Alignments for a candidate for aroB in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Cupriavidus basilensis 4G11

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate RR42_RS19005 RR42_RS19005 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__Cup4G11:RR42_RS19005
          Length = 368

 Score =  371 bits (953), Expect = e-107
 Identities = 192/341 (56%), Positives = 238/341 (69%), Gaps = 1/341 (0%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           M  + V+LGERSYPI I +GL ++   F P   G+  ++VTNET+ PLY  +V+  L   
Sbjct: 1   MITLEVSLGERSYPIHIGTGLLDQTELFRPHVRGQHAVIVTNETVGPLYAARVQASLAAL 60

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
           G  V +V LPDGE +K    L+ +F ALL     R TTL+ALGGGVVGD+TGFAAA Y R
Sbjct: 61  GKTVRTVTLPDGEAFKQWETLNLIFDALLSAGADRKTTLIALGGGVVGDMTGFAAACYMR 120

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           GV F+QVPTTLLSQVDSSVGGKT +NHPLGKNMIGAF+QP +V+ D+D L+TLP RELA+
Sbjct: 121 GVPFVQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFHQPNAVIADIDTLRTLPERELAA 180

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           GLAEVIK+G + D  +F W+E N+ AL   D   MA  ++R CE+KA VVA DERE GLR
Sbjct: 181 GLAEVIKHGAMADAGYFGWIEGNIRALNACDPDIMALAVKRSCEIKAAVVAQDEREGGLR 240

Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300
           A+LN GHTFGHAIEA MGYG WLHGEAV  GMVMAA  S RLG   +    R++ L++ A
Sbjct: 241 AMLNFGHTFGHAIEAGMGYGEWLHGEAVGCGMVMAADLSHRLGFIDTETRARVVHLIRAA 300

Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKS 341
            LPV  P E+    Y+  M  DKK  AG ++ IL   +G++
Sbjct: 301 MLPVVAP-ELGTDRYIELMKVDKKAEAGSIKFILLRKLGEA 340


Lambda     K      H
   0.320    0.136    0.392 

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: 327
Number of extensions: 9
Number of successful extensions: 3
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: 362
Length of database: 368
Length adjustment: 30
Effective length of query: 332
Effective length of database: 338
Effective search space:   112216
Effective search space used:   112216
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: 49 (23.5 bits)

Align candidate RR42_RS19005 RR42_RS19005 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.15738.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-124  401.6   0.0   1.7e-124  401.5   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS19005  RR42_RS19005 3-dehydroquinate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS19005  RR42_RS19005 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.5   0.0  1.7e-124  1.7e-124       1     339 [.      13     350 ..      13     355 .. 0.96

  Alignments for each domain:
  == domain 1  score: 401.5 bits;  conditional E-value: 1.7e-124
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                               y++++g+gll+++ e ++   + +++v++t+e+v  l+a+++++ l++lg +v ++++pdge  K++et
  lcl|FitnessBrowser__Cup4G11:RR42_RS19005  13 YPIHIGTGLLDQT-ELFRPhvRGQHAVIVTNETVGPLYAARVQASLAALGKTVRTVTLPDGEAFKQWET 80 
                                               689********66.44444355699******************************************** PP

                                 TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136
                                               ++ + d+ll+++++rk++l+a+GGGvvgD++GF+Aa y+RG+++vqvPTtll++vDssvGGKtgin+pl
  lcl|FitnessBrowser__Cup4G11:RR42_RS19005  81 LNLIFDALLSAGADRKTTLIALGGGVVGDMTGFAAACYMRGVPFVQVPTTLLSQVDSSVGGKTGINHPL 149
                                               ********************************************************************* PP

                                 TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205
                                               gkN+iGaf+qP+aV+ d+++l+tlperel++G+aEviKhg++ada  f ++e n ++l+  ++ ++++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS19005 150 GKNMIGAFHQPNAVIADIDTLRTLPERELAAGLAEVIKHGAMADAGYFGWIEGNIRALNA-CDPDIMAL 217
                                               *******************************************************97776.677***** PP

                                 TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273
                                               ++krs+e+Ka vV++De+e glRa+LNfGHt+gHaiEa ++y+ + HGeaV +Gmv++a ls++lg+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS19005 218 AVKRSCEIKAAVVAQDEREGGLRAMLNFGHTFGHAIEAGMGYGeWLHGEAVGCGMVMAADLSHRLGFID 286
                                               ********************************************************************* PP

                                 TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339
                                               +e + r+v+l++++ lp+  ++ l ++ +++ ++ DKK+e+++ik++ll+++G+a+++ +v++ +l
  lcl|FitnessBrowser__Cup4G11:RR42_RS19005 287 TETRARVVHLIRAAMLPVVAPE-LGTDRYIELMKVDKKAEAGSIKFILLRKLGEAFIT-TVPDPDL 350
                                               *******************996.********************************999.7766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (368 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.85
//
[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