Alignments for a candidate for aroC in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Phaeobacter inhibens BS107

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate GFF3353 PGA1_c34060 chorismate synthase AroC

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Phaeo:GFF3353
          Length = 368

 Score =  409 bits (1052), Expect = e-119
 Identities = 208/358 (58%), Positives = 265/358 (74%), Gaps = 8/358 (2%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ N+ G LFRVTT+GESHG ALG  VDG PP +P+    LQ  LD+RRPG ++  TQR 
Sbjct: 1   MSINSFGHLFRVTTWGESHGPALGATVDGCPPNVPVDAEMLQQWLDKRRPGQNKNMTQRN 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD VKILSGVFEG +TGT I L+IENTDQRS+DY  I   FRPGHAD TY QKYG RDY
Sbjct: 61  EPDAVKILSGVFEGKSTGTPIQLMIENTDQRSKDYGDIAQTFRPGHADITYFQKYGNRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYL-AEKFGIEIRGCLTQMGDIPLDIK--DWSQVEQNP 177
           RGGGRSSARETA RVAAG +A++ + A   G+EI+G +T+MG++ +D    DW  ++QN 
Sbjct: 121 RGGGRSSARETAARVAAGGVAREAIKALVPGLEIKGYMTRMGEMEIDRSRFDWDAIDQND 180

Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237
           F+ PD   +   +  ++ L+KE DS+GA + VVA GVPAG+G P++ +LD D+A A+MSI
Sbjct: 181 FWIPDAAAVQDWENYLQGLRKEHDSVGAVIEVVARGVPAGIGAPIYGKLDTDLASAMMSI 240

Query: 238 NAVKGVEIGDGFDVVALRGSQNRDEI--TKDG---FQSNHAGGILGGISSGQQIIAHMAL 292
           NAVK VEIG+G +   L+GS+N DEI   +DG   + SNH+GGILGGIS+GQ ++   A+
Sbjct: 241 NAVKAVEIGEGMNAALLKGSENADEIFLGEDGQPVYSSNHSGGILGGISTGQDVVVRFAV 300

Query: 293 KPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQ 350
           KPTSSI  P ++I + G   E+ITKGRHDPCVGIRAVP+AEAM+A V++DHLL  R Q
Sbjct: 301 KPTSSILTPRQSIRKDGSAAEVITKGRHDPCVGIRAVPVAEAMMACVILDHLLLHRGQ 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: 433
Number of extensions: 16
Number of successful extensions: 4
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: 368
Length adjustment: 29
Effective length of query: 332
Effective length of database: 339
Effective search space:   112548
Effective search space used:   112548
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 GFF3353 PGA1_c34060 (chorismate synthase AroC)
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.9123.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.9e-136  438.5   0.1   9.1e-136  438.3   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3353  PGA1_c34060 chorismate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3353  PGA1_c34060 chorismate synthase AroC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.3   0.1  9.1e-136  9.1e-136       1     349 [.      10     357 ..      10     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 438.3 bits;  conditional E-value: 9.1e-136
                          TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPialli 76 
                                        +r+tt+GeSHg+alga++dG+P+++++++e++q+ l++Rrpgq +  ++r+E D+v+ilsGvfeGk tG+Pi l+i
  lcl|FitnessBrowser__Phaeo:GFF3353  10 FRVTTWGESHGPALGATVDGCPPNVPVDAEMLQQWLDKRRPGQNKNMTQRNEPDAVKILSGVFEGKSTGTPIQLMI 85 
                                        89************************************************************************** PP

                          TIGR00033  77 kNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketa.gieivayvvkl 151
                                        +N+d+rskdy di++++RPgHad ty++KYg++d++gggrsSaReTaarvaaG va++ +k    g+ei++y++++
  lcl|FitnessBrowser__Phaeo:GFF3353  86 ENTDQRSKDYGDIAQTFRPGHADITYFQKYGNRDYRGGGRSSARETAARVAAGGVAREAIKALVpGLEIKGYMTRM 161
                                        **********************************************************99986449********** PP

                          TIGR00033 152 geveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaela 227
                                        ge+e++++ ++    +++d++ + +pda a +  e++++ ++k++dsvG+v+evv+++vp+g+G p++ kld+ la
  lcl|FitnessBrowser__Phaeo:GFF3353 162 GEMEIDRSRFDW---DAIDQNDFWIPDAAAVQDWENYLQGLRKEHDSVGAVIEVVARGVPAGIGAPIYGKLDTDLA 234
                                        ******998884...79*********************************************************** PP

                          TIGR00033 228 sallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGedirvriavKpiptikkpl 302
                                        sa++sinAvK+veiG+G +aa  +Gse  De+ l  d++    +n+sGGi+GGi++G+d++vr avKp+++i +p+
  lcl|FitnessBrowser__Phaeo:GFF3353 235 SAMMSINAVKAVEIGEGMNAALLKGSENADEIFLGeDGQPVYSSNHSGGILGGISTGQDVVVRFAVKPTSSILTPR 310
                                        *******************************998758888999********************************* PP

                          TIGR00033 303 ktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekra 349
                                        +++ ++++ +  +tkgRhDpcv +ravpv+Eam+a v++d+ll +r+
  lcl|FitnessBrowser__Phaeo:GFF3353 311 QSIRKDGSAAEVITKGRHDPCVGIRAVPVAEAMMACVILDHLLLHRG 357
                                        ******************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (368 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: 7.94
//
[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