Alignments for a candidate for aroG in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas simiae WCS417

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF1675 PS417_08525 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P29976
         (525 letters)



>FitnessBrowser__WCS417:GFF1675
          Length = 448

 Score =  559 bits (1441), Expect = e-164
 Identities = 265/442 (59%), Positives = 338/442 (76%), Gaps = 1/442 (0%)

Query: 75  WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134
           W+P+SW+     Q P YP+A  L  V + + ++PP+VFAGEAR L  + A+   G+AFLL
Sbjct: 5   WSPDSWRALPIQQQPQYPDAAHLLQVEQNLASYPPLVFAGEARELRRQFAEVTQGRAFLL 64

Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194
           QGGDCAESF EF+A  IRDTF+VLLQM+IV+TF    PV+KVGRMAGQFAKPRS   E  
Sbjct: 65  QGGDCAESFAEFSAAKIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSANDETI 124

Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254
           DG+ LP+Y+GD +NG  FDE SR+PDP+R++++Y QS ATLNLLRAFA GG+A + +V +
Sbjct: 125 DGITLPAYRGDIVNGIGFDETSRVPDPDRLLQSYHQSTATLNLLRAFAQGGFADLHQVHK 184

Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDHPLMTTTDFYTSHECLLLPYEQS 314
           WNLDF+  S  A++Y +LA+R+DE L FM ACG+ +  P +  T F+T+HE LLL YEQ+
Sbjct: 185 WNLDFIANSALAEKYSQLADRIDETLAFMRACGMDSS-PQLRETSFFTAHEALLLNYEQA 243

Query: 315 LTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVKLV 374
             R DS +  YYDCSAHM+W G+RTRQLDGAHVEFLRG+ NP+G+KV   M+P +L++L+
Sbjct: 244 FVRRDSLTNDYYDCSAHMLWIGDRTRQLDGAHVEFLRGVNNPIGVKVGPSMNPDDLIRLI 303

Query: 375 EILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCGLK 434
           +ILNP+N PGR+ +I RMGA  +   LP LIRAV+R G+ V W  DPMHGNTIKA  G K
Sbjct: 304 DILNPDNDPGRLNLIARMGAGKVGDHLPGLIRAVQREGKQVLWSSDPMHGNTIKASSGYK 363

Query: 435 TRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHTHC 494
           TR F  IL EV+ F  VH+ EG++AGGIH+EMTGQNVTECIGG+R +T D LS RYHTHC
Sbjct: 364 TRDFAQILGEVKEFFQVHQAEGTYAGGIHIEMTGQNVTECIGGARPITEDGLSDRYHTHC 423

Query: 495 DPRLNASQSLELAFIVAERLRK 516
           DPR+NA QSLELAF++AE L++
Sbjct: 424 DPRMNADQSLELAFLIAETLKQ 445


Lambda     K      H
   0.318    0.132    0.389 

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: 640
Number of extensions: 19
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: 525
Length of database: 448
Length adjustment: 34
Effective length of query: 491
Effective length of database: 414
Effective search space:   203274
Effective search space used:   203274
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 GFF1675 PS417_08525 (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.17376.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.1e-224  730.9   0.0   2.5e-224  730.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF1675  PS417_08525 phospho-2-dehydro-3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1675  PS417_08525 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.7   0.0  2.5e-224  2.5e-224       1     442 [.       5     446 ..       5     447 .. 1.00

  Alignments for each domain:
  == domain 1  score: 730.7 bits;  conditional E-value: 2.5e-224
                           TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkevead 75 
                                         ws++swr+ p +q+P+yPda++l +v+++l+s+PPlv+age+++l++++aev++G+afllqgGdcaesf e++a+
  lcl|FitnessBrowser__WCS417:GFF1675   5 WSPDSWRALPIQQQPQYPDAAHLLQVEQNLASYPPLVFAGEARELRRQFAEVTQGRAFLLQGGDCAESFAEFSAA 79 
                                         89************************************************************************* PP

                           TIGR01358  76 nirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpdperl 150
                                         +ird+++vllqma+v+t++a+ Pvvkvgr+aGq+akPrs++ e+ dg+tlp+yrGd++ng  fde +rvpdp+rl
  lcl|FitnessBrowser__WCS417:GFF1675  80 KIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSANDETIDGITLPAYRGDIVNGIGFDETSRVPDPDRL 154
                                         *************************************************************************** PP

                           TIGR01358 151 vrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeaealkrvel 225
                                         ++ y++s+atlnllra+++gG+adl++vh+Wnl+f+ +s  +++y +la++ide+l fm+a+g++++ +l+++ +
  lcl|FitnessBrowser__WCS417:GFF1675 155 LQSYHQSTATLNLLRAFAQGGFADLHQVHKWNLDFIANSALAEKYSQLADRIDETLAFMRACGMDSSPQLRETSF 229
                                         *************************************************************************** PP

                           TIGR01358 226 ytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsmeadellklie 300
                                         +t+healll+ye+a++r ds +++++d+sah+lWiG+rtrqldgahveflrgv+nPig+kvgpsm++d+l++li+
  lcl|FitnessBrowser__WCS417:GFF1675 230 FTAHEALLLNYEQAFVRRDSLTNDYYDCSAHMLWIGDRTRQLDGAHVEFLRGVNNPIGVKVGPSMNPDDLIRLID 304
                                         *************************************************************************** PP

                           TIGR01358 301 vldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkeffe 375
                                         +l+P+n+PGrl li+r+Ga k+ ++lP l++av+++G++v+W +dpmhGnt++a+sGyktr f +il evkeff+
  lcl|FitnessBrowser__WCS417:GFF1675 305 ILNPDNDPGRLNLIARMGAGKVGDHLPGLIRAVQREGKQVLWSSDPMHGNTIKASSGYKTRDFAQILGEVKEFFQ 379
                                         *************************************************************************** PP

                           TIGR01358 376 vhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflvaeklrea 442
                                         vh+aeGt+ GG+h+e+tG++vtec+GGar ite+ l++ry+t+cdPr+na+qslelafl+ae+l+++
  lcl|FitnessBrowser__WCS417:GFF1675 380 VHQAEGTYAGGIHIEMTGQNVTECIGGARPITEDGLSDRYHTHCDPRMNADQSLELAFLIAETLKQV 446
                                         ****************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (448 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: 7.35
//
[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