Alignments for a candidate for aroB in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Denitrovibrio acetiphilus DSM 12809

Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_013009414.1 DACET_RS00305 3-dehydroquinate synthase

Query= curated2:Q8RB14
         (356 letters)



>NCBI__GCF_000025725.1:WP_013009414.1
          Length = 349

 Score =  233 bits (595), Expect = 4e-66
 Identities = 144/343 (41%), Positives = 191/343 (55%), Gaps = 12/343 (3%)

Query: 1   MDEVIVELKERSYPIYFDYEGFDRVGDLIKKHVRSSKTFVITDSNVYPLYFEKIEESLRK 60
           M  V V LK+     Y    G     ++I+K +R+   F + D NV+ LY +        
Sbjct: 1   MKTVKVNLKKEVDTSYEITIGSSFAKEVIEK-MRAEGAFFMVDENVFELYSDLFTH---- 55

Query: 61  SGFDVLYEVIPAGETSKTMEMAQRLLEVAYDSGLLRDSSIIALGGGVVGDIAGFVAATYM 120
              D  +    A E +KT E    +L   +  G  RDS +  +GGG+ GD+ GFVAATYM
Sbjct: 56  ---DNTFR-FRADEHNKTHESVVAVLGFLFREGAKRDSLLSIVGGGITGDVGGFVAATYM 111

Query: 121 RGIDFIQIPTTLLAQVDSSVGGKVAVNLKKGKNIVGAFYQPKMVYIDTSVLGTLNKREVL 180
           RGI FIQ+PTTLL+ VDSSVGGK  +N +  KN VGAF QP+ VYID   L TL   E L
Sbjct: 112 RGISFIQMPTTLLSMVDSSVGGKTGINFRGAKNNVGAFAQPEHVYIDMDFLNTLTDEEFL 171

Query: 181 GGLAEVIKYGVIWDFDLFTYIEENLGDILRLKKEDLTYIVKRSCEIKAKVVSLDEKEENL 240
            G+AE+IKYG I+D D F Y+EE+   ++    E L+YIVKR CE+KA+VV  DEKE   
Sbjct: 172 NGVAEIIKYGAIFDKDFFRYLEEHREQVIARDTETLSYIVKRCCEMKAEVVRKDEKERGD 231

Query: 241 RAILNFGHTIGHAIEALTGYERYIHGEAVAIGMAYEARLAFNLGYIDEGYLERILNLIKR 300
           RA+LNFGHT  HAIE    +    HG AVA GM  E   A   G  D+  LE I  ++  
Sbjct: 232 RALLNFGHTFAHAIET-DSHHGVKHGFAVATGMYLETDYAVRAGEADKETLEAIGRILTD 290

Query: 301 AGLPADYEGIEKTDMLNAIKLDKKMREGRINFVL--PVGLGKV 341
            G    Y+  ++     A++ DKK  +  ++  L   +G GK+
Sbjct: 291 YGFALSYDIDDRELFFQAMQADKKAGKKGLSLALTPSIGSGKI 333


Lambda     K      H
   0.320    0.141    0.393 

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: 371
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 356
Length of database: 349
Length adjustment: 29
Effective length of query: 327
Effective length of database: 320
Effective search space:   104640
Effective search space used:   104640
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_013009414.1 DACET_RS00305 (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.30496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-105  337.1   0.3   7.3e-105  336.9   0.3    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013009414.1  DACET_RS00305 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013009414.1  DACET_RS00305 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.9   0.3  7.3e-105  7.3e-105       1     341 [.      16     344 ..      16     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 7.3e-105
                                 TIGR01357   1 ykvkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletva 69 
                                               y++++g+++ k++ e+++   + +++++de+v +l+++ + + +        ++ + + e++K+ e+v 
  lcl|NCBI__GCF_000025725.1:WP_013009414.1  16 YEITIGSSFAKEVIEKMRA--EGAFFMVDENVFELYSDLFTHDN--------TFRFRADEHNKTHESVV 74 
                                               6789999999988888885..78999********9988776555........68999************ PP

                                 TIGR01357  70 klldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgk 138
                                               ++l  l++e+++r+s+l ++GGG+ gD++GFvAaty+RGi+++q+PTtll+mvDssvGGKtgin+++ k
  lcl|NCBI__GCF_000025725.1:WP_013009414.1  75 AVLGFLFREGAKRDSLLSIVGGGITGDVGGFVAATYMRGISFIQMPTTLLSMVDSSVGGKTGINFRGAK 143
                                               ********************************************************************* PP

                                 TIGR01357 139 NliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeeli 207
                                               N +Gaf qP+ V+id+++l+tl+++e+ +G+aE+iK+g+i d+++f+ le++ +++  + ++e+l+ ++
  lcl|NCBI__GCF_000025725.1:WP_013009414.1 144 NNVGAFAQPEHVYIDMDFLNTLTDEEFLNGVAEIIKYGAIFDKDFFRYLEEHREQVIAR-DTETLSYIV 211
                                               ******************************************************98875.56******* PP

                                 TIGR01357 208 krsievKaevVeeDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkael 276
                                               kr++e+KaevV +Deke+g RalLNfGHt++HaiE+ ++++++HG aVa+Gm +e+ ++ ++g +++e 
  lcl|NCBI__GCF_000025725.1:WP_013009414.1 212 KRCCEMKAEVVRKDEKERGDRALLNFGHTFAHAIETDSHHGVKHGFAVATGMYLETDYAVRAGEADKET 280
                                               ********************************************************************* PP

                                 TIGR01357 277 lerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                               le + ++l  +g   ++    + e +++a++ DKK+ ++ + l l  +iG+ ++ ++++++ + +
  lcl|NCBI__GCF_000025725.1:WP_013009414.1 281 LEAIGRILTDYGFALSYD-IDDRELFFQAMQADKKAGKKGLSLALTPSIGSGKILKNIPQQSVVD 344
                                               *****************9.5999*****************************9999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (349 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: 7.52
//
[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