Alignments for a candidate for aroC in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Burkholderia phytofirmans PsJN

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate BPHYT_RS13705 BPHYT_RS13705 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__BFirm:BPHYT_RS13705
          Length = 366

 Score =  482 bits (1240), Expect = e-141
 Identities = 234/360 (65%), Positives = 284/360 (78%)

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

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

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

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P+   +  L+  M AL+K+GDSIGA++ VVASGVP GLGEP+FDRLDADIAHA+M INAV
Sbjct: 181 PNAQIVPQLETYMDALRKDGDSIGARINVVASGVPVGLGEPLFDRLDADIAHAMMGINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  +A RGS + DE+T +GF  NHAGG+LGGIS+GQ +   +A+KPTSSI  
Sbjct: 241 KGVEIGAGFASIAQRGSVHGDELTPEGFVGNHAGGVLGGISTGQDVTVSIAIKPTSSIRT 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360
           P R+I++ G+ V + T GRHDPCVGIRA PIAE+MLA+VL+DH LR RAQ  DV    P+
Sbjct: 301 PRRSIDKAGQPVVVETFGRHDPCVGIRATPIAESMLALVLIDHALRHRAQCGDVAVSTPK 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: 442
Number of extensions: 11
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 BPHYT_RS13705 BPHYT_RS13705 (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.19458.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.9e-144  466.3   0.0   3.3e-144  466.1   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13705  BPHYT_RS13705 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13705  BPHYT_RS13705 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.1   0.0  3.3e-144  3.3e-144       1     350 [.      10     350 ..      10     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 466.1 bits;  conditional E-value: 3.3e-144
                                TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGa 70 
                                              +++ttfGeSHg+a+g++idG+P+g+ l+e+diq el+rR+pg+sr+ ++r+EeD+veilsGvfeG+TtGa
  lcl|FitnessBrowser__BFirm:BPHYT_RS13705  10 FTVTTFGESHGPAIGCVIDGCPPGMALNEADIQFELDRRKPGTSRHVTQRQEEDKVEILSGVFEGQTTGA 79 
                                              789******************************************************************* PP

                                TIGR00033  71 PiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketa 140
                                              Pialli+N+d+rskdy +i++++RPgHadyty++KYgi+d++gggrsSaR Ta  vaaGavakk+L+e+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13705  80 PIALLIRNTDQRSKDYGNIADTFRPGHADYTYWQKYGIRDYRGGGRSSARLTAPTVAAGAVAKKWLREKF 149
                                              ********************************************************************** PP

                                TIGR00033 141 gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnv 210
                                              g+ei +y+  lge+++++         ++ ++p+++p+a+   ++e ++d ++kdgds+G++++vv+s+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS13705 150 GTEIHGYMAALGEIDVPFVDW-----AHVRENPFFAPNAQIVPQLETYMDALRKDGDSIGARINVVASGV 214
                                              *****************8544.....57999*************************************** PP

                                TIGR00033 211 pvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGi 280
                                              pvglGeplfd+lda +a+a+++inAvKgveiG+GF++  +rGs + Del+       ++ n+ GG++GGi
  lcl|FitnessBrowser__BFirm:BPHYT_RS13705 215 PVGLGEPLFDRLDADIAHAMMGINAVKGVEIGAGFASIAQRGSVHGDELTP----EGFVGNHAGGVLGGI 280
                                              ***********************************************7754....4799*********** PP

                                TIGR00033 281 tnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                              ++G+d++v+ia+Kp+++i++p++++d+++++ +  t gRhDpcv +ra+p++E+m+alvl+d++l++ra+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13705 281 STGQDVTVSIAIKPTSSIRTPRRSIDKAGQPVVVETFGRHDPCVGIRATPIAESMLALVLIDHALRHRAQ 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.18
//
[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