Alignments for a candidate for aroG in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Denitrovibrio acetiphilus DSM 12809

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_013009607.1 DACET_RS01305 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9WYH8
         (338 letters)



>NCBI__GCF_000025725.1:WP_013009607.1
          Length = 338

 Score =  344 bits (882), Expect = 2e-99
 Identities = 176/339 (51%), Positives = 237/339 (69%), Gaps = 9/339 (2%)

Query: 1   MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIG-----DDRYVVADKFES 55
           MIVV+K G+++E++  V + AE      H+ +G+ER V+G++G     D   V+      
Sbjct: 1   MIVVMKIGASQEELNNVTQAAEELGFSSHVIEGKERNVVGLVGIAGQRDKMNVIGQ---- 56

Query: 56  LDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAH 115
           L  VE++V + KPYKL SRE  PE ++ID+  VK G     +IAGPCSVE  E +++TA 
Sbjct: 57  LAGVENIVPISKPYKLASREVKPEPSIIDVCGVKFGGENIPVIAGPCSVENEEGVIKTAE 116

Query: 116 FLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVA 175
           F+   G ++LRGGA+KPRTSPYSFQGL E GL+ L +A +  G+ +VTE      +  V 
Sbjct: 117 FIKAAGAQMLRGGAFKPRTSPYSFQGLEEDGLKILAKAREATGLPIVTEVTNPRYVDMVY 176

Query: 176 EYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILC 235
           +YAD+ Q+GARN QNF LLS+ G  +KPVLLKRG   TIEE+L + EYI + GN  +ILC
Sbjct: 177 KYADMFQVGARNVQNFALLSELGKTDKPVLLKRGMSTTIEEYLNATEYILSEGNKNVILC 236

Query: 236 ERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGI 295
           ERG+RTFE ATRNTLDISAVP+I+++SHLPI++DPSH+ G    V PLS+AA+A+GA G+
Sbjct: 237 ERGLRTFETATRNTLDISAVPVIKEKSHLPIIIDPSHAAGHWQYVGPLSKAAVAIGADGL 296

Query: 296 IVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334
           I+EVHPEPEKA SDG QSL    F +L+  M+ +A A+G
Sbjct: 297 IIEVHPEPEKAWSDGAQSLTPTQFLKLMGSMRSIALAIG 335


Lambda     K      H
   0.318    0.138    0.388 

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: 353
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_013009607.1 DACET_RS01305 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR01361 (aroF: 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR01361.hmm
# target sequence database:        /tmp/gapView.336351.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01361  [M=260]
Accession:   TIGR01361
Description: DAHP_synth_Bsub: 3-deoxy-7-phosphoheptulonate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-126  406.3   0.0   3.3e-126  405.9   0.0    1.1  1  NCBI__GCF_000025725.1:WP_013009607.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025725.1:WP_013009607.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.9   0.0  3.3e-126  3.3e-126       2     259 ..      72     329 ..      71     330 .. 0.99

  Alignments for each domain:
  == domain 1  score: 405.9 bits;  conditional E-value: 3.3e-126
                             TIGR01361   2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlg 74 
                                           las++vk+e +++dv +vk+G++++ viaGPCsve+ee +++ta+++k+aGa++lrGgafkPrtsPysfqGl+
  NCBI__GCF_000025725.1:WP_013009607.1  72 LASREVKPEPSIIDVCGVKFGGENIPVIAGPCSVENEEGVIKTAEFIKAAGAQMLRGGAFKPRTSPYSFQGLE 144
                                           789********************************************************************** PP

                             TIGR01361  75 eeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatiee 147
                                           e+glk+l++a+++tgl++vtev ++r+v++v +y+D++q+Garn+qnf+lL+e+gk++kPvlLkrg+++tiee
  NCBI__GCF_000025725.1:WP_013009607.1 145 EDGLKILAKAREATGLPIVTEVTNPRYVDMVYKYADMFQVGARNVQNFALLSELGKTDKPVLLKRGMSTTIEE 217
                                           ************************************************************************* PP

                             TIGR01361 148 wleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlplakaava 220
                                           +l+a+eYilsegn+nvilcerG+rtfe+atr+tld+sav+++k+++hlP+i+DpshaaG++++v pl+kaava
  NCBI__GCF_000025725.1:WP_013009607.1 218 YLNATEYILSEGNKNVILCERGLRTFETATRNTLDISAVPVIKEKSHLPIIIDPSHAAGHWQYVGPLSKAAVA 290
                                           ************************************************************************* PP

                             TIGR01361 221 vGadgllievhpdPekalsDseqqltpeefkelvkelka 259
                                           +Gadgl+ievhp+Peka+sD++q+ltp++f +l+ ++++
  NCBI__GCF_000025725.1:WP_013009607.1 291 IGADGLIIEVHPEPEKAWSDGAQSLTPTQFLKLMGSMRS 329
                                           *********************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (338 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: 00:00:00.00
# Mc/sec: 28.74
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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