Alignments for a candidate for aroC in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Dyella japonica UNC79MFTsu3.2

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate N515DRAFT_0107 N515DRAFT_0107 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0107
          Length = 362

 Score =  477 bits (1227), Expect = e-139
 Identities = 233/360 (64%), Positives = 286/360 (79%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ N+ G++F VTTFGESHG A+GC++DG PPG+ + E++ ++DLDRR  G SR+T+QRR
Sbjct: 1   MSSNSFGKIFTVTTFGESHGPAIGCVIDGCPPGLAIDESEFRNDLDRRATGKSRHTSQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D V+ILSGV+EG TTGT I LLI NTDQRS+DY  I + FRPGHADY+Y QKYG+RD 
Sbjct: 61  EADDVEILSGVYEGRTTGTPIALLIRNTDQRSKDYGDIVNTFRPGHADYSYWQKYGIRDP 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARET MRVAA  IAKK+LAE+ G+ +RG L Q+G+I     DW+ VEQNPFF 
Sbjct: 121 RGGGRSSARETTMRVAAAVIAKKWLAERHGVRVRGYLAQLGEIAPQGFDWAAVEQNPFFW 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P   ++ AL++ M AL+K GDS+GA+V VVA GVP G GEP++ +LD D+A ALMSINAV
Sbjct: 181 PHAAQVPALEKAMDALRKSGDSVGARVNVVADGVPPGWGEPIYGKLDGDLAAALMSINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIGDGF  VA RGS++RDE++  GF SNHAGGILGGIS+GQ + A +ALKPTSSI +
Sbjct: 241 KGVEIGDGFAAVAQRGSEHRDEMSPAGFASNHAGGILGGISTGQAVTASIALKPTSSILI 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360
           PG ++N  GE VE++TKGRHDPCVGIRA PIAEAM+A+VLMDH LR RAQ  DV    PR
Sbjct: 301 PGHSVNLAGEPVEVVTKGRHDPCVGIRATPIAEAMMALVLMDHALRHRAQCGDVGEVSPR 360


Lambda     K      H
   0.319    0.138    0.404 

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: 439
Number of extensions: 11
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: 361
Length of database: 362
Length adjustment: 29
Effective length of query: 332
Effective length of database: 333
Effective search space:   110556
Effective search space used:   110556
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate N515DRAFT_0107 N515DRAFT_0107 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

# 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/TIGR00033.hmm
# target sequence database:        /tmp/gapView.13258.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00033  [M=351]
Accession:   TIGR00033
Description: aroC: chorismate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.7e-138  445.9   0.0   5.4e-138  445.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0107  N515DRAFT_0107 chorismate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0107  N515DRAFT_0107 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.7   0.0  5.4e-138  5.4e-138       1     350 [.      10     350 ..      10     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 445.7 bits;  conditional E-value: 5.4e-138
                                    TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGk 66 
                                                  +++ttfGeSHg+a+g++idG+P+gl ++e++++++l+rR  g+sr+t++r+E+D veilsGv+eG+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0107  10 FTVTTFGESHGPAIGCVIDGCPPGLAIDESEFRNDLDRRATGKSRHTSQRREADDVEILSGVYEGR 75 
                                                  789*************************************************************** PP

                                    TIGR00033  67 TtGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGava 132
                                                  TtG+Pialli+N+d+rskdy di +++RPgHady y++KYgi+d +gggrsSaReT++rvaa ++a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0107  76 TTGTPIALLIRNTDQRSKDYGDIVNTFRPGHADYSYWQKYGIRDPRGGGRSSARETTMRVAAAVIA 141
                                                  ****************************************************************** PP

                                    TIGR00033 133 kklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgds 198
                                                  kk+L+e +g+++ +y+ +lge++ +   ++     +++++p++ p a +  ++e+ +d ++k+gds
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0107 142 KKWLAERHGVRVRGYLAQLGEIAPQG--FD---WAAVEQNPFFWPHAAQVPALEKAMDALRKSGDS 202
                                                  ***********************996..33...4589***************************** PP

                                    TIGR00033 199 vGgvvevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvledd 264
                                                  vG++v+vv+ +vp g+Gep++ kld+ la+al+sinAvKgveiGdGF+a+ +rGse+ De+     
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0107 203 VGARVNVVADGVPPGWGEPIYGKLDGDLAAALMSINAVKGVEIGDGFAAVAQRGSEHRDEMS---- 264
                                                  ***********************************************************875.... PP

                                    TIGR00033 265 kirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravp 330
                                                     + +n+ GGi+GGi++G+ ++ +ia+Kp+++i  p ++v+l++++   +tkgRhDpcv +ra+p
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0107 265 PAGFASNHAGGILGGISTGQAVTASIALKPTSSILIPGHSVNLAGEPVEVVTKGRHDPCVGIRATP 330
                                                  6789***************************************999999999************** PP

                                    TIGR00033 331 vvEamvalvladallekras 350
                                                  ++Eam+alvl+d++l++ra+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0107 331 IAEAMMALVLMDHALRHRAQ 350
                                                  ****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (362 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.28
//
[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