Alignments for a candidate for aroC in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Acidovorax sp. GW101-3H11

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate Ac3H11_2925 Chorismate synthase (EC 4.2.3.5)

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2925
          Length = 365

 Score =  465 bits (1197), Expect = e-136
 Identities = 225/359 (62%), Positives = 282/359 (78%), Gaps = 1/359 (0%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNTIG LF VT FGESHG A+GC++DG PPG+ L+EAD+Q DLDRRRPGTSR+ TQR 
Sbjct: 1   MSGNTIGTLFAVTNFGESHGPAIGCVIDGCPPGMLLSEADIQADLDRRRPGTSRHVTQRN 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD V+ILSGV+EG TTGT I LLI NTDQRS+DYS I + FRPGHADYTY  KYG+RD 
Sbjct: 61  EPDAVEILSGVYEGKTTGTPIALLIRNTDQRSKDYSNIAESFRPGHADYTYWHKYGIRDP 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSAR TA  VAAGA+AKK+LA+++G + R C+TQ+G++P+  + W  V  NPFF 
Sbjct: 121 RGGGRSSARLTAPTVAAGAVAKKWLAQQYGAQFRACMTQLGELPIPFESWDHVRSNPFFA 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P  D +   ++ M AL+K GDS GA++ V A+GVP GLGEP++D+LDADIAHA+M +NAV
Sbjct: 181 PVAD-VQQYEDYMDALRKAGDSCGARIRVQATGVPVGLGEPLYDKLDADIAHAMMGLNAV 239

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  VA RG+ + D +T  GF++N+AGG+LGGIS+GQ +   +A+KPTSSI  
Sbjct: 240 KGVEIGAGFASVAHRGTMHGDSMTPQGFRTNNAGGVLGGISTGQDLEVSIAIKPTSSIIS 299

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
           P  +I+  G+  E+ITKGRHDPCVGIRA PIAEA+LA+V+M+H LR RAQ  DV   +P
Sbjct: 300 PRESIDIHGQSTEVITKGRHDPCVGIRAAPIAEALLALVVMEHALRHRAQCGDVVPPVP 358


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: 457
Number of extensions: 13
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: 365
Length adjustment: 29
Effective length of query: 332
Effective length of database: 336
Effective search space:   111552
Effective search space used:   111552
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 Ac3H11_2925 (Chorismate synthase (EC 4.2.3.5))
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.12925.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.3e-136  441.2   0.0   1.5e-136  441.0   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925  Chorismate synthase (EC 4.2.3.5)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925  Chorismate synthase (EC 4.2.3.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.0   0.0  1.5e-136  1.5e-136       1     350 [.      10     349 ..      10     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 441.0 bits;  conditional E-value: 1.5e-136
                                        TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGv 62 
                                                      + +t fGeSHg+a+g++idG+P+g+ l+e+diq +l+rRrpg+sr+ ++r+E D+veilsGv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925  10 FAVTNFGESHGPAIGCVIDGCPPGMLLSEADIQADLDRRRPGTSRHVTQRNEPDAVEILSGV 71 
                                                      6799********************************************************** PP

                                        TIGR00033  63 feGkTtGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaa 124
                                                      +eGkTtG+Pialli+N+d+rskdy++i+e++RPgHadyty++KYgi+d +gggrsSaR Ta 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925  72 YEGKTTGTPIALLIRNTDQRSKDYSNIAESFRPGHADYTYWHKYGIRDPRGGGRSSARLTAP 133
                                                      ************************************************************** PP

                                        TIGR00033 125 rvaaGavakklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekeme 186
                                                       vaaGavakk+L++++g +  a +++lge+ +++es +     ++ ++p+++p a+  ++ e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925 134 TVAAGAVAKKWLAQQYGAQFRACMTQLGELPIPFESWD-----HVRSNPFFAPVAD-VQQYE 189
                                                      *********************************97666.....6889999999865.5679* PP

                                        TIGR00033 187 eeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaa 248
                                                      +++d ++k+gds G+++ v++++vpvglGepl+dklda +a+a++++nAvKgveiG+GF+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925 190 DYMDALRKAGDSCGARIRVQATGVPVGLGEPLYDKLDADIAHAMMGLNAVKGVEIGAGFASV 251
                                                      ************************************************************** PP

                                        TIGR00033 249 svrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletk 310
                                                        rG  + D +    + + ++tnn GG++GGi++G+d++v+ia+Kp+++i  p++++d++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925 252 AHRGTMHGDSM----TPQGFRTNNAGGVLGGISTGQDLEVSIAIKPTSSIISPRESIDIHGQ 309
                                                      *********65....56789****************************************** PP

                                        TIGR00033 311 ekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                                       +  +tkgRhDpcv +ra+p++Ea++alv+++++l++ra+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2925 310 STEVITKGRHDPCVGIRAAPIAEALLALVVMEHALRHRAQ 349
                                                      ************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (365 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: 00:00:00.01
# Mc/sec: 9.91
//
[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