GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Enterococcus termitis LMG 8895

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_069665193.1 BCR25_RS19025 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9WYH8
         (338 letters)



>NCBI__GCF_001730305.1:WP_069665193.1
          Length = 341

 Score =  355 bits (911), Expect = e-103
 Identities = 172/333 (51%), Positives = 241/333 (72%)

Query: 1   MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60
           MIV++K  +T+  I+ V++  +   L+ H+S+G+E+T+IG++GD R +    F S D VE
Sbjct: 1   MIVIMKSEATKAQIKSVIERVKKEGLEVHLSEGKEQTIIGLVGDTRKMQDVAFNSYDGVE 60

Query: 61  SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120
           + VR+   YKL SREFHPE+T++D+  VKIG+G  T++AGPCS+EG + + E A      
Sbjct: 61  NAVRISLTYKLTSREFHPENTIVDVDGVKIGDGSMTMMAGPCSIEGLDQIRECARIAKAG 120

Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADI 180
           G  +LRGGA+KPRTSPY+FQGL E+GL+Y+R+AAD++ M V+TE + E  +  +AEY+DI
Sbjct: 121 GATILRGGAFKPRTSPYAFQGLEEEGLKYIRQAADEFDMKVITEVMDEGHIDMIAEYSDI 180

Query: 181 IQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIR 240
           +QIGARN QNF+LL   G   KP+ LKRG   TI+E+L +AEYIA  GN  +I  ERGIR
Sbjct: 181 LQIGARNMQNFKLLQAVGKTGKPIGLKRGISGTIDEWLNAAEYIAAQGNFNVIFIERGIR 240

Query: 241 TFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVH 300
           T+E ATRNTLD+SAVP+I+K SH PI+VDPSH  G  DLV  ++RA +A GA G+IVE+H
Sbjct: 241 TYETATRNTLDLSAVPLIKKLSHFPIIVDPSHGVGIWDLVPSMARAGVAAGADGLIVEIH 300

Query: 301 PEPEKALSDGKQSLDFELFKELVQEMKKLADAL 333
           P+P  A SDG QSL+ + +  ++QE+  +  A+
Sbjct: 301 PDPVNAWSDGPQSLNEKTYMRMMQEVHIMEKAM 333


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: 327
Number of extensions: 7
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: 338
Length of database: 341
Length adjustment: 28
Effective length of query: 310
Effective length of database: 313
Effective search space:    97030
Effective search space used:    97030
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_069665193.1 BCR25_RS19025 (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.2215536.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-129  415.2   0.0   6.6e-129  414.8   0.0    1.2  1  NCBI__GCF_001730305.1:WP_069665193.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069665193.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.8   0.0  6.6e-129  6.6e-129       2     259 ..      71     328 ..      70     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 414.8 bits;  conditional E-value: 6.6e-129
                             TIGR01361   2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlg 74 
                                           l+s+++++e+t+vdv++vkiG+g+++++aGPCs+e  +qi+e+a+  k+ Ga++lrGgafkPrtsPy+fqGl+
  NCBI__GCF_001730305.1:WP_069665193.1  71 LTSREFHPENTIVDVDGVKIGDGSMTMMAGPCSIEGLDQIRECARIAKAGGATILRGGAFKPRTSPYAFQGLE 143
                                           78*********************************************************************** PP

                             TIGR01361  75 eeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatiee 147
                                           eeglk++++a+de++++v+tev+de +++++aey DilqiGarnmqnf+lL++vgk+ kP+ Lkrg++ ti+e
  NCBI__GCF_001730305.1:WP_069665193.1 144 EEGLKYIRQAADEFDMKVITEVMDEGHIDMIAEYSDILQIGARNMQNFKLLQAVGKTGKPIGLKRGISGTIDE 216
                                           ************************************************************************* PP

                             TIGR01361 148 wleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlplakaava 220
                                           wl+aaeYi+++gn nvi++erGirt+e+atr+tldlsav+l+kkl+h+P+ivDpsh++G +dlv+++a+a+va
  NCBI__GCF_001730305.1:WP_069665193.1 217 WLNAAEYIAAQGNFNVIFIERGIRTYETATRNTLDLSAVPLIKKLSHFPIIVDPSHGVGIWDLVPSMARAGVA 289
                                           ************************************************************************* PP

                             TIGR01361 221 vGadgllievhpdPekalsDseqqltpeefkelvkelka 259
                                           +Gadgl++e+hpdP +a+sD++q+l+++++ ++++e+++
  NCBI__GCF_001730305.1:WP_069665193.1 290 AGADGLIVEIHPDPVNAWSDGPQSLNEKTYMRMMQEVHI 328
                                           ************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (341 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: 19.36
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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