Alignments for a candidate for aroC in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Desulfarculus baarsii DSM 2075

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013260008.1 DEBA_RS16085 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000143965.1:WP_013260008.1
          Length = 356

 Score =  347 bits (889), Expect = e-100
 Identities = 179/351 (50%), Positives = 232/351 (66%), Gaps = 3/351 (0%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M G+ +GQ+ R+ TFGESHG A+G ++DG+P G+ + E  +Q DLDRRRPGTS Y TQR+
Sbjct: 1   MFGSFMGQILRIATFGESHGPAVGVVIDGLPAGLAIDETLIQRDLDRRRPGTSPYVTQRK 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D  +ILSG+ +G T GT + +++ NTD RS+DY  +  VFRPGHAD+ Y  KYG    
Sbjct: 61  EADTAQILSGLADGRTLGTPLCVVVHNTDARSKDYGELLGVFRPGHADFAYHAKYGAPPQ 120

Query: 121 RGGG--RSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPF 178
            GGG  RSS RET  RVAAGA+A+  LA   G+ IR C   +G +     DW    Q+P 
Sbjct: 121 PGGGAGRSSGRETVGRVAAGAVARAILAP-LGVVIRACTAAVGQVRAARLDWDFAAQDPL 179

Query: 179 FCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSIN 238
            CPDPD   A+ E +   + EGDS+G  V +V SG PAGLG+PVF +LDA +  A+ SI 
Sbjct: 180 RCPDPDAAPAMAERIAQARAEGDSVGGLVRLVVSGAPAGLGDPVFGKLDARLGGAMFSIG 239

Query: 239 AVKGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSI 298
            VKGVEIG GF V    G QN D + ++GF+ N+AGG+LGGIS+GQ+I   +A+KPT SI
Sbjct: 240 GVKGVEIGAGFAVAQRSGGQNNDAMDENGFRGNNAGGVLGGISTGQEITMLLAVKPTPSI 299

Query: 299 TVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRA 349
             P +TI   G+   +  KGRHDPC+  R  P+AEAM A+VL D  L QRA
Sbjct: 300 GRPQQTIGLDGQPRLIQIKGRHDPCLCPRIAPVAEAMAALVLADAYLAQRA 350


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: 380
Number of extensions: 16
Number of successful extensions: 4
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: 356
Length adjustment: 29
Effective length of query: 332
Effective length of database: 327
Effective search space:   108564
Effective search space used:   108564
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_013260008.1 DEBA_RS16085 (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.16927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-124  400.3   0.0   3.7e-124  400.1   0.0    1.0  1  lcl|NCBI__GCF_000143965.1:WP_013260008.1  DEBA_RS16085 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000143965.1:WP_013260008.1  DEBA_RS16085 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.1   0.0  3.7e-124  3.7e-124       1     349 [.      10     350 ..      10     352 .. 0.96

  Alignments for each domain:
  == domain 1  score: 400.1 bits;  conditional E-value: 3.7e-124
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr+ tfGeSHg+a+g++idGlPagl ++e  iq++l+rRrpg+s + ++rkE+D+ +ilsG+  G+T G
  lcl|NCBI__GCF_000143965.1:WP_013260008.1  10 LRIATFGESHGPAVGVVIDGLPAGLAIDETLIQRDLDRRRPGTSPYVTQRKEADTAQILSGLADGRTLG 78 
                                               6899***************************************************************** PP

                                 TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregg..grsSaReTaarvaaGavakklL 136
                                               +P++++++N+d rskdy ++  ++RPgHad++y  KYg   + gg  grsS+ReT++rvaaGava++ L
  lcl|NCBI__GCF_000143965.1:WP_013260008.1  79 TPLCVVVHNTDARSKDYGELLGVFRPGHADFAYHAKYGAPPQPGGgaGRSSGRETVGRVAAGAVARAIL 147
                                               ***************************************996654238********************* PP

                                 TIGR00033 137 ketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvev 205
                                               +   g+ i a +  +g+v++ +   +      ++++p+rcpd++a+ +m e i +a+ +gdsvGg v +
  lcl|NCBI__GCF_000143965.1:WP_013260008.1 148 AP-LGVVIRACTAAVGQVRAARLDWD-----FAAQDPLRCPDPDAAPAMAERIAQARAEGDSVGGLVRL 210
                                               **.88**************9986665.....47889********************************* PP

                                 TIGR00033 206 vvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsG 274
                                               vvs+ p+glG+p+f klda+l+ a++si  vKgveiG+GF+ a++ G + nD +    d+  ++ nn G
  lcl|NCBI__GCF_000143965.1:WP_013260008.1 211 VVSGAPAGLGDPVFGKLDARLGGAMFSIGGVKGVEIGAGFAVAQRSGGQNNDAM----DENGFRGNNAG 275
                                               ****************************************************54....566799***** PP

                                 TIGR00033 275 GieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvlada 343
                                               G++GGi++G++i++  avKp+p+i++p++t+ l++++     kgRhDpc  pr++pv+Eam alvlada
  lcl|NCBI__GCF_000143965.1:WP_013260008.1 276 GVLGGISTGQEITMLLAVKPTPSIGRPQQTIGLDGQPRLIQIKGRHDPCLCPRIAPVAEAMAALVLADA 344
                                               ***********************************9999999*************************** PP

                                 TIGR00033 344 llekra 349
                                               +l++ra
  lcl|NCBI__GCF_000143965.1:WP_013260008.1 345 YLAQRA 350
                                               **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (356 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: 7.86
//
[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