Alignments for a candidate for aroC in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Rhodomicrobium vannielii ATCC 17100

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013418144.1 RVAN_RS02255 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000166055.1:WP_013418144.1
          Length = 362

 Score =  438 bits (1127), Expect = e-128
 Identities = 229/362 (63%), Positives = 273/362 (75%), Gaps = 15/362 (4%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ NT G +FRVTT+GESHG A+GC++DG PPGIPLTEAD+Q  LD+RRPG SR+TTQR+
Sbjct: 1   MSYNTFGHMFRVTTWGESHGPAIGCVIDGCPPGIPLTEADIQPFLDKRRPGQSRFTTQRQ 60

Query: 61  EPDQVKILSGVFEG-----VTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKY 115
           E D+V+ILSGVF       VTTGT + L I+NTDQRS+DYS IKD FRPGHAD+TY +KY
Sbjct: 61  EEDRVRILSGVFPNEAGVQVTTGTPVALEIQNTDQRSKDYSDIKDKFRPGHADFTYVEKY 120

Query: 116 GLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQV 173
           G+RDYRGGGRSSARETAMRVAAGA+A+K +    GI IRG L Q+G   +D    DW++V
Sbjct: 121 GIRDYRGGGRSSARETAMRVAAGAVARKVVP---GIAIRGALVQVGAEQIDRARWDWAEV 177

Query: 174 EQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHA 233
           E+NPFF PD   ++     +  ++K G S GA V VVA G PAGLG P++ +LD DIA A
Sbjct: 178 ERNPFFAPDAGIVERWTAYLDGVRKAGSSCGAVVEVVAEGAPAGLGAPLYGKLDQDIAAA 237

Query: 234 LMSINAVKGVEIGDGFDVVALRGSQNRDE--ITKDG---FQSNHAGGILGGISSGQQIIA 288
            MSINAVKGVEIG+GF   AL G  N DE  I  DG   F SNHAGGILGGIS+GQ I+A
Sbjct: 238 FMSINAVKGVEIGEGFASAALSGEDNADEMRIGPDGQPVFLSNHAGGILGGISTGQPIVA 297

Query: 289 HMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQR 348
             A+KPTSSI  P RTI+  G + E++TKGRHDPCVGIRAVP+ EAM+AIVL DH LR R
Sbjct: 298 RFAVKPTSSILTPRRTIDTQGHDAEILTKGRHDPCVGIRAVPVGEAMMAIVLADHWLRHR 357

Query: 349 AQ 350
           AQ
Sbjct: 358 AQ 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: 459
Number of extensions: 19
Number of successful extensions: 5
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 WP_013418144.1 RVAN_RS02255 (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.3065759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-133  428.4   0.0   1.1e-132  428.2   0.0    1.0  1  NCBI__GCF_000166055.1:WP_013418144.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_013418144.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.2   0.0  1.1e-132  1.1e-132       1     350 [.      10     359 ..      10     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 428.2 bits;  conditional E-value: 1.1e-132
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvf...eG..kTt 68 
                                           +r+tt+GeSHg+a+g++idG+P+g++lte+diq+ l++Rrpgqsr+t++r+EeD+v+ilsGvf    G   Tt
  NCBI__GCF_000166055.1:WP_013418144.1  10 FRVTTWGESHGPAIGCVIDGCPPGIPLTEADIQPFLDKRRPGQSRFTTQRQEEDRVRILSGVFpneAGvqVTT 82 
                                           89************************************************************933334335** PP

                             TIGR00033  69 GaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketag 141
                                           G+P+al i+N+d+rskdy+dik+++RPgHad+ty++KYgi+d++gggrsSaReTa+rvaaGava+k +     
  NCBI__GCF_000166055.1:WP_013418144.1  83 GTPVALEIQNTDQRSKDYSDIKDKFRPGHADFTYVEKYGIRDYRGGGRSSARETAMRVAAGAVARKVVPG--- 152
                                           ******************************************************************9876... PP

                             TIGR00033 142 ieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvgl 214
                                           i i + +v++g  ++++   +     +++++p+++pda   ++  +++d ++k+g s G+vvevv+++ p+gl
  NCBI__GCF_000166055.1:WP_013418144.1 153 IAIRGALVQVGAEQIDRARWD---WAEVERNPFFAPDAGIVERWTAYLDGVRKAGSSCGAVVEVVAEGAPAGL 222
                                           99**************97777...478999******************************************* PP

                             TIGR00033 215 GeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGedi 286
                                           G pl+ kld  +a+a++sinAvKgveiG+GF++a   G +  De+ +  d++  + +n+ GGi+GGi++G++i
  NCBI__GCF_000166055.1:WP_013418144.1 223 GAPLYGKLDQDIAAAFMSINAVKGVEIGEGFASAALSGEDNADEMRIGpDGQPVFLSNHAGGILGGISTGQPI 295
                                           ***********************************************989999******************** PP

                             TIGR00033 287 rvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                           + r avKp+++i +p++t+d++++++   tkgRhDpcv +ravpv Eam+a+vlad+ l++ra+
  NCBI__GCF_000166055.1:WP_013418144.1 296 VARFAVKPTSSILTPRRTIDTQGHDAEILTKGRHDPCVGIRAVPVGEAMMAIVLADHWLRHRAQ 359
                                           ************************************************************9986 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.92
//
[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