Alignments for a candidate for aroD in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroD in Stenotrophomonas chelatiphaga DSM 21508

Align Catabolic 3-dehydroquinate dehydratase; 3-dehydroquinase; EC 4.2.1.10 (characterized)
to candidate WP_057508481.1 ABB28_RS09905 type I 3-dehydroquinate dehydratase

Query= SwissProt::Q59087
         (272 letters)



>NCBI__GCF_001431535.1:WP_057508481.1
          Length = 283

 Score =  240 bits (612), Expect = 3e-68
 Identities = 124/262 (47%), Positives = 172/262 (65%)

Query: 7   STTYAAENTVPASKSTYVVKNLNIGDLPVKTLVPITAKTREQALAQAKVIAENKDADIAE 66
           +T+  A    P +     +  + IG+   KT+VPITA T EQAL QAKVIA +   DIAE
Sbjct: 14  ATSIPAVQAAPPAIRPLQIGTMRIGEGMPKTIVPITAATAEQALQQAKVIAASASTDIAE 73

Query: 67  FRIDLLEFASDTKKVIALGQELNQILKDKPLLATIRTSNEGGKLKVTDQEYEKIYSEYLK 126
           +RID L+ A+D   ++ALG+ + Q L  KPL+ T RT  EGG   ++D +Y  +Y+  L+
Sbjct: 74  WRIDYLDIATDGTALLALGKRIEQALAGKPLIVTFRTQAEGGSKAISDADYGALYATLLR 133

Query: 127 KPFMQLLDIEMFRDQAAVAKLTKLAHQKKVLVVMSNHDFDKTPSEQEIVSRLLKQDQMGA 186
             F+Q+LD+EMFRD+  V  L   AH     VVMS+HDF  TP  +EIV+RLL+Q  MGA
Sbjct: 134 GGFVQMLDVEMFRDRQVVQSLVDAAHGAGAKVVMSSHDFHATPPREEIVARLLRQQAMGA 193

Query: 187 DILKIAVMPKSKQDVFTLMNATLKVSEQSTKPLLTMSMGRLGTISRIATANMGGSLSFGM 246
           D+LKIAVMP+   DV  L++AT +V +QS +PLLTM+MG  G +SR+A    G +++FGM
Sbjct: 194 DVLKIAVMPRDAGDVLALLDATWQVRQQSDRPLLTMAMGGTGVVSRLAGETFGQAMTFGM 253

Query: 247 IGEASAPGQIDVTALKQFLKTV 268
           IG  SAPGQ++V  L+  L+ +
Sbjct: 254 IGTPSAPGQVEVEQLQSVLQVI 275


Lambda     K      H
   0.314    0.129    0.341 

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: 206
Number of extensions: 5
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: 272
Length of database: 283
Length adjustment: 25
Effective length of query: 247
Effective length of database: 258
Effective search space:    63726
Effective search space used:    63726
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 bits)

Align candidate WP_057508481.1 ABB28_RS09905 (type I 3-dehydroquinate dehydratase)
to HMM TIGR01093 (aroD: 3-dehydroquinate dehydratase, type I (EC 4.2.1.10))

# 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/TIGR01093.hmm
# target sequence database:        /tmp/gapView.22122.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01093  [M=229]
Accession:   TIGR01093
Description: aroD: 3-dehydroquinate dehydratase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.7e-72  229.1   0.0    4.3e-72  228.9   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508481.1  ABB28_RS09905 type I 3-dehydroqu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508481.1  ABB28_RS09905 type I 3-dehydroquinate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.9   0.0   4.3e-72   4.3e-72       1     228 [.      43     271 ..      43     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 228.9 bits;  conditional E-value: 4.3e-72
                                 TIGR01093   1 kilvpltakdleealeelekik.evgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtq 68 
                                               k++vp+ta ++e+al++++ i+     Di E+R+D+l+ + +   + a+ + ++++l+ +pli+T+Rtq
  lcl|NCBI__GCF_001431535.1:WP_057508481.1  43 KTIVPITAATAEQALQQAKVIAaSASTDIAEWRIDYLDIATDGTALLALGKRIEQALAGKPLIVTFRTQ 111
                                               689*****************9977899****************************************** PP

                                 TIGR01093  69 keGGkfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskee 137
                                                eGG+ + ++ ++ +++  ++  ++v+++D+E++++ ++v+ l+  a+ a+ k+++S+Hdf+ tp+ ee
  lcl|NCBI__GCF_001431535.1:WP_057508481.1 112 AEGGSKAISDADYGALYATLLRGGFVQMLDVEMFRDRQVVQSLVDAAHGAGAKVVMSSHDFHATPPREE 180
                                               ********************************************************************* PP

                                 TIGR01093 138 lverlekaqsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvl 206
                                               +v+rl ++q+++aD++Kiavm++++ Dvl+Ll +t +v+++ d+pl+++ Mg +G +sR++g+ +g ++
  lcl|NCBI__GCF_001431535.1:WP_057508481.1 181 IVARLLRQQAMGADVLKIAVMPRDAGDVLALLDATWQVRQQSDRPLLTMAMGGTGVVSRLAGETFGQAM 249
                                               **************************************9888*************************** PP

                                 TIGR01093 207 tfgslgkasAPGQisvkelrel 228
                                               tfg++g  sAPGQ++v++l+ +
  lcl|NCBI__GCF_001431535.1:WP_057508481.1 250 TFGMIGTPSAPGQVEVEQLQSV 271
                                               *******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (229 nodes)
Target sequences:                          1  (283 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: 00:00:00.00
# Mc/sec: 7.22
//
[ok]

This GapMind analysis is from Apr 10 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