Alignments for a candidate for aroG in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Desulfarculus baarsii DSM 2075

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_013257309.1 DEBA_RS02400 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9YEJ7
         (270 letters)



>NCBI__GCF_000143965.1:WP_013257309.1
          Length = 296

 Score =  301 bits (772), Expect = 8e-87
 Identities = 160/258 (62%), Positives = 188/258 (72%)

Query: 8   KLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGA 67
           KL  + +   +TVV V  V IGGG+  VIAGPCSVES EQ+ E A AV++ G  +LRGGA
Sbjct: 29  KLHAREQHPEDTVVRVGDVAIGGGAFVVIAGPCSVESEEQMVETAQAVRQGGGAILRGGA 88

Query: 68  FKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQ 127
           +KPRTSPYSFQGLG  GL LL  AG   GLP VTE++D   +  +   ADM+QIGARN+Q
Sbjct: 89  YKPRTSPYSFQGLGPNGLTLLGLAGKATGLPYVTELMDAEDLPLLEEQADMIQIGARNIQ 148

Query: 128 NFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFT 187
           NF LL++VGRS KPVLLKRG   TV+ELL +AEYIL  GN  VVL ERGIRTFE +TR T
Sbjct: 149 NFSLLKKVGRSSKPVLLKRGLMTTVDELLMSAEYILDGGNQSVVLCERGIRTFETATRNT 208

Query: 188 LDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSD 247
           LD++ V VLKE THLPVIVDPSH  G+R  V  +AKA LA GADG++VEVH  PE AL D
Sbjct: 209 LDLSVVPVLKERTHLPVIVDPSHAVGKRRYVAPMAKAALAVGADGIMVEVHCRPEAALCD 268

Query: 248 AKQQLTPGEFARLMGELR 265
            +Q L P EFA LM +LR
Sbjct: 269 GEQSLHPSEFAELMAQLR 286


Lambda     K      H
   0.318    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: 218
Number of extensions: 4
Number of successful extensions: 1
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: 270
Length of database: 296
Length adjustment: 26
Effective length of query: 244
Effective length of database: 270
Effective search space:    65880
Effective search space used:    65880
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: 47 (22.7 bits)

Align candidate WP_013257309.1 DEBA_RS02400 (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.3743500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-123  396.7   0.0   2.6e-123  396.5   0.0    1.0  1  NCBI__GCF_000143965.1:WP_013257309.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013257309.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.5   0.0  2.6e-123  2.6e-123       2     258 ..      30     286 ..      29     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.5 bits;  conditional E-value: 2.6e-123
                             TIGR01361   2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlg 74 
                                           l++++ ++e+tvv+v dv+iG+g ++viaGPCsveseeq+veta+av++ G  +lrGga+kPrtsPysfqGlg
  NCBI__GCF_000143965.1:WP_013257309.1  30 LHAREQHPEDTVVRVGDVAIGGGAFVVIAGPCSVESEEQMVETAQAVRQGGGAILRGGAYKPRTSPYSFQGLG 102
                                           688999******************************************************************* PP

                             TIGR01361  75 eeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatiee 147
                                            +gl+ll  a ++tgl+ vte++d++d+ +++e +D++qiGarn+qnf+lLk+vg+s+kPvlLkrgl++t++e
  NCBI__GCF_000143965.1:WP_013257309.1 103 PNGLTLLGLAGKATGLPYVTELMDAEDLPLLEEQADMIQIGARNIQNFSLLKKVGRSSKPVLLKRGLMTTVDE 175
                                           ************************************************************************* PP

                             TIGR01361 148 wleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlplakaava 220
                                           +l++aeYil  gn+ v+lcerGirtfe+atr+tldls+v++lk+ thlPvivDpsha+G+r +v p+akaa+a
  NCBI__GCF_000143965.1:WP_013257309.1 176 LLMSAEYILDGGNQSVVLCERGIRTFETATRNTLDLSVVPVLKERTHLPVIVDPSHAVGKRRYVAPMAKAALA 248
                                           ************************************************************************* PP

                             TIGR01361 221 vGadgllievhpdPekalsDseqqltpeefkelvkelk 258
                                           vGadg+++evh  Pe al+D+eq+l+p+ef+el+ +l+
  NCBI__GCF_000143965.1:WP_013257309.1 249 VGADGIMVEVHCRPEAALCDGEQSLHPSEFAELMAQLR 286
                                           **********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (296 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.12
//
[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 2024 update 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 original 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