Alignments for a candidate for aroB in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Acidovorax sp. GW101-3H11

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate Ac3H11_4705 3-dehydroquinate synthase (EC 4.2.3.4)

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4705
          Length = 367

 Score =  357 bits (915), Expect = e-103
 Identities = 192/347 (55%), Positives = 235/347 (67%), Gaps = 3/347 (0%)

Query: 2   ERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQAG 61
           E + + L  RSY I +  G  +   +F  L S    ++V+N T+APLY   +R  ++   
Sbjct: 6   ECVSIDLEGRSYNIVVGEGSLHAATTFEGLPSAHAALIVSNTTIAPLYAATLRSAIKSRF 65

Query: 62  VNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRG 121
             V  V+LPDGE YK+   L  +F ALL     R T L ALGGGVVGD+TGFAAASY RG
Sbjct: 66  PVVHEVLLPDGEAYKNWETLQLIFDALLSNACDRKTVLFALGGGVVGDMTGFAAASYMRG 125

Query: 122 VRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASG 181
           V F+QVPTTLL+QVDSSVGGKTA+NHP GKNMIGAFYQP  VV DL  L +LP REL++G
Sbjct: 126 VPFVQVPTTLLAQVDSSVGGKTAINHPQGKNMIGAFYQPRLVVCDLATLDSLPLRELSAG 185

Query: 182 LAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRA 241
           LAEVIKYG I D  F +WLE +++ L+  D  A+A+ +RR CE+KA VV+ DE+ETGLRA
Sbjct: 186 LAEVIKYGPIADVDFLDWLESSIEDLMARDRAALAHAVRRSCEIKAWVVSQDEKETGLRA 245

Query: 242 LLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAG 301
           +LN GHTFGHAIEA MGYG WLHGE VAAGMVMAA  S RLG   +A  +R+  L+ RAG
Sbjct: 246 ILNFGHTFGHAIEAGMGYGVWLHGEGVAAGMVMAAELSRRLGLVDAAFVERLTALIARAG 305

Query: 302 LPVNGP---REMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRS 345
           LP  GP      +A  YL  M  DKK   GE+R +L    GK+ VR+
Sbjct: 306 LPTKGPVLDAADNAGRYLELMRIDKKSEGGEIRFVLIDGPGKAVVRA 352


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: 328
Number of extensions: 8
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: 367
Length adjustment: 29
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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 Ac3H11_4705 (3-dehydroquinate synthase (EC 4.2.3.4))
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.1273.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.2e-119  384.7   0.0   2.5e-119  384.5   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705  3-dehydroquinate synthase (EC 4.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705  3-dehydroquinate synthase (EC 4.2.3.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.5   0.0  2.5e-119  2.5e-119       1     334 [.      17     353 ..      17     363 .. 0.94

  Alignments for each domain:
  == domain 1  score: 384.5 bits;  conditional E-value: 2.5e-119
                                        TIGR01357   1 ykvkvgegllk..klveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdge 60 
                                                      y+++vgeg l+  +++e l  +a+ ++++++ +++ l+a++l++a ks+   v+++++pdge
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705  17 YNIVVGEGSLHaaTTFEGLP-SAHAALIVSNTTIAPLYAATLRSAIKSRFPVVHEVLLPDGE 77 
                                                      67899999887333344444.57899**********************9999********** PP

                                        TIGR01357  61 esKsletvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamv 122
                                                       +K++et++ + d+ll++ ++rk+vl a+GGGvvgD++GF+Aa+y+RG+++vqvPTtlla+v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705  78 AYKNWETLQLIFDALLSNACDRKTVLFALGGGVVGDMTGFAAASYMRGVPFVQVPTTLLAQV 139
                                                      ************************************************************** PP

                                        TIGR01357 123 DssvGGKtginlplgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelf 184
                                                      DssvGGKt+in+p+gkN+iGafyqP++V++dl++l +lp rel++G+aEviK+g iad +++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705 140 DSSVGGKTAINHPQGKNMIGAFYQPRLVVCDLATLDSLPLRELSAGLAEVIKYGPIADVDFL 201
                                                      ************************************************************** PP

                                        TIGR01357 185 eelekneklllklaelealeelikrsievKaevVeeDekesglRalLNfGHtlgHaiEallk 246
                                                      ++le+  ++l  + + +al+++++rs+e+Ka vV++Deke+glRa+LNfGHt+gHaiEa ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705 202 DWLESSIEDLMAR-DRAALAHAVRRSCEIKAWVVSQDEKETGLRAILNFGHTFGHAIEAGMG 262
                                                      *****99998875.559********************************************* PP

                                        TIGR01357 247 yk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkk...klsveellk 304
                                                      y+ + HGe Va Gmv++a+ls++lgl++a  +erl+al+ ++glptk +      ++  +l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705 263 YGvWLHGEGVAAGMVMAAELSRRLGLVDAAFVERLTALIARAGLPTKGPVldaADNAGRYLE 324
                                                      ***********************************************9987667788999** PP

                                        TIGR01357 305 allkDKKnegskiklvlleeiGkaalasev 334
                                                       +  DKK+eg++i++vl++  Gka+++   
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4705 325 LMRIDKKSEGGEIRFVLIDGPGKAVVR-AA 353
                                                      ***********************9987.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (367 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: 11.25
//
[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