Alignments for a candidate for aroG in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Trichormus variabilis ATCC 29413

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011321312.1 AVA_RS23605 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9WYH8
         (338 letters)



>NCBI__GCF_000204075.1:WP_011321312.1
          Length = 352

 Score =  300 bits (767), Expect = 5e-86
 Identities = 163/342 (47%), Positives = 226/342 (66%), Gaps = 8/342 (2%)

Query: 1   MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLD-CV 59
           MIVV+K GS E +I ++     S+ L      G+ + VIG++G+   +   + + +   +
Sbjct: 1   MIVVMKVGSPEVEINRINDELTSWGLTPEKIIGKHKVVIGLVGETADLDPLQIQEVSPWI 60

Query: 60  ESVVRVLKPYKLVSREF-HPEDTVIDL----GDVKIG-NGYFTIIAGPCSVEGREMLMET 113
           E V+RV  PYK  SR++ H E + + +    G V  G N    ++AGPCSVE  EM++ET
Sbjct: 61  EQVLRVELPYKRASRQYRHGEASEVVVNTPDGPVVFGENQALVVVAGPCSVENEEMIIET 120

Query: 114 AHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPK 173
           A  +   G K LRGGAYKPRTSPY+FQG GE  LE L +A D  G+ ++TE +   +L  
Sbjct: 121 AQRVKAAGAKFLRGGAYKPRTSPYAFQGHGESALELLAKARDVSGLGIITEVMDASELDI 180

Query: 174 VAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKII 233
           +AE AD+IQ+GARN QNF LL K G+  KPVLLKRG   TIE++L++AEY+  +GN  +I
Sbjct: 181 IAEVADVIQVGARNMQNFSLLKKVGAQPKPVLLKRGMAATIEDWLMAAEYVLAAGNPNVI 240

Query: 234 LCERGIRTFEKA-TRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGA 292
           LCERGIRTF++  TRNTLD+S VP++RK +HLPI++DPSH  G  + V  ++ AAIA G 
Sbjct: 241 LCERGIRTFDRQYTRNTLDLSVVPVLRKLTHLPIMIDPSHGTGWAEYVPSMAMAAIAAGT 300

Query: 293 HGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334
             +++EVHP P+KALSDG QSL  E F  L+QE+  +  A+G
Sbjct: 301 DSLMIEVHPNPKKALSDGPQSLTPEHFDRLMQELAVIGKAVG 342


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: 298
Number of extensions: 8
Number of successful extensions: 4
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: 352
Length adjustment: 29
Effective length of query: 309
Effective length of database: 323
Effective search space:    99807
Effective search space used:    99807
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_011321312.1 AVA_RS23605 (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.5812.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-124  399.9   0.0   2.8e-124  399.6   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011321312.1  AVA_RS23605 3-deoxy-7-phosphohep


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011321312.1  AVA_RS23605 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.6   0.0  2.8e-124  2.8e-124       3     259 ..      73     336 ..      71     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 399.6 bits;  conditional E-value: 2.8e-124
                                 TIGR01361   3 askkvkkeetvvdved.....vkiGege.liviaGPCsveseeqivetakavkeaGakllrGgafkPrt 65 
                                               as+++++ e+ + v +     v +Ge++ l+v+aGPCsve+ee+i+eta++vk+aGak+lrGga+kPrt
  lcl|NCBI__GCF_000204075.1:WP_011321312.1  73 ASRQYRHGEASEVVVNtpdgpVVFGENQaLVVVAGPCSVENEEMIIETAQRVKAAGAKFLRGGAYKPRT 141
                                               67777766555444444558899***997899************************************* PP

                                 TIGR01361  66 sPysfqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkP 134
                                               sPy+fqG+ge++l+ll++a+d  gl ++tev+d+++++i+ae++D++q+Garnmqnf+lLk+vg++ kP
  lcl|NCBI__GCF_000204075.1:WP_011321312.1 142 SPYAFQGHGESALELLAKARDVSGLGIITEVMDASELDIIAEVADVIQVGARNMQNFSLLKKVGAQPKP 210
                                               ********************************************************************* PP

                                 TIGR01361 135 vlLkrglaatieewleaaeYilsegnenvilcerGirtfe.katrftldlsavallkklthlPvivDps 202
                                               vlLkrg+aatie+wl+aaeY+l++gn+nvilcerGirtf+ ++tr+tldls+v++l+klthlP+++Dps
  lcl|NCBI__GCF_000204075.1:WP_011321312.1 211 VLLKRGMAATIEDWLMAAEYVLAAGNPNVILCERGIRTFDrQYTRNTLDLSVVPVLRKLTHLPIMIDPS 279
                                               ****************************************889************************** PP

                                 TIGR01361 203 haaGrrdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelka 259
                                               h++G  ++v+++a+aa+a+G+d+l+ievhp+P+kalsD++q+ltpe+f++l++el++
  lcl|NCBI__GCF_000204075.1:WP_011321312.1 280 HGTGWAEYVPSMAMAAIAAGTDSLMIEVHPNPKKALSDGPQSLTPEHFDRLMQELAV 336
                                               *****************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (352 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: 7.87
//
[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