Alignments for a candidate for aroC in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Paraburkholderia bryophila 376MFSha3.1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate H281DRAFT_04489 H281DRAFT_04489 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Burk376:H281DRAFT_04489
          Length = 366

 Score =  485 bits (1249), Expect = e-142
 Identities = 238/360 (66%), Positives = 286/360 (79%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNT+G LF VTTFGESHG A+GC++DG PPG+ LTEAD+Q +LDRR+PGTSR+ TQR+
Sbjct: 1   MSGNTLGTLFTVTTFGESHGPAIGCVIDGCPPGMALTEADIQLELDRRKPGTSRHVTQRQ 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D+V+ILSGVFEG TTG  I LLI NTDQRS+DY  I D FRPGHADYTY QKYG+RDY
Sbjct: 61  EEDKVEILSGVFEGATTGAPIALLIRNTDQRSKDYGNIVDTFRPGHADYTYWQKYGIRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSAR TA  VAAGA+AKK+L EKFG EIRG +  +G+I +   DW+ V +NPFF 
Sbjct: 121 RGGGRSSARLTAPTVAAGAVAKKWLREKFGTEIRGYMAALGEIDVPFVDWAHVRENPFFV 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P+ D +  L+  M AL+KEGDSIGA++ VVASGVP GLGEP+FDRLDADIAHA+M INAV
Sbjct: 181 PNADIVPQLEAYMDALRKEGDSIGARINVVASGVPVGLGEPLFDRLDADIAHAMMGINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  VA RGS + DE+T +GF  N+AGG+LGGIS+GQ I   +A+KPTSSI  
Sbjct: 241 KGVEIGAGFASVAQRGSVHGDELTPEGFVGNNAGGVLGGISTGQDITVSIAIKPTSSIRT 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360
           P R+I++ G+   + T GRHDPCVGIRA PIAE+MLA+VL+DH LR RAQ  DV    P+
Sbjct: 301 PRRSIDKAGQPAMVETFGRHDPCVGIRATPIAESMLALVLIDHALRHRAQCGDVSVSTPK 360


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: 455
Number of extensions: 12
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: 366
Length adjustment: 29
Effective length of query: 332
Effective length of database: 337
Effective search space:   111884
Effective search space used:   111884
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 H281DRAFT_04489 H281DRAFT_04489 (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.31718.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.5e-145  468.0   0.0   9.8e-145  467.8   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04489  H281DRAFT_04489 chorismate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04489  H281DRAFT_04489 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.8   0.0  9.8e-145  9.8e-145       1     350 [.      10     350 ..      10     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.8 bits;  conditional E-value: 9.8e-145
                                    TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGk 66 
                                                  +++ttfGeSHg+a+g++idG+P+g+ lte+diq el+rR+pg+sr+ ++r+EeD+veilsGvfeG 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04489  10 FTVTTFGESHGPAIGCVIDGCPPGMALTEADIQLELDRRKPGTSRHVTQRQEEDKVEILSGVFEGA 75 
                                                  789*************************************************************** PP

                                    TIGR00033  67 TtGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGava 132
                                                  TtGaPialli+N+d+rskdy +i +++RPgHadyty++KYgi+d++gggrsSaR Ta  vaaGava
  lcl|FitnessBrowser__Burk376:H281DRAFT_04489  76 TTGAPIALLIRNTDQRSKDYGNIVDTFRPGHADYTYWQKYGIRDYRGGGRSSARLTAPTVAAGAVA 141
                                                  ****************************************************************** PP

                                    TIGR00033 133 kklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgds 198
                                                  kk+L+e+ g+ei +y+  lge+++++         ++ ++p+++p+a+   ++e+++d ++k+gds
  lcl|FitnessBrowser__Burk376:H281DRAFT_04489 142 KKWLREKFGTEIRGYMAALGEIDVPFVDW-----AHVRENPFFVPNADIVPQLEAYMDALRKEGDS 202
                                                  *************************8544.....57999*************************** PP

                                    TIGR00033 199 vGgvvevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvledd 264
                                                  +G++++vv+s+vpvglGeplfd+lda +a+a+++inAvKgveiG+GF+++ +rGs + Del+    
  lcl|FitnessBrowser__Burk376:H281DRAFT_04489 203 IGARINVVASGVPVGLGEPLFDRLDADIAHAMMGINAVKGVEIGAGFASVAQRGSVHGDELTP--- 265
                                                  ***********************************************************7754... PP

                                    TIGR00033 265 kirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravp 330
                                                     ++ nn GG++GGi++G+di+v+ia+Kp+++i++p++++d+++++++  t gRhDpcv +ra+p
  lcl|FitnessBrowser__Burk376:H281DRAFT_04489 266 -EGFVGNNAGGVLGGISTGQDITVSIAIKPTSSIRTPRRSIDKAGQPAMVETFGRHDPCVGIRATP 330
                                                  .4799************************************************************* PP

                                    TIGR00033 331 vvEamvalvladallekras 350
                                                  ++E+m+alvl+d++l++ra+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04489 331 IAESMLALVLIDHALRHRAQ 350
                                                  ****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (366 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.04
//
[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