Alignments for a candidate for aroB in Beijerinckia mobilis UQM 1969

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Beijerinckia mobilis UQM 1969

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_084704786.1 DL88_RS19705 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_000745425.1:WP_084704786.1
          Length = 597

 Score =  256 bits (654), Expect = 1e-72
 Identities = 161/359 (44%), Positives = 207/359 (57%), Gaps = 10/359 (2%)

Query: 2   ERIVVTLGERSYPITIASGLFNEPASFLP-LKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           E + V LG RSY I I   L  E  + +  L       +VT+E +A  +L  +   L   
Sbjct: 230 EIVPVDLGPRSYKIHIGPDLIAEAGALIAALDPKAACAIVTDENVAREHLPALEQSLRNQ 289

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
           G+  +++++  GE  KS A    V  A++     R   +VALGGG+VGDL GF AAS +R
Sbjct: 290 GIRYETIVVRPGEGSKSFATFAEVCDAVIAGKFERRDLIVALGGGIVGDLAGFVAASVRR 349

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           G+RF+QVPTTLLSQVDSSVGGKT +N P GKN+IGAF+QP+ V+ D   L+TLP RE  +
Sbjct: 350 GMRFVQVPTTLLSQVDSSVGGKTGINSPHGKNLIGAFHQPSLVLADSAVLETLPKREFRA 409

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           G AEV+KYG+I D AFF WLE +   + +  G    + I   C  KA +V  DE ETG R
Sbjct: 410 GYAEVVKYGLINDPAFFVWLEVHWPNVFQ-GGVDRVHAIATSCRAKAAIVKRDEFETGDR 468

Query: 241 ALLNLGHTFGHAIEAEMGYG--NWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLK 298
           ALLNLGHTFGHA EA   +     +HGE VA GM  A R S R G  S+ +  R+   L+
Sbjct: 469 ALLNLGHTFGHAFEALTHFDGIRLVHGEGVAIGMACAFRFSVRRGYCSAEDALRVENHLR 528

Query: 299 RAGLPVNGPREMS-----AQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELV 352
             GLP +  RE+S     A A L  M +DKKV  G +  IL   IG   V   V  + V
Sbjct: 529 AVGLPTH-IREISDFDADAAAILAAMYQDKKVERGALTFILARGIGDCFVEKKVEGDEV 586


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: 452
Number of extensions: 14
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: 597
Length adjustment: 33
Effective length of query: 329
Effective length of database: 564
Effective search space:   185556
Effective search space used:   185556
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: 51 (24.3 bits)

Align candidate WP_084704786.1 DL88_RS19705 (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.25903.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-113  364.9   0.0   2.7e-113  364.6   0.0    1.1  1  lcl|NCBI__GCF_000745425.1:WP_084704786.1  DL88_RS19705 3-dehydroquinate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745425.1:WP_084704786.1  DL88_RS19705 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.6   0.0  2.7e-113  2.7e-113       1     341 [.     241     588 ..     241     591 .. 0.96

  Alignments for each domain:
  == domain 1  score: 364.6 bits;  conditional E-value: 2.7e-113
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                               yk+++g +l++++ + +a    +    ++tde+v++++   le+ l+++g++ +++vv +ge sKs++t
  lcl|NCBI__GCF_000745425.1:WP_084704786.1 241 YKIHIGPDLIAEAGALIAAldPKAACAIVTDENVAREHLPALEQSLRNQGIRYETIVVRPGEGSKSFAT 309
                                               78*********9999999965458899****************************************** PP

                                 TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136
                                               +a++ d++++ k+er++++va+GGG+vgDlaGFvAa+  RG+r+vqvPTtll++vDssvGGKtgin p+
  lcl|NCBI__GCF_000745425.1:WP_084704786.1 310 FAEVCDAVIAGKFERRDLIVALGGGIVGDLAGFVAASVRRGMRFVQVPTTLLSQVDSSVGGKTGINSPH 378
                                               ********************************************************************* PP

                                 TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205
                                               gkNliGaf+qP++Vl d +vletlp+re+r+G+aEv+K+gli+d ++f +le ++ ++ +        +
  lcl|NCBI__GCF_000745425.1:WP_084704786.1 379 GKNLIGAFHQPSLVLADSAVLETLPKREFRAGYAEVVKYGLINDPAFFVWLEVHWPNVFQ--GGVDRVH 445
                                               *******************************************************98875..4456678 PP

                                 TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgl 271
                                               +i+ s++ Ka +V++De e+g RalLN+GHt+gHa Eal++++   l HGe VaiGm++++++s + g+
  lcl|NCBI__GCF_000745425.1:WP_084704786.1 446 AIATSCRAKAAIVKRDEFETGDRALLNLGHTFGHAFEALTHFDgirLVHGEGVAIGMACAFRFSVRRGY 514
                                               99***************************************9999999********************* PP

                                 TIGR01357 272 lkaellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevte 336
                                               ++ae++ r+++ l+++glpt++++    + ++ ++l+a+ +DKK e++ ++++l++ iG+++++++v  
  lcl|NCBI__GCF_000745425.1:WP_084704786.1 515 CSAEDALRVENHLRAVGLPTHIREisdfDADAAAILAAMYQDKKVERGALTFILARGIGDCFVEKKVEG 583
                                               ************************9988899999******************************99987 PP

                                 TIGR01357 337 eelle 341
                                               +e+++
  lcl|NCBI__GCF_000745425.1:WP_084704786.1 584 DEVKA 588
                                               77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (597 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: 11.65
//
[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