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.14320.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.06
//
[ok]

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

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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:

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