Alignments for a candidate for aroC in Desulfobacca acetoxidans DSM 11109

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Desulfobacca acetoxidans DSM 11109

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013707610.1 DESAC_RS13365 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000195295.1:WP_013707610.1
          Length = 353

 Score =  361 bits (927), Expect = e-104
 Identities = 182/349 (52%), Positives = 242/349 (69%), Gaps = 1/349 (0%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNT G++FRVTT+GESHG ALG ++DG PP +PLT AD+  +L +RRPG    +T RR
Sbjct: 1   MSGNTFGRIFRVTTWGESHGPALGAVIDGCPPRLPLTTADIAVELAKRRPGGGLASTTRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD V+ILSGVF   TTGT I L+I N D + + Y  +K++FRPGH D+TY+ KYG+RDY
Sbjct: 61  EPDAVEILSGVFADQTTGTPISLIIYNKDAKIEAYEPLKEIFRPGHGDFTYQAKYGIRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETA RVAAGA+A+K L +  GI +     ++G +     DW++++QN F+C
Sbjct: 121 RGGGRSSARETAARVAAGAVAQKVL-DTGGIRVLAYTLELGGVRAQTFDWTEIDQNQFYC 179

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           PD +   ++   ++ +KK+GDS+G  V V   G PAGLGEPVFD+LDA +A A+MSI AV
Sbjct: 180 PDSEAAASMAARVQDIKKQGDSLGGIVEVRVQGCPAGLGEPVFDKLDAVLAQAVMSIGAV 239

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF    L GS++ D +T  GF SN+AGGIL GIS+G +II   A+KP  SI  
Sbjct: 240 KGVEIGAGFAAARLTGSEHNDPLTPKGFVSNNAGGILAGISNGDEIIVRAAVKPIPSIAK 299

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRA 349
             +TI++ G+   +   GRHD     R  P+  AM+ + L D LLRQ+A
Sbjct: 300 LQQTIDQHGQPQTISIAGRHDISAIPRITPVIAAMVKLTLADFLLRQKA 348


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: 365
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: 353
Length adjustment: 29
Effective length of query: 332
Effective length of database: 324
Effective search space:   107568
Effective search space used:   107568
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 WP_013707610.1 DESAC_RS13365 (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.19109.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-131  422.3   0.1   7.8e-131  422.1   0.1    1.0  1  lcl|NCBI__GCF_000195295.1:WP_013707610.1  DESAC_RS13365 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195295.1:WP_013707610.1  DESAC_RS13365 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.1   0.1  7.8e-131  7.8e-131       1     349 [.      10     348 ..      10     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 422.1 bits;  conditional E-value: 7.8e-131
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +r+tt+GeSHg+alga+idG+P+ l+lt++di+ el++Rrpg +  +++r+E D+veilsGvf  +TtG
  lcl|NCBI__GCF_000195295.1:WP_013707610.1  10 FRVTTWGESHGPALGAVIDGCPPRLPLTTADIAVELAKRRPGGGLASTTRREPDAVEILSGVFADQTTG 78 
                                               89******************************************************************* PP

                                 TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138
                                               +Pi+l+i+Nkd + + ye +ke++RPgH d+ty+ KYgi+d++gggrsSaReTaarvaaGava+k L+ 
  lcl|NCBI__GCF_000195295.1:WP_013707610.1  79 TPISLIIYNKDAKIEAYEPLKEIFRPGHGDFTYQAKYGIRDYRGGGRSSARETAARVAAGAVAQKVLDT 147
                                               *******************************************************************99 PP

                                 TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207
                                                 gi+++ay+ +lg v++++         ++d++++ cpd ea++ m + ++ +kk+gds+Gg+vev v
  lcl|NCBI__GCF_000195295.1:WP_013707610.1 148 -GGIRVLAYTLELGGVRAQTFD-----WTEIDQNQFYCPDSEAAASMAARVQDIKKQGDSLGGIVEVRV 210
                                               .99*************999644.....4579************************************** PP

                                 TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276
                                               ++ p+glGep+fdklda la+a++si AvKgveiG+GF+aa+ +Gse+nD+l+       +++nn GGi
  lcl|NCBI__GCF_000195295.1:WP_013707610.1 211 QGCPAGLGEPVFDKLDAVLAQAVMSIGAVKGVEIGAGFAAARLTGSEHNDPLT----PKGFVSNNAGGI 275
                                               **************************************************985....5579******** PP

                                 TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345
                                               + Gi+nG +i vr+avKpip+i+k ++t+d ++++++    gRhD +++pr++pv+ amv+l+lad ll
  lcl|NCBI__GCF_000195295.1:WP_013707610.1 276 LAGISNGDEIIVRAAVKPIPSIAKLQQTIDQHGQPQTISIAGRHDISAIPRITPVIAAMVKLTLADFLL 344
                                               ********************************99999999***************************** PP

                                 TIGR00033 346 ekra 349
                                               +++a
  lcl|NCBI__GCF_000195295.1:WP_013707610.1 345 RQKA 348
                                               9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (353 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: 10.66
//
[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