Aligments for a candidate for cysK in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Aligments for a candidate for cysK in Escherichia coli BW25113

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 16513 b2414 cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI)

Query= BRENDA::P0ABK5
         (323 letters)



>lcl|FitnessBrowser__Keio:16513 b2414 cysteine synthase A,
           O-acetylserine sulfhydrolase A subunit (NCBI)
          Length = 323

 Score =  626 bits (1614), Expect = 0.0
 Identities = 323/323 (100%), Positives = 323/323 (100%)

Query: 1   MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60
           MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK
Sbjct: 1   MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60

Query: 61  PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120
           PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM
Sbjct: 61  PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120

Query: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180
           KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG
Sbjct: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180

Query: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240
           TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD
Sbjct: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240

Query: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300
           LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP
Sbjct: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300

Query: 301 SSGERYLSTALFADLFTEKELQQ 323
           SSGERYLSTALFADLFTEKELQQ
Sbjct: 301 SSGERYLSTALFADLFTEKELQQ 323


Lambda     K      H
   0.313    0.133    0.368 

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: 507
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: 323
Length of database: 323
Length adjustment: 28
Effective length of query: 295
Effective length of database: 295
Effective search space:    87025
Effective search space used:    87025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate 16513 b2414 (cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI))
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))

# 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/TIGR01139.hmm
# target sequence database:        /tmp/gapView.14734.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01139  [M=298]
Accession:   TIGR01139
Description: cysK: cysteine synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.3e-150  485.8   1.1   2.6e-150  485.7   1.1    1.0  1  lcl|FitnessBrowser__Keio:16513  b2414 cysteine synthase A, O-ace


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16513  b2414 cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.7   1.1  2.6e-150  2.6e-150       2     298 .]       9     312 ..       8     312 .. 0.98

  Alignments for each domain:
  == domain 1  score: 485.7 bits;  conditional E-value: 2.6e-150
                       TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaaarg 80 
                                     s +iG+tPlvrLn +++ ++++l+k+es+nPs+svk+ri+++mi+daek+g+lk+g ++ve+tsGntGiala+vaaarg
  lcl|FitnessBrowser__Keio:16513   9 SLTIGHTPLVRLN-RIG-NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLKPGVELVEPTSGNTGIALAYVAAARG 85 
                                     569**********.666.89*********************************************************** PP

                       TIGR01139  81 ykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttapeilkd 159
                                     ykl+ltmpetms+errkllka+Ga+lvLt+ga+gmkgai+kaee+v+++p+kylll+qf+npanpeih+ktt+pei++d
  lcl|FitnessBrowser__Keio:16513  86 YKLTLTMPETMSIERRKLLKALGANLVLTEGAKGMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWED 164
                                     ******************************************************************************* PP

                       TIGR01139 160 ldgkldafvagvGtGGtitGvgevlkekkp..dikvvavePaespvlsgg......kpgphkiqGigagfiPkvLdkev 230
                                     +dg++d+f+agvGtGGt+tGv++++k +k+  d+ +vaveP++spv++++      kpgphkiqGigagfiP++Ld ++
  lcl|FitnessBrowser__Keio:16513 165 TDGQVDVFIAGVGTGGTLTGVSRYIKGTKGktDLISVAVEPTDSPVIAQAlageeiKPGPHKIQGIGAGFIPANLDLKL 243
                                     **************************99887799***************9999************************** PP

                       TIGR01139 231 idevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298
                                     +d+vi +++eeai+tarrl++eeGil+GissGaavaaalk++++++ ++k+ivvilp++gerYlstaLf
  lcl|FitnessBrowser__Keio:16513 244 VDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESfTNKNIVVILPSSGERYLSTALF 312
                                     ********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (323 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.88
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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, or view the source code, or see 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