Alignments for a candidate for aroB in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Pseudarthrobacter sulfonivorans Ar51

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_058932360.1 AU252_RS20930 3-dehydroquinate synthase

Query= BRENDA::P9WPX9
         (362 letters)



>NCBI__GCF_001484605.1:WP_058932360.1
          Length = 363

 Score =  411 bits (1056), Expect = e-119
 Identities = 214/345 (62%), Positives = 252/345 (73%), Gaps = 1/345 (0%)

Query: 18  YPVVIGTGLLDELEDLLADR-HKVAVVHQPGLAETAEEIRKRLAGKGVDAHRIEIPDAEA 76
           Y VV+G GLL  L  LL +R  +V V+H   L  T + +R  LA  G  +   EIPDAE 
Sbjct: 19  YDVVVGRGLLGNLPALLGERVRRVLVIHPRALRLTGDTVRDELAAAGFTSLTAEIPDAEE 78

Query: 77  GKDLPVVGFIWEVLGRIGIGRKDALVSLGGGAATDVAGFAAATWLRGVSIVHLPTTLLGM 136
           GK + V  F W+VLG+    R DA+V++GGGA TD+AGF AATWLRGV ++H+PT+LLGM
Sbjct: 79  GKHIQVAAFCWQVLGQNDFTRSDAIVAVGGGAVTDLAGFVAATWLRGVKVIHMPTSLLGM 138

Query: 137 VDAAVGGKTGINTDAGKNLVGAFHQPLAVLVDLATLQTLPRDEMICGMAEVVKAGFIADP 196
           VDA+VGGKTGINT  GKNLVG+FH P  VLVDL TL TLPR+E+I GMAEV+K GFIADP
Sbjct: 139 VDASVGGKTGINTAEGKNLVGSFHPPAGVLVDLDTLNTLPRNEIISGMAEVIKCGFIADP 198

Query: 197 VILDLIEADPQAALDPAGDVLPELIRRAITVKAEVVAADEKESELREILNYGHTLGHAIE 256
            ILDL+E DP AA DP  D L ELI RAI VKA+VV+ D KES LREILNYGHTL HAIE
Sbjct: 199 AILDLVEKDPAAATDPGSDALRELIERAIAVKAKVVSEDLKESGLREILNYGHTLAHAIE 258

Query: 257 RRERYRWRHGAAVSVGLVFAAELARLAGRLDDATAQRHRTILSSLGLPVSYDPDALPQLL 316
             ERY WRHGAAVSVG++FAAELAR  GRL DA A RHR+IL +LGLPV+Y  D    LL
Sbjct: 259 LVERYSWRHGAAVSVGMMFAAELARSVGRLSDADADRHRSILETLGLPVTYRRDRWQGLL 318

Query: 317 EIMAGDKKTRAGVLRFVVLDGLAKPGRMVGPDPGLLVTAYAGVCA 361
           + M  DKK+R  +LRFVVLDG+AKPG +  PD  LL  AY  + +
Sbjct: 319 DGMRRDKKSRGDLLRFVVLDGIAKPGILDVPDTSLLFAAYQEIAS 363


Lambda     K      H
   0.320    0.139    0.406 

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: 469
Number of extensions: 21
Number of successful extensions: 2
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: 363
Length adjustment: 29
Effective length of query: 333
Effective length of database: 334
Effective search space:   111222
Effective search space used:   111222
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 WP_058932360.1 AU252_RS20930 (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.23923.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-112  361.4   0.0     3e-112  361.2   0.0    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058932360.1  AU252_RS20930 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058932360.1  AU252_RS20930 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.2   0.0    3e-112    3e-112       1     334 [.      19     348 ..      19     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 361.2 bits;  conditional E-value: 3e-112
                                 TIGR01357   1 ykvkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletva 69 
                                               y+v+vg+gll +l + l e+  + v++++ ++ +l ++++++ l+++g++ l++ +pd+ee K+++++a
  lcl|NCBI__GCF_001484605.1:WP_058932360.1  19 YDVVVGRGLLGNLPALLGER-VRRVLVIHPRALRLTGDTVRDELAAAGFTSLTAEIPDAEEGKHIQVAA 86 
                                               7899*******999999985.56677888999999********************************** PP

                                 TIGR01357  70 klldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgk 138
                                                +++ l +++++r++++va+GGG+v+DlaGFvAat+lRG++++++PT+ll+mvD+svGGKtgin+++gk
  lcl|NCBI__GCF_001484605.1:WP_058932360.1  87 FCWQVLGQNDFTRSDAIVAVGGGAVTDLAGFVAATWLRGVKVIHMPTSLLGMVDASVGGKTGINTAEGK 155
                                               ********************************************************************* PP

                                 TIGR01357 139 NliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeeli 207
                                               Nl+G+f+ P  Vl+dl++l+tlp++e+++GmaEviK g+iad ++++ +ek  ++ ++    +al+eli
  lcl|NCBI__GCF_001484605.1:WP_058932360.1 156 NLVGSFHPPAGVLVDLDTLNTLPRNEIISGMAEVIKCGFIADPAILDLVEKDPAAATDP-GSDALRELI 223
                                               ***************************************************99988875.66******* PP

                                 TIGR01357 208 krsievKaevVeeDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkael 276
                                               +r+i vKa+vV+eD kesglR++LN+GHtl+HaiE +  y+++HG aV++Gm+++a+l++++g l+  +
  lcl|NCBI__GCF_001484605.1:WP_058932360.1 224 ERAIAVKAKVVSEDLKESGLREILNYGHTLAHAIELVERYSWRHGAAVSVGMMFAAELARSVGRLSDAD 292
                                               ********************************************************************* PP

                                 TIGR01357 277 lerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasev 334
                                               ++r++++l++lglp+++++  + + ll+ + +DKK++g+ +++v+l+ i+k+ +  +v
  lcl|NCBI__GCF_001484605.1:WP_058932360.1 293 ADRHRSILETLGLPVTYRR-DRWQGLLDGMRRDKKSRGDLLRFVVLDGIAKPGIL-DV 348
                                               ******************8.999**************************998776.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (363 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: 10.87
//
[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