GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Escherichia coli BW25113

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate 17452 b3389 3-dehydroquinate synthase (NCBI)

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__Keio:17452
          Length = 362

 Score =  708 bits (1827), Expect = 0.0
 Identities = 362/362 (100%), Positives = 362/362 (100%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA
Sbjct: 1   MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
           GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR
Sbjct: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS
Sbjct: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR
Sbjct: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240

Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300
           ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA
Sbjct: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300

Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ 360
           GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ
Sbjct: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ 360

Query: 361 SA 362
           SA
Sbjct: 361 SA 362


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: 569
Number of extensions: 6
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: 362
Length of database: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
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 17452 b3389 (3-dehydroquinate synthase (NCBI))
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.17559.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.8e-127  409.3   0.0   7.7e-127  409.2   0.0    1.0  1  lcl|FitnessBrowser__Keio:17452  b3389 3-dehydroquinate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17452  b3389 3-dehydroquinate synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.2   0.0  7.7e-127  7.7e-127       1     341 [.      13     354 ..      13     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: 409.2 bits;  conditional E-value: 7.7e-127
                       TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqllee 78 
                                     y++++ +gl+++ ++ l   + ++++++t+e+++ l+ +k++ +l+++gv+v+ +++pdge++Ksl+++ ++ ++ll++
  lcl|FitnessBrowser__Keio:17452  13 YPITIASGLFNEPASFLPLkSGEQVMLVTNETLAPLYLDKVRGVLEQAGVNVDSVILPDGEQYKSLAVLDTVFTALLQK 91 
                                     67999999999888888763459******************************************************** PP

                       TIGR01357  79 klerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidlkvl 157
                                      + r+++lva+GGGvvgDl+GF+Aa+y+RG+r++qvPTtll++vDssvGGKt++n+plgkN+iGafyqP  V++dl++l
  lcl|FitnessBrowser__Keio:17452  92 PHGRDTTLVALGGGVVGDLTGFAAASYQRGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCL 170
                                     ******************************************************************************* PP

                       TIGR01357 158 etlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRalLNfGHt 236
                                     +tlp rel++G+aEviK+g+i d ++f++le+n ++ll+l +  a++ +i+r++e+KaevV++De+e+glRalLN+GHt
  lcl|FitnessBrowser__Keio:17452 171 KTLPPRELASGLAEVIKYGIILDGAFFNWLEENLDALLRL-DGPAMAYCIRRCCELKAEVVAADERETGLRALLNLGHT 248
                                     ***********************************99986.66************************************ PP

                       TIGR01357 237 lgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkallkDKKneg 314
                                     +gHaiEa+++y+ + HGeaVa Gmv++a++se+lg++++ +++r+++llk++glp++ ++++s++++l ++l+DKK  +
  lcl|FitnessBrowser__Keio:17452 249 FGHAIEAEMGYGnWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAGLPVNGPREMSAQAYLPHMLRDKKVLA 327
                                     ******************************************************************************* PP

                       TIGR01357 315 skiklvlleeiGkaalasevteeelle 341
                                     ++++l+l+ +iGk +++s v++e +l+
  lcl|FitnessBrowser__Keio:17452 328 GEMRLILPLAIGKSEVRSGVSHELVLN 354
                                     ****************99988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (362 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.12
//
[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:

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:

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:

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:

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