GapMind for Amino acid biosynthesis

 

Aligments for a candidate for aroG in Azospirillum brasilense Sp245

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate AZOBR_RS09730 AZOBR_RS09730 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::A0A0D5ZBC4
         (539 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS09730 AZOBR_RS09730
           phospho-2-dehydro-3-deoxyheptonate aldolase
          Length = 461

 Score =  578 bits (1489), Expect = e-169
 Identities = 272/447 (60%), Positives = 350/447 (78%), Gaps = 1/447 (0%)

Query: 82  KWTVDSWKSKKALQLPEYPDQAELESVLKTLDAFPPIVFAGEARSLEEKLGEAAMGNAFL 141
           +W+ DSW+SK A QLP YPD +++E+V + L ++PP+VFAGEAR L++ L  AA GNAFL
Sbjct: 4   RWSPDSWRSKPAKQLPTYPDPSKVEAVEQRLSSYPPLVFAGEARRLKDSLAAAAAGNAFL 63

Query: 142 LQGGDCAESFKEFNANNIRDTFRILLQMGAVLMFGGQMPVIKVGRMAGQFAKPRSDPFEE 201
           LQGGDCAESF EF+ NNIRDTFR+LLQM  VL FG  +PV+KVGRMAGQFAKPRS   E 
Sbjct: 64  LQGGDCAESFAEFHPNNIRDTFRVLLQMAVVLTFGAAIPVVKVGRMAGQFAKPRSADTEV 123

Query: 202 KNGVKLPSYRGDNVNGDSFDEKSRIPDPQRMIRAYCQSAATLNLLRAFATGGYAAMQRVT 261
             G++LPSYRGD +NG  F   +R+PDP+RM++AY Q+AATLNLLRAF+ GGYA + +V 
Sbjct: 124 LEGIELPSYRGDIINGFDFTPDARVPDPERMMQAYTQAAATLNLLRAFSQGGYADLHKVH 183

Query: 262 QWNLDFTEHSEQGDRYRELASRVDEALGFMAAAGLTVDH-PIMTTTEFWTSHECLLLPYE 320
           QW L F E S  G+++RE+A+R+DE LGFMAA G+T    P +  TEF+TSHE LLLP+E
Sbjct: 184 QWTLGFVERSPAGEQFREIANRLDETLGFMAACGITAQTTPQIRETEFFTSHEALLLPFE 243

Query: 321 QSLTRLDSTSGRYYDCSAHFLWAGERTRQLDGAHVEFLRGVANPLGIKVSDKMDPNELVK 380
           Q++TR+DST+G +YD SAH LW G+RTRQLDGAHVEFLRGV NP+G+K     DP+EL++
Sbjct: 244 QAMTRVDSTTGDWYDVSAHMLWIGDRTRQLDGAHVEFLRGVKNPIGLKCGPTTDPDELIR 303

Query: 381 LIEILNPQNKAGRITVITRMGAENMRVKLPHLIRAVRRAGQIVTWVSDPMHGNTIKAPCG 440
           LI++LNP N+ GR+T+I RMGA+ +  K P L+R V+R G++V W SDPMHGNT+K+  G
Sbjct: 304 LIDLLNPTNEPGRLTLIVRMGADKVAEKFPPLLRKVQREGRVVVWSSDPMHGNTVKSSSG 363

Query: 441 LKTRPFDSIRAEVRAFFDVHEQEGSHPGGVHLEMTGQNVTECIGGSRTVTFDDLGSRYHT 500
            KTRP + + +E R FF VHE EG+H GGVH E+TGQ+VTEC GG++ +T   L  RYHT
Sbjct: 364 YKTRPVEKVLSEARDFFAVHEAEGTHAGGVHFELTGQDVTECTGGAQAITDHKLALRYHT 423

Query: 501 HCDPRLNASQSLELAFIIAERLRKRRI 527
            CDPRLNASQ+LELAF++AE L++ R+
Sbjct: 424 ACDPRLNASQALELAFLLAEELKRARL 450


Lambda     K      H
   0.318    0.133    0.393 

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: 683
Number of extensions: 16
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: 539
Length of database: 461
Length adjustment: 34
Effective length of query: 505
Effective length of database: 427
Effective search space:   215635
Effective search space used:   215635
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: 52 (24.6 bits)

Align candidate AZOBR_RS09730 AZOBR_RS09730 (phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR01358 (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/TIGR01358.hmm
# target sequence database:        /tmp/gapView.22448.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-229  745.3   0.0     1e-228  745.1   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS09730  AZOBR_RS09730 phospho-2-dehydro-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS09730  AZOBR_RS09730 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  745.1   0.0    1e-228    1e-228       1     442 [.       5     448 ..       5     449 .. 0.99

  Alignments for each domain:
  == domain 1  score: 745.1 bits;  conditional E-value: 1e-228
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               ws++swrskpa+qlP+yPd +++eav++ l+s+PPlv+age+++lk++la++a+G+afllqgGdcaesf
  lcl|FitnessBrowser__azobra:AZOBR_RS09730   5 WSPDSWRSKPAKQLPTYPDPSKVEAVEQRLSSYPPLVFAGEARRLKDSLAAAAAGNAFLLQGGDCAESF 73 
                                               89******************************************************************* PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                                e++ +nird++rvllqmavvlt+ga +Pvvkvgr+aGq+akPrs+++e+ +g++lpsyrGd+ing++f
  lcl|FitnessBrowser__azobra:AZOBR_RS09730  74 AEFHPNNIRDTFRVLLQMAVVLTFGAAIPVVKVGRMAGQFAKPRSADTEVLEGIELPSYRGDIINGFDF 142
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               + +arvpdper+++ay+++aatlnllra+ +gGyadl+kvh+W+l fv++spag++++++a+++de+l 
  lcl|FitnessBrowser__azobra:AZOBR_RS09730 143 TPDARVPDPERMMQAYTQAAATLNLLRAFSQGGYADLHKVHQWTLGFVERSPAGEQFREIANRLDETLG 211
                                               ********************************************************************* PP

                                 TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274
                                               fm a+g++ ++  +++++e++tshealll++e+a+trvds++g+++d+sah+lWiG+rtrqldgahvef
  lcl|FitnessBrowser__azobra:AZOBR_RS09730 212 FMAACGITAQTtpQIRETEFFTSHEALLLPFEQAMTRVDSTTGDWYDVSAHMLWIGDRTRQLDGAHVEF 280
                                               *******9998899******************************************************* PP

                                 TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343
                                               lrgvknPig+k+gp++ +del++li+ l+P nePGrltli+r+Ga+k+aek+P+ll++v+++Gr vvW 
  lcl|FitnessBrowser__azobra:AZOBR_RS09730 281 LRGVKNPIGLKCGPTTDPDELIRLIDLLNPTNEPGRLTLIVRMGADKVAEKFPPLLRKVQREGRVVVWS 349
                                               ********************************************************************* PP

                                 TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412
                                               +dpmhGnt++++sGyktr ++++lse + ff+vh+aeGth GGvh eltG+dvtec+GGa++it+++la
  lcl|FitnessBrowser__azobra:AZOBR_RS09730 350 SDPMHGNTVKSSSGYKTRPVEKVLSEARDFFAVHEAEGTHAGGVHFELTGQDVTECTGGAQAITDHKLA 418
                                               ********************************************************************* PP

                                 TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442
                                                ry+tacdPrlna+q+lelafl+ae l+ a
  lcl|FitnessBrowser__azobra:AZOBR_RS09730 419 LRYHTACDPRLNASQALELAFLLAEELKRA 448
                                               **************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (461 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.05
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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