Alignments for a candidate for aroG in Hippea alviniae EP5-r

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Hippea alviniae EP5-r

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_022670181.1 G415_RS0103360 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9WYH8
         (338 letters)



>NCBI__GCF_000420385.1:WP_022670181.1
          Length = 344

 Score =  376 bits (965), Expect = e-109
 Identities = 193/342 (56%), Positives = 248/342 (72%), Gaps = 13/342 (3%)

Query: 1   MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLD--- 57
           MI+V+K  + EEDI+++ +  ES  LK HISKG  +TVIG+IGD    +  K E+LD   
Sbjct: 1   MIIVMKSTAKEEDIQRLKEKIESLELKAHISKGSTKTVIGVIGD----IDSKTENLDLIA 56

Query: 58  ------CVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLM 111
                  VESV RV KPYKL SRE    DT+ID+  VKIG   FT+IAGPCSVE RE +M
Sbjct: 57  VLSLDKAVESVHRVSKPYKLASREHRDSDTIIDVNGVKIGGNRFTVIAGPCSVENREQVM 116

Query: 112 ETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDL 171
            TA  + +    +LRGGA+KPRTSPYSFQGLGE+GL+ L+EA+++ GM VVTE +   DL
Sbjct: 117 TTALGIKKCSAHMLRGGAFKPRTSPYSFQGLGEEGLKILKEASEETGMPVVTEVMNPRDL 176

Query: 172 PKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTK 231
             V +YAD++QIGARN QNF LL + G  +KPVLLKRG   TI+EFL+SAEYI + GN  
Sbjct: 177 DVVLKYADVLQIGARNIQNFALLKEVGKTDKPVLLKRGMATTIQEFLMSAEYIMSEGNAD 236

Query: 232 IILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVG 291
           +ILCERGIRTFE ATRNTLDISAVP+++KE+HLP+++DPSH+ G+RD V  LSRAAIA G
Sbjct: 237 VILCERGIRTFETATRNTLDISAVPVLKKETHLPVIIDPSHAAGKRDYVPALSRAAIAAG 296

Query: 292 AHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADAL 333
           A G+++EVH  P+ A+SD  Q L  E F  L++E+K + + +
Sbjct: 297 ADGLLIEVHYNPQIAVSDAAQQLTIEEFCNLMKELKAIGEVV 338


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: 376
Number of extensions: 7
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: 344
Length adjustment: 29
Effective length of query: 309
Effective length of database: 315
Effective search space:    97335
Effective search space used:    97335
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_022670181.1 G415_RS0103360 (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.85859.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-131  421.8   0.1   6.1e-131  421.5   0.1    1.1  1  NCBI__GCF_000420385.1:WP_022670181.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022670181.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.5   0.1  6.1e-131  6.1e-131       2     259 ..      76     333 ..      75     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 421.5 bits;  conditional E-value: 6.1e-131
                             TIGR01361   2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlg 74 
                                           las++ + ++t++dv++vkiG+++++viaGPCsve++eq+++ta  +k+  a++lrGgafkPrtsPysfqGlg
  NCBI__GCF_000420385.1:WP_022670181.1  76 LASREHRDSDTIIDVNGVKIGGNRFTVIAGPCSVENREQVMTTALGIKKCSAHMLRGGAFKPRTSPYSFQGLG 148
                                           789********************************************************************** PP

                             TIGR01361  75 eeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatiee 147
                                           eeglk+lk+a +etg++vvtev+++rd+++v +y+D+lqiGarn+qnf+lLkevgk++kPvlLkrg+a+ti+e
  NCBI__GCF_000420385.1:WP_022670181.1 149 EEGLKILKEASEETGMPVVTEVMNPRDLDVVLKYADVLQIGARNIQNFALLKEVGKTDKPVLLKRGMATTIQE 221
                                           ************************************************************************* PP

                             TIGR01361 148 wleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlplakaava 220
                                           +l++aeYi+segn +vilcerGirtfe+atr+tld+sav++lkk+thlPvi+DpshaaG+rd+v++l++aa+a
  NCBI__GCF_000420385.1:WP_022670181.1 222 FLMSAEYIMSEGNADVILCERGIRTFETATRNTLDISAVPVLKKETHLPVIIDPSHAAGKRDYVPALSRAAIA 294
                                           ************************************************************************* PP

                             TIGR01361 221 vGadgllievhpdPekalsDseqqltpeefkelvkelka 259
                                           +Gadgllievh +P+ a+sD++qqlt+eef +l+kelka
  NCBI__GCF_000420385.1:WP_022670181.1 295 AGADGLLIEVHYNPQIAVSDAAQQLTIEEFCNLMKELKA 333
                                           ***********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (344 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: 00:00:00.00
# Mc/sec: 15.18
//
[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