Alignments for a candidate for aroC in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Shewanella oneidensis MR-1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate 370251 SO3078.2 hypothetical chorismate synthase (NCBI ptt file)

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__MR1:370251
          Length = 261

 Score =  410 bits (1053), Expect = e-119
 Identities = 201/258 (77%), Positives = 226/258 (87%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GN+IGQ F VTTFGESHG+ALGCI+DG PPG+ LTEAD+QHDLDRRRPGTSRYTT RR
Sbjct: 1   MSGNSIGQNFVVTTFGESHGVALGCIIDGCPPGLELTEADMQHDLDRRRPGTSRYTTARR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD+V+ILSGVFEG TTGTSIGLLIENTDQRSQDYS IKD+FRPGHADYTY+QKYGLRDY
Sbjct: 61  EPDEVRILSGVFEGKTTGTSIGLLIENTDQRSQDYSNIKDLFRPGHADYTYQQKYGLRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETAMRVAAGA+AKKYL +  GI I+G ++Q+G I  +  D+SQ+EQN FF 
Sbjct: 121 RGGGRSSARETAMRVAAGAVAKKYLKQVHGISIQGYMSQLGPICAETLDFSQIEQNAFFF 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           PD  K++ALDE MR LKK GDSIGAK++VVA+ VP GLGEPVFDRLDADIAHALM INAV
Sbjct: 181 PDASKLEALDEYMRELKKSGDSIGAKISVVATNVPVGLGEPVFDRLDADIAHALMGINAV 240

Query: 241 KGVEIGDGFDVVALRGSQ 258
           KGVEIGDGF VV  R  +
Sbjct: 241 KGVEIGDGFGVVTQRAQK 258


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: 363
Number of extensions: 6
Number of successful extensions: 1
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: 261
Length adjustment: 27
Effective length of query: 334
Effective length of database: 234
Effective search space:    78156
Effective search space used:    78156
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: 48 (23.1 bits)

Align candidate 370251 SO3078.2 (hypothetical chorismate synthase (NCBI ptt file))
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.6172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-109  351.3   0.1   3.3e-109  351.0   0.1    1.0  1  lcl|FitnessBrowser__MR1:370251  SO3078.2 hypothetical chorismate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:370251  SO3078.2 hypothetical chorismate synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.0   0.1  3.3e-109  3.3e-109       1     251 [.      10     255 ..      10     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 351.0 bits;  conditional E-value: 3.3e-109
                       TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiallikNk 79 
                                     + +ttfGeSHg alg+iidG+P+glelte+d+q++l+rRrpg+sr+t+ r+E Dev+ilsGvfeGkTtG+ i lli+N+
  lcl|FitnessBrowser__MR1:370251  10 FVVTTFGESHGVALGCIIDGCPPGLELTEADMQHDLDRRRPGTSRYTTARREPDEVRILSGVFEGKTTGTSIGLLIENT 88 
                                     569**************************************************************************** PP

                       TIGR00033  80 dvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvklgevelee 158
                                     d+rs+dy++ik+l+RPgHadyty++KYg++d++gggrsSaReTa+rvaaGavakk+Lk+ +gi i +y+++lg +++e+
  lcl|FitnessBrowser__MR1:370251  89 DQRSQDYSNIKDLFRPGHADYTYQQKYGLRDYRGGGRSSARETAMRVAAGAVAKKYLKQVHGISIQGYMSQLGPICAET 167
                                     ****************************************************************************997 PP

                       TIGR00033 159 esakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelasallsinAvK 237
                                       +      +++++ +++pda++ +++ e++ ++kk+gds+G++++vv++nvpvglGep+fd+lda +a+al++inAvK
  lcl|FitnessBrowser__MR1:370251 168 LDF-----SQIEQNAFFFPDASKLEALDEYMRELKKSGDSIGAKISVVATNVPVGLGEPVFDRLDADIAHALMGINAVK 241
                                     444.....5799******************************************************************* PP

                       TIGR00033 238 gveiGdGFeaasvr 251
                                     gveiGdGF  +++r
  lcl|FitnessBrowser__MR1:370251 242 GVEIGDGFGVVTQR 255
                                     ********988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (261 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: 6.60
//
[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