Alignments for a candidate for aroC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Herbaspirillum seropedicae SmR1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate HSERO_RS16525 HSERO_RS16525 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__HerbieS:HSERO_RS16525
          Length = 362

 Score =  459 bits (1181), Expect = e-134
 Identities = 224/359 (62%), Positives = 278/359 (77%)

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

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD V+ILSG +EG TTGT I LLI N DQRS+DY  I D FRPGHADYTY  KYG+RD 
Sbjct: 61  EPDTVEILSGTYEGKTTGTPIALLIRNQDQRSKDYGNILDTFRPGHADYTYWHKYGIRDP 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSAR TA  V A A+AKK+L E++G   +GC++Q+G+I +  + W  V  NPFF 
Sbjct: 121 RGGGRSSARLTAPVVGAAAVAKKWLFEQYGTTFKGCMSQLGEIAIPFESWEHVPNNPFFA 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
            +   I+ L+  M AL+K+GDSIGA++ VVA  VP GLGEP++D+LDA+IA ALM INAV
Sbjct: 181 ANASIIERLEAYMDALRKDGDSIGARIDVVAQNVPVGLGEPLYDKLDAEIAFALMGINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  VA +GS++ D +T +GF  N+AGG+LGGIS+GQ I A +A+KPTSSI  
Sbjct: 241 KGVEIGAGFRSVAQKGSEHGDALTPEGFVGNNAGGVLGGISTGQDITASIAIKPTSSIRT 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
           P  +I++ G+ + + T GRHDPCVGIRA PIAEAMLA+VLMDH LR RAQ  DVK D P
Sbjct: 301 PRPSIDKSGQPIAVETFGRHDPCVGIRATPIAEAMLALVLMDHALRHRAQCGDVKVDTP 359


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: 447
Number of extensions: 15
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: 362
Length adjustment: 29
Effective length of query: 332
Effective length of database: 333
Effective search space:   110556
Effective search space used:   110556
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 HSERO_RS16525 HSERO_RS16525 (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.2039843.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-139  450.3   0.0   2.4e-139  450.1   0.0    1.0  1  FitnessBrowser__HerbieS:HSERO_RS16525  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS16525  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.1   0.0  2.4e-139  2.4e-139       1     350 [.      10     350 ..      10     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 450.1 bits;  conditional E-value: 2.4e-139
                              TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPi 72 
                                            +++ttfGeSHg+a+g++idG+P+g++l+e+diq+el+rRrpg+sr+ ++r+E D+veilsG++eGkTtG+Pi
  FitnessBrowser__HerbieS:HSERO_RS16525  10 FTVTTFGESHGPAIGCVIDGCPPGMTLSEADIQPELDRRRPGTSRHVTQRQEPDTVEILSGTYEGKTTGTPI 81 
                                            789********************************************************************* PP

                              TIGR00033  73 allikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagiei 144
                                            alli+N+d+rskdy +i +++RPgHadyty++KYgi+d +gggrsSaR Ta  v a avakk+L e++g+  
  FitnessBrowser__HerbieS:HSERO_RS16525  82 ALLIRNQDQRSKDYGNILDTFRPGHADYTYWHKYGIRDPRGGGRSSARLTAPVVGAAAVAKKWLFEQYGTTF 153
                                            ************************************************************************ PP

                              TIGR00033 145 vayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGe 216
                                            ++ +++lge+++++e     s e++ ++p+++++a+  +++e+++d ++kdgds+G++++vv++nvpvglGe
  FitnessBrowser__HerbieS:HSERO_RS16525 154 KGCMSQLGEIAIPFE-----SWEHVPNNPFFAANASIIERLEAYMDALRKDGDSIGARIDVVAQNVPVGLGE 220
                                            *************84.....4568999********************************************* PP

                              TIGR00033 217 plfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirv 288
                                            pl+dkldae+a al++inAvKgveiG+GF+++ ++Gse+ D l+       ++ nn GG++GGi++G+di+ 
  FitnessBrowser__HerbieS:HSERO_RS16525 221 PLYDKLDAEIAFALMGINAVKGVEIGAGFRSVAQKGSEHGDALT----PEGFVGNNAGGVLGGISTGQDITA 288
                                            *****************************************554....45799******************* PP

                              TIGR00033 289 riavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                            +ia+Kp+++i++p+ ++d+++++ a  t gRhDpcv +ra+p++Eam+alvl+d++l++ra+
  FitnessBrowser__HerbieS:HSERO_RS16525 289 SIAIKPTSSIRTPRPSIDKSGQPIAVETFGRHDPCVGIRATPIAEAMLALVLMDHALRHRAQ 350
                                            **********************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (362 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.19
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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