Alignments for a candidate for aroG in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Azospirillum brasilense Sp245

Align Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2; DAHP synthase 2; PhDAHP2; Phospho-2-keto-3-deoxyheptonate aldolase 2; EC 2.5.1.54 (characterized)
to candidate AZOBR_RS09730 AZOBR_RS09730 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= SwissProt::A0A067XGX8
         (512 letters)



>FitnessBrowser__azobra:AZOBR_RS09730
          Length = 461

 Score =  580 bits (1495), Expect = e-170
 Identities = 275/447 (61%), Positives = 352/447 (78%), Gaps = 1/447 (0%)

Query: 61  KWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGNAFL 120
           +W+ +SW++KPA QLP YPD  ++E+V + LS+YPP+VFAGEAR L++ L  AA GNAFL
Sbjct: 4   RWSPDSWRSKPAKQLPTYPDPSKVEAVEQRLSSYPPLVFAGEARRLKDSLAAAAAGNAFL 63

Query: 121 LQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDPFEE 180
           LQGGDCAESF EF  NNIRDTFRV+LQM VVL FG  +PV+KVGRMAGQFAKPRS   E 
Sbjct: 64  LQGGDCAESFAEFHPNNIRDTFRVLLQMAVVLTFGAAIPVVKVGRMAGQFAKPRSADTEV 123

Query: 181 KDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQRVN 240
            +G++LPSYRGD +NG  F   +R+PDP RM++AYTQ+ ATLNLLRAF+ GGYA + +V+
Sbjct: 124 LEGIELPSYRGDIINGFDFTPDARVPDPERMMQAYTQAAATLNLLRAFSQGGYADLHKVH 183

Query: 241 QWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVDHTI-MTTTDFWTSHECLLLPYE 299
           QW L F ++S  G+++RE+A+R+DE +GFM A G+T   T  +  T+F+TSHE LLLP+E
Sbjct: 184 QWTLGFVERSPAGEQFREIANRLDETLGFMAACGITAQTTPQIRETEFFTSHEALLLPFE 243

Query: 300 QALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDELVK 359
           QA+TR DST+G +YD SAHM+W+G+RTRQLDGAHVEFLRG+ NP+G+K     DPDEL++
Sbjct: 244 QAMTRVDSTTGDWYDVSAHMLWIGDRTRQLDGAHVEFLRGVKNPIGLKCGPTTDPDELIR 303

Query: 360 LIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKAPCG 419
           LID+LNP N+PGR+T+I RMGAD +  K P L+R V+  G++V W SDPMHGNT K+  G
Sbjct: 304 LIDLLNPTNEPGRLTLIVRMGADKVAEKFPPLLRKVQREGRVVVWSSDPMHGNTVKSSSG 363

Query: 420 LKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSRYHT 479
            KTR  + + +E R FF VHE EG++ GGVH E+TGQ+VTEC GG++ IT + L+ RYHT
Sbjct: 364 YKTRPVEKVLSEARDFFAVHEAEGTHAGGVHFELTGQDVTECTGGAQAITDHKLALRYHT 423

Query: 480 HCDPRLNASQALELAFAIAERLRRRRL 506
            CDPRLNASQALELAF +AE L+R RL
Sbjct: 424 ACDPRLNASQALELAFLLAEELKRARL 450


Lambda     K      H
   0.319    0.134    0.401 

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: 716
Number of extensions: 21
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: 512
Length of database: 461
Length adjustment: 34
Effective length of query: 478
Effective length of database: 427
Effective search space:   204106
Effective search space used:   204106
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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.25054.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.07
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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