQSRVSEVFAVDIHPAVSIG 143
                                               799****************************************************************** PP

                                 TIGR01172  72 rgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenaki 140
                                               rgvliDh+tGvviGetav+gddvsi+qgvtLGgtgke+g+RhP+v++gv+++agakvLGnievg +ak+
  lcl|FitnessBrowser__azobra:AZOBR_RS25375 144 RGVLIDHGTGVVIGETAVVGDDVSILQGVTLGGTGKEHGDRHPKVRDGVLLAAGAKVLGNIEVGRHAKV 212
                                               ********************************************************************* PP

                                 TIGR01172 141 GansvvlkdvpaeatvvGvpar 162
                                               Ga+svvlk+vp++atv+Gvpar
  lcl|FitnessBrowser__azobra:AZOBR_RS25375 213 GAGSVVLKPVPPGATVAGVPAR 234
                                               ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (162 nodes)
Target sequences:                          1  (260 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: 10.99
//
[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