Alignments for a candidate for aroG in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Phaeobacter inhibens BS107

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF1565 PGA1_c15860 phospho-2-dehydro-3-deoxyheptonate aldolase AroH

Query= BRENDA::A0A0D5ZBC4
         (539 letters)



>FitnessBrowser__Phaeo:GFF1565
          Length = 456

 Score =  521 bits (1343), Expect = e-152
 Identities = 259/453 (57%), Positives = 330/453 (72%), Gaps = 2/453 (0%)

Query: 82  KWTVDSWKSKKALQLPEYPDQAELESVLKTLDAFPPIVFAGEARSLEEKLGEAAMGNAFL 141
           +W   +W+ K  +Q+P+Y +   L +V   L  +PP+VFAGEAR L++ LG A  G AFL
Sbjct: 3   EWQKSTWRQKPRVQMPDYTNADALSAVEAQLSKYPPLVFAGEARRLKQHLGAAGRGEAFL 62

Query: 142 LQGGDCAESFKEFNANNIRDTFRILLQMGAVLMFGGQMPVIKVGRMAGQFAKPRSDPFEE 201
           LQGGDCAESF +F+A+ IRDTF+++LQM  VL +G ++PVIKVGRMAGQFAKPRS P E 
Sbjct: 63  LQGGDCAESFDQFSADAIRDTFKVMLQMAMVLTYGAKVPVIKVGRMAGQFAKPRSAPTET 122

Query: 202 KNGVKLPSYRGDNVNGDSFDEKSRIPDPQRMIRAYCQSAATLNLLRAFATGGYAAMQRVT 261
            NGV+LPSYRGD +N  +F E SR+PDPQRM++AY Q+AAT+NL+RAF+TGGYA + +V 
Sbjct: 123 VNGVELPSYRGDIINDLAFTETSRVPDPQRMLQAYTQAAATVNLIRAFSTGGYADVNQVH 182

Query: 262 QWNLDFTEHSEQGDRYRELASRVDEALGFMAAAGLTVDHP-IMTTTEFWTSHECLLLPYE 320
            W L FTE  E+ + YRE+A+R+ + L FM AAG+  D    + + EF+TSHE LLL YE
Sbjct: 183 AWTLGFTE-GEKAESYREMANRITDTLDFMKAAGINNDTAHTLQSVEFYTSHEGLLLEYE 241

Query: 321 QSLTRLDSTSGRYYDCSAHFLWAGERTRQLDGAHVEFLRGVANPLGIKVSDKMDPNELVK 380
           ++LTRLDSTSG++   S H LW G+RTRQ DGAHVEF RGV NP+G+K        +L  
Sbjct: 242 EALTRLDSTSGKWLAGSGHMLWIGDRTRQPDGAHVEFCRGVQNPIGLKCGPTTTAEDLKV 301

Query: 381 LIEILNPQNKAGRITVITRMGAENMRVKLPHLIRAVRRAGQIVTWVSDPMHGNTIKAPCG 440
           L+  LNP+N+ GR+T+I R GA      LP LI+AV+  G  VTWV DPMHGNTIK+  G
Sbjct: 302 LMAKLNPENEEGRLTLIARFGAGKAGEHLPRLIKAVQDEGAKVTWVCDPMHGNTIKSSSG 361

Query: 441 LKTRPFDSIRAEVRAFFDVHEQEGSHPGGVHLEMTGQNVTECIGGSRTVTFDDLGSRYHT 500
            KTRPF+S+  EVR FF +H  EG+ PGGVH EMTGQ+VTEC GG R VT +DL  RYHT
Sbjct: 362 YKTRPFESVLREVRDFFAIHTAEGTIPGGVHFEMTGQDVTECTGGVRAVTDEDLSDRYHT 421

Query: 501 HCDPRLNASQSLELAFIIAERLRKRRINSPQLQ 533
            CDPRLNASQSLELAF++AE + + R  + + Q
Sbjct: 422 ACDPRLNASQSLELAFLVAEEVSQLRARTSERQ 454


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: 667
Number of extensions: 21
Number of successful extensions: 3
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: 456
Length adjustment: 34
Effective length of query: 505
Effective length of database: 422
Effective search space:   213110
Effective search space used:   213110
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 GFF1565 PGA1_c15860 (phospho-2-dehydro-3-deoxyheptonate aldolase AroH)
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.22141.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.5e-212  690.6   0.0   4.2e-212  690.4   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1565  PGA1_c15860 phospho-2-dehydro-3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1565  PGA1_c15860 phospho-2-dehydro-3-deoxyheptonate aldolase AroH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  690.4   0.0  4.2e-212  4.2e-212       1     441 [.       4     445 ..       4     447 .. 0.99

  Alignments for each domain:
  == domain 1  score: 690.4 bits;  conditional E-value: 4.2e-212
                          TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkeveadn 76 
                                        w++++wr+kp +q+P+y +a+al+av+++l+++PPlv+age+++lk++l+++ +GeafllqgGdcaesf++++ad 
  lcl|FitnessBrowser__Phaeo:GFF1565   4 WQKSTWRQKPRVQMPDYTNADALSAVEAQLSKYPPLVFAGEARRLKQHLGAAGRGEAFLLQGGDCAESFDQFSADA 79 
                                        7889************************************************************************ PP

                          TIGR01358  77 irdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpdperlvr 152
                                        ird+++v+lqma+vltyga++Pv+kvgr+aGq+akPrs+p+e+ +gv+lpsyrGd+in  af+e +rvpdp+r+++
  lcl|FitnessBrowser__Phaeo:GFF1565  80 IRDTFKVMLQMAMVLTYGAKVPVIKVGRMAGQFAKPRSAPTETVNGVELPSYRGDIINDLAFTETSRVPDPQRMLQ 155
                                        **************************************************************************** PP

                          TIGR01358 153 ayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae..alkrvely 226
                                        ay+++aat+nl+ra+ +gGyad+++vh+W+l f++  ++++ y+++a++i+++l fm+a+g+++++  +l+ ve+y
  lcl|FitnessBrowser__Phaeo:GFF1565 156 AYTQAAATVNLIRAFSTGGYADVNQVHAWTLGFTE-GEKAESYREMANRITDTLDFMKAAGINNDTahTLQSVEFY 230
                                        *********************************86.7899*********************98876669******* PP

                          TIGR01358 227 tsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsmeadellklievl 302
                                        tshe lll+yeealtr ds++g++   s+h+lWiG+rtrq dgahvef rgv+nPig+k+gp+++a++l  l+ +l
  lcl|FitnessBrowser__Phaeo:GFF1565 231 TSHEGLLLEYEEALTRLDSTSGKWLAGSGHMLWIGDRTRQPDGAHVEFCRGVQNPIGLKCGPTTTAEDLKVLMAKL 306
                                        **************************************************************************** PP

                          TIGR01358 303 dPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkeffevhk 378
                                        +Pene Grltli+r+Ga k  e+lP+l++av+++G++v+Wv+dpmhGnt++++sGyktr f+++l ev+ ff++h+
  lcl|FitnessBrowser__Phaeo:GFF1565 307 NPENEEGRLTLIARFGAGKAGEHLPRLIKAVQDEGAKVTWVCDPMHGNTIKSSSGYKTRPFESVLREVRDFFAIHT 382
                                        **************************************************************************** PP

                          TIGR01358 379 aeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflvaeklre 441
                                        aeGt pGGvh e+tG+dvtec+GG r++t++dl++ry+tacdPrlna+qslelaflvae + +
  lcl|FitnessBrowser__Phaeo:GFF1565 383 AEGTIPGGVHFEMTGQDVTECTGGVRAVTDEDLSDRYHTACDPRLNASQSLELAFLVAEEVSQ 445
                                        ***********************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (456 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: 7.74
//
[ok]

This GapMind analysis is from Apr 09 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