Alignments for a candidate for aroC in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Clostridium acetobutylicum ATCC 824

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate NP_347532.1 CA_C0896 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000008765.1:NP_347532.1
          Length = 356

 Score =  259 bits (662), Expect = 8e-74
 Identities = 147/350 (42%), Positives = 214/350 (61%), Gaps = 15/350 (4%)

Query: 7   GQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRREPDQVK 66
           G   +++ FGESHG A+G +++G+ PG+ L    +  +++RR PG ++Y+TQR E D  +
Sbjct: 6   GNKIKLSIFGESHGKAIGIVINGLEPGVELDLEFINSEMERRAPGRTKYSTQRNEKDNFE 65

Query: 67  ILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKY-GLRDYRGGGR 125
           I+SG F G TTGT +  +I N +Q S+DYS +KD  RPGH+DYT   KY G  DYRGGG 
Sbjct: 66  IVSGFFNGKTTGTPLCAIIWNGNQHSKDYSNVKDFARPGHSDYTGFIKYKGFNDYRGGGH 125

Query: 126 SSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGD--------IPLDIKDWSQVEQNP 177
            S R TA  V AGA+AK+ L  K  I I   +  + D        + +D +    + +  
Sbjct: 126 FSGRLTAPLVFAGAVAKQILF-KDNIIIGSHILSIKDTKEKYFDKVNIDSETLISLTKKA 184

Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237
           F   D  K + + E++   K + DS+G  +   A  +PAG G+P FD  ++ ++H L SI
Sbjct: 185 FPVLDDKKGEEMKEVILKAKNDLDSVGGIIECCALNLPAGKGDPFFDSCESILSHMLFSI 244

Query: 238 NAVKGVEIGDGFDVVALRGSQ-NRDEITKDGF---QSNHAGGILGGISSGQQIIAHMALK 293
            AVKGVE G+GF++  ++GS+ N D  TK+G     SN+ GGILGGI+SG  ++   A K
Sbjct: 245 PAVKGVEFGEGFNITKMKGSEANDDFYTKNGIVKTYSNNNGGILGGITSGMPLVFRAAFK 304

Query: 294 PTSSITVPGRTIN-RFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMD 342
           PT+SI  P +TIN +  E  E+  KGRHDPC+ +RAVP+ EA  A+ ++D
Sbjct: 305 PTASIYKPQKTINMKTMENEEISIKGRHDPCIVLRAVPVVEAACALSILD 354


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: 334
Number of extensions: 16
Number of successful extensions: 5
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 NP_347532.1 CA_C0896 (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.6581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   2.5e-124  400.7   0.0   2.7e-124  400.6   0.0    1.0  1  lcl|NCBI__GCF_000008765.1:NP_347532.1  CA_C0896 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_347532.1  CA_C0896 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.6   0.0  2.7e-124  2.7e-124       2     343 ..      10     355 ..       9     356 .] 0.95

  Alignments for each domain:
  == domain 1  score: 400.6 bits;  conditional E-value: 2.7e-124
                              TIGR00033   2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPia 73 
                                            +l +fGeSHgka+g +i+Gl +g+el+ e i++e++rR pg ++++++r+E+D++ei+sG f+GkTtG+P++
  lcl|NCBI__GCF_000008765.1:NP_347532.1  10 KLSIFGESHGKAIGIVINGLEPGVELDLEFINSEMERRAPGRTKYSTQRNEKDNFEIVSGFFNGKTTGTPLC 81 
                                            789********************************************************************* PP

                              TIGR00033  74 llikNkdvrskdyedikelpRPgHadytylkKYgikd.regggrsSaReTaarvaaGavakklLketagiei 144
                                             +i N +++skdy+++k++ RPgH+dyt++ KY+  + ++ggg  S+R Ta +v aGavak+ L + ++i i
  lcl|NCBI__GCF_000008765.1:NP_347532.1  82 AIIWNGNQHSKDYSNVKDFARPGHSDYTGFIKYKGFNdYRGGGHFSGRLTAPLVFAGAVAKQILFK-DNIII 152
                                            *********************************85544**************************99.99*** PP

                              TIGR00033 145 vayvvklge.veleeesak..eiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvg 213
                                             +++ ++ + +e  +++++  +++  +l k+ + ++d ++ +em+e+i kak+d dsvGg++e+ + n+p+g
  lcl|NCBI__GCF_000008765.1:NP_347532.1 153 GSHILSIKDtKEKYFDKVNidSETLISLTKKAFPVLDDKKGEEMKEVILKAKNDLDSVGGIIECCALNLPAG 224
                                            *******984333333333335555667779***************************************** PP

                              TIGR00033 214 lGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGed 285
                                             G+p+fd+ ++ l++ l+si+AvKgve+G+GF+ ++++GseanD+++++++ +++ +nn+GGi+GGit G++
  lcl|NCBI__GCF_000008765.1:NP_347532.1 225 KGDPFFDSCESILSHMLFSIPAVKGVEFGEGFNITKMKGSEANDDFYTKNGIVKTYSNNNGGILGGITSGMP 296
                                            ************************************************************************ PP

                              TIGR00033 286 irvriavKpiptikkplktvdletkekakat.kgRhDpcvvpravpvvEamvalvlada 343
                                            +++r+a+Kp+++i+kp+kt++++t+e+ +++ kgRhDpc+v+ravpvvEa+ al ++d 
  lcl|NCBI__GCF_000008765.1:NP_347532.1 297 LVFRAAFKPTASIYKPQKTINMKTMENEEISiKGRHDPCIVLRAVPVVEAACALSILDI 355
                                            ******************************************************99986 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: 9.88
//
[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