GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Pseudomonas simiae WCS417

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate GFF3772 PS417_19315 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__WCS417:GFF3772
          Length = 363

 Score =  510 bits (1313), Expect = e-149
 Identities = 254/359 (70%), Positives = 298/359 (83%), Gaps = 1/359 (0%)

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

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD+V+ILSGVFEG TTG +IGLLI NTDQ+S+DYSAIKD+FRP HADYTY  KYG RDY
Sbjct: 61  EPDEVEILSGVFEGRTTGCAIGLLIRNTDQKSKDYSAIKDLFRPAHADYTYHHKYGERDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETAMRVAAGAIAKKYLA + GI IRG ++Q+G I +  K W  V+ N FF 
Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLATQ-GIVIRGYMSQLGPIEIPFKTWDSVDDNAFFS 179

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

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  V+ RG+++RDE+T +GF SN+AGGILGGISSGQ I+AH+ALK TSSIT 
Sbjct: 240 KGVEIGAGFACVSQRGTEHRDELTPEGFLSNNAGGILGGISSGQPIVAHLALKATSSITT 299

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
           PGR+I+  G  V++ITKGRHDPCVGIRA PIAEAM+AIVLMDHLLR R QNADV+   P
Sbjct: 300 PGRSIDVHGNPVDVITKGRHDPCVGIRATPIAEAMMAIVLMDHLLRNRGQNADVRVSTP 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: 476
Number of extensions: 17
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: 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 GFF3772 PS417_19315 (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.1133.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-139  451.3   0.0   1.2e-139  451.1   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF3772  PS417_19315 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3772  PS417_19315 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.1   0.0  1.2e-139  1.2e-139       1     350 [.      10     349 ..      10     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 451.1 bits;  conditional E-value: 1.2e-139
                           TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiall 75 
                                         +++tt+GeSHg+al+ai+dG+P+glel+ ed+q++l+rR+pg+sr+t++r+E DeveilsGvfeG+TtG  i ll
  lcl|FitnessBrowser__WCS417:GFF3772  10 FTVTTAGESHGPALVAIVDGCPPGLELSLEDLQRDLDRRKPGTSRHTTQRQEPDEVEILSGVFEGRTTGCAIGLL 84 
                                         789************************************************************************ PP

                           TIGR00033  76 ikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvk 150
                                         i+N+d++skdy+ ik+l+RP+Hadyty +KYg +d++gggrsSaReTa+rvaaGa+akk+L+  +gi i +y+++
  lcl|FitnessBrowser__WCS417:GFF3772  85 IRNTDQKSKDYSAIKDLFRPAHADYTYHHKYGERDYRGGGRSSARETAMRVAAGAIAKKYLAT-QGIVIRGYMSQ 158
                                         **************************************************************9.99********* PP

                           TIGR00033 151 lgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldae 225
                                         lg +e+++++ +     ++d++ ++ pd+++  e+e+++d++++d+dsvG++++vv+++v  glGep+fd+ldae
  lcl|FitnessBrowser__WCS417:GFF3772 159 LGPIEIPFKTWD-----SVDDNAFFSPDPDKVPELEAYMDQLRRDQDSVGAKITVVAEGVKPGLGEPIFDRLDAE 228
                                         *******86665.....6999****************************************************** PP

                           TIGR00033 226 lasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikk 300
                                         la+al+sinAvKgveiG+GF+ +s+rG e+ Del+       + +nn GGi+GGi+ G++i+ + a+K++++i++
  lcl|FitnessBrowser__WCS417:GFF3772 229 LAHALMSINAVKGVEIGAGFACVSQRGTEHRDELTP----EGFLSNNAGGILGGISSGQPIVAHLALKATSSITT 299
                                         ********************************7754....479******************************** PP

                           TIGR00033 301 plktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                         p +++d+++++   +tkgRhDpcv +ra+p++Eam+a+vl+d+ll++r++
  lcl|FitnessBrowser__WCS417:GFF3772 300 PGRSIDVHGNPVDVITKGRHDPCVGIRATPIAEAMMAIVLMDHLLRNRGQ 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: 9.52
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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