Alignments for a candidate for aroC in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Pseudomonas stutzeri RCH2

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate GFF1864 Psest_1903 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__psRCH2:GFF1864
          Length = 363

 Score =  512 bits (1318), Expect = e-150
 Identities = 256/359 (71%), Positives = 297/359 (82%), Gaps = 1/359 (0%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNT G+LF VTT GESHG AL  IVDG PPG+ L+  DLQ DLDRR+PGTSR+TTQR+
Sbjct: 1   MSGNTYGKLFTVTTAGESHGPALVAIVDGCPPGLELSLEDLQRDLDRRKPGTSRHTTQRQ 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D+V+ILSGVFEG TTG  IGLLI NTDQ+S+DYSAIKD FRP HADYTY  KYG+RDY
Sbjct: 61  EADEVEILSGVFEGKTTGCPIGLLIRNTDQKSKDYSAIKDQFRPAHADYTYHHKYGVRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETAMRVAAGAIAKKYLA   GI++RG ++Q+G I +  K W  VEQN FF 
Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLAT-LGIQVRGYMSQLGPIEIPFKTWDSVEQNAFFS 179

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           PDPDK+  L+  M  L+++ DS+GAK+TVVA GVP GLGEP+FDRLDA++AHALMSINAV
Sbjct: 180 PDPDKVAELEAYMDQLRRDQDSVGAKITVVAEGVPPGLGEPIFDRLDAELAHALMSINAV 239

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  VA RG+++RDE+T  GF SN+AGGILGGISSGQ IIAH+ALKPTSSIT 
Sbjct: 240 KGVEIGAGFASVAQRGTEHRDELTPQGFLSNNAGGILGGISSGQPIIAHLALKPTSSITT 299

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
           PG +I+  G  V++ITKGRHDPCVGIRA PIAEAM+AIVL+DHLLR R QNADV+   P
Sbjct: 300 PGHSIDVSGAPVDVITKGRHDPCVGIRATPIAEAMMAIVLLDHLLRNRGQNADVQVTTP 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: 475
Number of extensions: 17
Number of successful extensions: 3
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: 363
Length adjustment: 29
Effective length of query: 332
Effective length of database: 334
Effective search space:   110888
Effective search space used:   110888
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 GFF1864 Psest_1903 (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.5374.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.1e-144  466.8   0.0   2.4e-144  466.6   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1864  Psest_1903 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1864  Psest_1903 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.6   0.0  2.4e-144  2.4e-144       1     350 [.      10     349 ..      10     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 466.6 bits;  conditional E-value: 2.4e-144
                           TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiall 75 
                                         +++tt+GeSHg+al+ai+dG+P+glel+ ed+q++l+rR+pg+sr+t++r+E+DeveilsGvfeGkTtG Pi ll
  lcl|FitnessBrowser__psRCH2:GFF1864  10 FTVTTAGESHGPALVAIVDGCPPGLELSLEDLQRDLDRRKPGTSRHTTQRQEADEVEILSGVFEGKTTGCPIGLL 84 
                                         789************************************************************************ PP

                           TIGR00033  76 ikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvk 150
                                         i+N+d++skdy+ ik+++RP+Hadyty +KYg++d++gggrsSaReTa+rvaaGa+akk+L+   gi++ +y+++
  lcl|FitnessBrowser__psRCH2:GFF1864  85 IRNTDQKSKDYSAIKDQFRPAHADYTYHHKYGVRDYRGGGRSSARETAMRVAAGAIAKKYLAT-LGIQVRGYMSQ 158
                                         **************************************************************9.88********* PP

                           TIGR00033 151 lgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldae 225
                                         lg +e+++++ +     +++++ ++ pd+++ +e+e+++d++++d+dsvG++++vv+++vp glGep+fd+ldae
  lcl|FitnessBrowser__psRCH2:GFF1864 159 LGPIEIPFKTWD-----SVEQNAFFSPDPDKVAELEAYMDQLRRDQDSVGAKITVVAEGVPPGLGEPIFDRLDAE 228
                                         *******86665.....6999****************************************************** PP

                           TIGR00033 226 lasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikk 300
                                         la+al+sinAvKgveiG+GF+++ +rG e+ Del    + + + +nn GGi+GGi+ G++i  + a+Kp+++i++
  lcl|FitnessBrowser__psRCH2:GFF1864 229 LAHALMSINAVKGVEIGAGFASVAQRGTEHRDEL----TPQGFLSNNAGGILGGISSGQPIIAHLALKPTSSITT 299
                                         ********************************66....5789********************************* PP

                           TIGR00033 301 plktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                         p +++d+++ +   +tkgRhDpcv +ra+p++Eam+a+vl+d+ll++r++
  lcl|FitnessBrowser__psRCH2:GFF1864 300 PGHSIDVSGAPVDVITKGRHDPCVGIRATPIAEAMMAIVLLDHLLRNRGQ 349
                                         *********************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (363 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: 7.87
//
[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