Alignments for a candidate for aroB in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Dyella japonica UNC79MFTsu3.2

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate N515DRAFT_1794 N515DRAFT_1794 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1794
          Length = 366

 Score =  323 bits (827), Expect = 6e-93
 Identities = 180/362 (49%), Positives = 233/362 (64%), Gaps = 2/362 (0%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           +  I V LG+RSYP+ I  GL ++ A +  +  G   ++++N T+APLYL++V   LE  
Sbjct: 7   LRSIDVALGQRSYPVWIGPGLLDDRARWRAMLRGRHALVISNTTVAPLYLERVAAGLE-- 64

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
           G+   + +L DGE +K+   +     AL Q    RD  +VALGGGVVGDL GF+AA + R
Sbjct: 65  GLQWSAFLLDDGEAHKTFDNVGRALDALAQLGATRDACVVALGGGVVGDLAGFSAACWMR 124

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           G+ FIQ+PTTLL+ VDSSVGGKT VN P GKN++GAF+QP +V+ D+D L TLP RE  +
Sbjct: 125 GIDFIQMPTTLLAMVDSSVGGKTGVNLPAGKNLVGAFHQPRAVIADIDTLATLPQREYRA 184

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           GLAEV+K   I D  FF WLE++ DAL   D   +   I R  + KA VVA DE E G R
Sbjct: 185 GLAEVVKGAAIGDLPFFAWLEQHADALAARDTAPLIEAIARKVQYKAGVVARDETEQGER 244

Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300
           ALLNLGHTFGHA+E    Y   LHGE VA GM++AAR SERLG  ++A+T R+  LL+R 
Sbjct: 245 ALLNLGHTFGHALETAGKYTTLLHGEGVAVGMLLAARLSERLGMSAAADTARLQRLLERL 304

Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ 360
           GLPV  P  M  QA L  M  DKK  AG +RLIL   IG++E+  GV    VL  + +  
Sbjct: 305 GLPVAIPPGMDPQALLALMRLDKKNTAGTLRLILWRGIGRAEIVGGVDEREVLATLHEAT 364

Query: 361 SA 362
           +A
Sbjct: 365 AA 366


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: 317
Number of extensions: 10
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: 366
Length adjustment: 29
Effective length of query: 333
Effective length of database: 337
Effective search space:   112221
Effective search space used:   112221
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 N515DRAFT_1794 N515DRAFT_1794 (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.14791.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.8e-114  366.2   0.0   9.9e-114  366.0   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_1794  N515DRAFT_1794 3-dehydroquinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1794  N515DRAFT_1794 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.0   0.0  9.9e-114  9.9e-114       1     341 [.      19     358 ..      19     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 366.0 bits;  conditional E-value: 9.9e-114
                                    TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsl 65 
                                                  y+v +g gll+  +++ a  + ++++vi++ +v+ l+ e++++ l+  g +   +++ dge +K++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1794  19 YPVWIGPGLLDDRARWRAMlRGRHALVISNTTVAPLYLERVAAGLE--GLQWSAFLLDDGEAHKTF 82 
                                                  678899999998877777756699*******************996..799999************ PP

                                    TIGR01357  66 etvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtg 131
                                                  ++v + ld+l++ +++r+ ++va+GGGvvgDlaGF Aa ++RGi+++q+PTtllamvDssvGGKtg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1794  83 DNVGRALDALAQLGATRDACVVALGGGVVGDLAGFSAACWMRGIDFIQMPTTLLAMVDSSVGGKTG 148
                                                  ****************************************************************** PP

                                    TIGR01357 132 inlplgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllkl 197
                                                  +nlp gkNl+Gaf+qP+aV+ d+++l+tlp+re+r+G+aEv+K ++i d  +f++le+++++l  +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1794 149 VNLPAGKNLVGAFHQPRAVIADIDTLATLPQREYRAGLAEVVKGAAIGDLPFFAWLEQHADALAAR 214
                                                  *************************************************************98875 PP

                                    TIGR01357 198 aelealeelikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvve 262
                                                   +++ l e+i+r +++Ka vV++De+e+g RalLN+GHt+gHa+E++ ky+ l HGe Va+Gm ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1794 215 -DTAPLIEAIARKVQYKAGVVARDETEQGERALLNLGHTFGHALETAGKYTtLLHGEGVAVGMLLA 279
                                                  .569***********************************************9************** PP

                                    TIGR01357 263 aklseklgllkaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGka 328
                                                  a+lse+lg+  a ++ rl++ll++lglp+ +++ ++ ++ll+ +  DKKn +++++l+l + iG+a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1794 280 ARLSERLGMSAAADTARLQRLLERLGLPVAIPPGMDPQALLALMRLDKKNTAGTLRLILWRGIGRA 345
                                                  ****************************************************************** PP

                                    TIGR01357 329 alasevteeelle 341
                                                  ++   v+e+e+l+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1794 346 EIVGGVDEREVLA 358
                                                  *999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (366 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: 11.62
//
[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:

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