Alignments for a candidate for aroG in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Desulfobulbus mediterraneus DSM 13871

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_028584204.1 G494_RS0108580 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::A0A0D5ZBC4
         (539 letters)



>NCBI__GCF_000429965.1:WP_028584204.1
          Length = 449

 Score =  492 bits (1267), Expect = e-143
 Identities = 235/442 (53%), Positives = 314/442 (71%)

Query: 82  KWTVDSWKSKKALQLPEYPDQAELESVLKTLDAFPPIVFAGEARSLEEKLGEAAMGNAFL 141
           +WT  SW+   ALQ P +PDQA+ + V+  L   PP+VFAGE R L+  LG+A+ G+AFL
Sbjct: 6   EWTKSSWQQYTALQQPNWPDQAQYDEVIDALSTLPPLVFAGEIRDLKTLLGKASQGDAFL 65

Query: 142 LQGGDCAESFKEFNANNIRDTFRILLQMGAVLMFGGQMPVIKVGRMAGQFAKPRSDPFEE 201
           LQGGDC+E F    A NIR+  ++LLQM  +L + G  PV+KVGR+AGQ+AKPRS   E 
Sbjct: 66  LQGGDCSEEFSRCTAPNIREKLKVLLQMAVILTYAGNKPVVKVGRIAGQYAKPRSSDTEI 125

Query: 202 KNGVKLPSYRGDNVNGDSFDEKSRIPDPQRMIRAYCQSAATLNLLRAFATGGYAAMQRVT 261
            +GV++PSYRGD  N    + ++RIPDPQR+++ Y  SAATLNLLRAF  GG++++ RV 
Sbjct: 126 VDGVEIPSYRGDMANSIEPNLEARIPDPQRLMKGYNMSAATLNLLRAFTRGGFSSLHRVH 185

Query: 262 QWNLDFTEHSEQGDRYRELASRVDEALGFMAAAGLTVDHPIMTTTEFWTSHECLLLPYEQ 321
            WN +F + S  G  Y  LA ++  AL FM   G++ D P M   +F+TSHE L L YE+
Sbjct: 186 AWNQEFVKRSPMGRSYDRLAKQISHALKFMETIGISTDIPQMKQAQFFTSHEALFLGYEE 245

Query: 322 SLTRLDSTSGRYYDCSAHFLWAGERTRQLDGAHVEFLRGVANPLGIKVSDKMDPNELVKL 381
           +LTR DS  G +Y CS H LW G+RTRQLDGAH+EFLRG+ NPLG+K+    D +E++++
Sbjct: 246 ALTREDSIEGGWYGCSGHMLWIGDRTRQLDGAHIEFLRGINNPLGMKIGPNHDVDEVLRI 305

Query: 382 IEILNPQNKAGRITVITRMGAENMRVKLPHLIRAVRRAGQIVTWVSDPMHGNTIKAPCGL 441
           ++ LNP+N+AGR+T+ITR GA  +   LP L+RAV+ AG+ V W  DPMH NT  A  G 
Sbjct: 306 LDRLNPENEAGRMTLITRFGAGQIEKHLPGLLRAVKSAGKNVLWCCDPMHANTFTAESGH 365

Query: 442 KTRPFDSIRAEVRAFFDVHEQEGSHPGGVHLEMTGQNVTECIGGSRTVTFDDLGSRYHTH 501
           KTR F++I +E+R FF++H  EG+ PGGVH E+TG +VTECIGG+R ++ + LG RY T 
Sbjct: 366 KTRDFENILSELRCFFELHWAEGTVPGGVHFELTGDDVTECIGGARQLSDEQLGLRYLTT 425

Query: 502 CDPRLNASQSLELAFIIAERLR 523
           CDPRLNA QSLE+AF IAE +R
Sbjct: 426 CDPRLNAEQSLEMAFQIAEMIR 447


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: 629
Number of extensions: 20
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: 539
Length of database: 449
Length adjustment: 34
Effective length of query: 505
Effective length of database: 415
Effective search space:   209575
Effective search space used:   209575
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 WP_028584204.1 G494_RS0108580 (3-deoxy-7-phosphoheptulonate synthase class II)
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.15838.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.5e-211  686.2   0.0   8.4e-211  686.1   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028584204.1  G494_RS0108580 3-deoxy-7-phospho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028584204.1  G494_RS0108580 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.1   0.0  8.4e-211  8.4e-211       1     441 [.       7     448 ..       7     449 .] 0.99

  Alignments for each domain:
  == domain 1  score: 686.1 bits;  conditional E-value: 8.4e-211
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               w+++sw++ +a+q+P++Pd+++ ++v+d l++lPPlv+agei++lk+ l+++++G+afllqgGdc+e+f
  lcl|NCBI__GCF_000429965.1:WP_028584204.1   7 WTKSSWQQYTALQQPNWPDQAQYDEVIDALSTLPPLVFAGEIRDLKTLLGKASQGDAFLLQGGDCSEEF 75 
                                               8999***************************************************************** PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                               + ++a+nir+kl+vllqmav+lty++++PvvkvgriaGqyakPrs+++e  dgv++psyrGd+ n+ ++
  lcl|NCBI__GCF_000429965.1:WP_028584204.1  76 SRCTAPNIREKLKVLLQMAVILTYAGNKPVVKVGRIAGQYAKPRSSDTEIVDGVEIPSYRGDMANSIEP 144
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               + +ar+pdp+rl++ y+ saatlnllra+t gG+++l++vh+Wn+efvk+sp g  y++la++i++al+
  lcl|NCBI__GCF_000429965.1:WP_028584204.1 145 NLEARIPDPQRLMKGYNMSAATLNLLRAFTRGGFSSLHRVHAWNQEFVKRSPMGRSYDRLAKQISHALK 213
                                               ********************************************************************* PP

                                 TIGR01358 208 fmsavgvaeae.alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvefl 275
                                               fm+++g++++  ++k+++++tsheal+l yeealtr+ds eg+++ +s+h+lWiG+rtrqldgah+efl
  lcl|NCBI__GCF_000429965.1:WP_028584204.1 214 FMETIGISTDIpQMKQAQFFTSHEALFLGYEEALTREDSIEGGWYGCSGHMLWIGDRTRQLDGAHIEFL 282
                                               *******99988********************************************************* PP

                                 TIGR01358 276 rgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvt 344
                                               rg++nP+g+k+gp+  +de+l+++++l+Pene Gr+tli+r+Ga +i ++lP ll+avk+aG++v+W +
  lcl|NCBI__GCF_000429965.1:WP_028584204.1 283 RGINNPLGMKIGPNHDVDEVLRILDRLNPENEAGRMTLITRFGAGQIEKHLPGLLRAVKSAGKNVLWCC 351
                                               ********************************************************************* PP

                                 TIGR01358 345 dpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlas 413
                                               dpmh nt++a sG+ktr f++ilse++ ffe+h aeGt pGGvh eltG+dvtec+GGar++++++l  
  lcl|NCBI__GCF_000429965.1:WP_028584204.1 352 DPMHANTFTAESGHKTRDFENILSELRCFFELHWAEGTVPGGVHFELTGDDVTECIGGARQLSDEQLGL 420
                                               ********************************************************************* PP

                                 TIGR01358 414 ryetacdPrlnaeqslelaflvaeklre 441
                                               ry t+cdPrlnaeqsle+af +ae++r 
  lcl|NCBI__GCF_000429965.1:WP_028584204.1 421 RYLTTCDPRLNAEQSLEMAFQIAEMIRT 448
                                               *************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (449 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: 00:00:00.02
# Mc/sec: 6.96
//
[ok]

This GapMind analysis is from Apr 10 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