Alignments for a candidate for aroB in Frankia alni ACN14A

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Frankia alni ACN14A

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_011606336.1 FRAAL_RS22880 3-dehydroquinate synthase

Query= BRENDA::P9WPX9
         (362 letters)



>NCBI__GCF_000058485.1:WP_011606336.1
          Length = 371

 Score =  383 bits (984), Expect = e-111
 Identities = 202/356 (56%), Positives = 249/356 (69%), Gaps = 12/356 (3%)

Query: 8   VTVQVAVDPPYPVVIGTGLLDELEDLLADRHKVAVVHQPGLAETAEEIRKRL-AGKGVDA 66
           + V+   +  Y VV+G GLL +L + +A R + AV+H   L  TA+ +   L A  GV+A
Sbjct: 13  IPVRPGGERAYDVVLGEGLLGDLAETVAGRTRAAVIHPAALRTTADAVVADLRANAGVEA 72

Query: 67  HRIEIPDAEAGKDLPVVGFIWEVLGRIGIGRKDALVSLGGGAATDVAGFAAATWLRGVSI 126
           H +E+PD E  K L + GF W+VLGRIG  R D ++ LGGG  TD+AGF AA+WLRGV +
Sbjct: 73  HAVEVPDGEEAKQLRIAGFCWDVLGRIGFTRDDVIIGLGGGTVTDLAGFVAASWLRGVDV 132

Query: 127 VHLPTTLLGMVDAAVGGKTGINTDAGKNLVGAFHQPLAVLVDLATLQTLPRDEMICGMAE 186
           V +PTT+LGMVDAAVGGKTG++ DAGKNLVGAFHQPL VL DLA L TLP  E+  G+AE
Sbjct: 133 VQVPTTVLGMVDAAVGGKTGVDIDAGKNLVGAFHQPLTVLCDLAALATLPAVEVRAGLAE 192

Query: 187 VVKAGFIADPVILDLIEADPQAALDPAGDVLPELIRRAITVKAEVVAADEKESELREILN 246
           VVK GFIAD  ILDL++ DP  A       LPEL+ R+I VKAEVV+ D +E+  REILN
Sbjct: 193 VVKTGFIADAAILDLLDDDPTGAAH-----LPELVERSIRVKAEVVSGDPREAGRREILN 247

Query: 247 YGHTLGHAIERRERYRWRHGAAVSVGLVFAAELARLAGRLDDATAQRHRTILSSLGLPVS 306
           YGHTLGHAIE+ E + WRHGAA+SVG+VFAAEL+RL   LDDATA RHR +L+ +GLPVS
Sbjct: 248 YGHTLGHAIEKVEHFTWRHGAAISVGMVFAAELSRLVAGLDDATADRHRELLTRIGLPVS 307

Query: 307 YDPDALPQLLEIMAGDKKTRAGVLRFVVLDGLAKPGRMV---GPDPGLLVTAYAGV 359
           Y  D  P LL+ M  DKK+R   LRF+   GLA  G  V    PD GLL+ A+  V
Sbjct: 308 YRGDRWPALLDAMRVDKKSRGRRLRFI---GLAAQGETVILDSPDTGLLIAAFTAV 360


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: 495
Number of extensions: 22
Number of successful extensions: 3
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: 371
Length adjustment: 30
Effective length of query: 332
Effective length of database: 341
Effective search space:   113212
Effective search space used:   113212
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_011606336.1 FRAAL_RS22880 (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.25337.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-108  348.8   0.0     2e-108  348.6   0.0    1.0  1  lcl|NCBI__GCF_000058485.1:WP_011606336.1  FRAAL_RS22880 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_011606336.1  FRAAL_RS22880 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.6   0.0    2e-108    2e-108       1     331 [.      23     345 ..      23     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 348.6 bits;  conditional E-value: 2e-108
                                 TIGR01357   1 ykvkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletva 69 
                                               y+v++gegll  l+e++a  ++++ vi+  ++++++++ ++++++++gve++ + vpdgee+K+l+ + 
  lcl|NCBI__GCF_000058485.1:WP_011606336.1  23 YDVVLGEGLLGDLAETVAG-RTRAAVIHPAALRTTADAVVADLRANAGVEAHAVEVPDGEEAKQLRIAG 90 
                                               7899**************7.678999999999999********************************** PP

                                 TIGR01357  70 klldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgk 138
                                                ++d l + +++r++v++++GGG+v+DlaGFvAa++lRG+++vqvPTt+l+mvD++vGGKtg++ + gk
  lcl|NCBI__GCF_000058485.1:WP_011606336.1  91 FCWDVLGRIGFTRDDVIIGLGGGTVTDLAGFVAASWLRGVDVVQVPTTVLGMVDAAVGGKTGVDIDAGK 159
                                               ********************************************************************* PP

                                 TIGR01357 139 NliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeeli 207
                                               Nl+Gaf+qP +Vl+dl+ l+tlp  e+r+G+aEv+K+g+iada++++ l +           ++l el+
  lcl|NCBI__GCF_000058485.1:WP_011606336.1 160 NLVGAFHQPLTVLCDLAALATLPAVEVRAGLAEVVKTGFIADAAILDLLDDDPT------GAAHLPELV 222
                                               *************************************************99665......2479***** PP

                                 TIGR01357 208 krsievKaevVeeDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkael 276
                                               +rsi+vKaevV+ D++e+g R++LN+GHtlgHaiE++ +++++HG a+++Gmv++a+ls+ ++ l+   
  lcl|NCBI__GCF_000058485.1:WP_011606336.1 223 ERSIRVKAEVVSGDPREAGRREILNYGHTLGHAIEKVEHFTWRHGAAISVGMVFAAELSRLVAGLDDAT 291
                                               ********************************************************************* PP

                                 TIGR01357 277 lerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaala 331
                                               ++r+++ll ++glp++++   +  +ll+a+  DKK++g +++++ l + G++++ 
  lcl|NCBI__GCF_000058485.1:WP_011606336.1 292 ADRHRELLTRIGLPVSYRG-DRWPALLDAMRVDKKSRGRRLRFIGLAAQGETVIL 345
                                               ******************7.999***********************999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (371 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.99
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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