Alignments for a candidate for aroC in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Malonomonas rubra DSM 5091

Align Chorismate synthase ARO2; 5-enolpyruvylshikimate-3-phosphate phospholyase; Aromatic amino acid requiring protein 2; EC 1.5.1.38; EC 4.2.3.5 (characterized)
to candidate WP_072907971.1 BUB13_RS08745 chorismate synthase

Query= SwissProt::P28777
         (376 letters)



>NCBI__GCF_900142125.1:WP_072907971.1
          Length = 359

 Score =  451 bits (1161), Expect = e-131
 Identities = 234/367 (63%), Positives = 276/367 (75%), Gaps = 11/367 (2%)

Query: 2   STFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRRPGQSKLSTPRDEKD 61
           S+FG+ F+++T+GESHC  VG +VDGVPP M L+EADIQ QL RRRPG +KL T R+E D
Sbjct: 3   SSFGRFFKISTFGESHCAGVGVVVDGVPPRMQLSEADIQVQLDRRRPGGNKLGTERNEAD 62

Query: 62  RVEIQSGTEFGKTLGTPIAMMIKNEDQRPHDYSDMDKFPRPSHADFTYSEKYGIKASSGG 121
           +V+I SG E G TLG+PI M++KN+DQRP DY  M + PRPSHAD+TY  KYGI ASSGG
Sbjct: 63  QVQILSGVENGLTLGSPIGMLVKNKDQRPGDYGSMSQIPRPSHADYTYRAKYGIHASSGG 122

Query: 122 GRASARETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITR 181
           GR+SARETIGRVA+GAIAEKFL +   +EIVA+V+ +G      D  D      + T+TR
Sbjct: 123 GRSSARETIGRVAAGAIAEKFLLEQYGIEIVAWVSGVG--LQQTDEID------MATVTR 174

Query: 182 EKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAM 241
           E+VD+   +RCPDA  A  M +EI   R +KDSIGGVVTCV RNLP GLGEP FD+LEA 
Sbjct: 175 EQVDA-SDVRCPDAVAAEKMTEEIVAARADKDSIGGVVTCVCRNLPAGLGEPAFDRLEAK 233

Query: 242 LAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYFEKETNRLRTKTNNSGGVQGGISNG 301
           LAHAMLS+PA+KGFEIGSGF G    GS HNDP+  + E  RL T +N SGGVQGGISNG
Sbjct: 234 LAHAMLSLPATKGFEIGSGFAGTCQRGSVHNDPYVMKGE--RLGTLSNRSGGVQGGISNG 291

Query: 302 ENIYFSVPFKSVATISQEQKTATYDGEEGILAAKGRHDPAVTPRAIPIVEAMTALVLADA 361
           E+ YF V FK  ATI QEQKT  Y+G E ILAAKGRHDP V PRA+PIVE+M ALVLAD 
Sbjct: 292 EDAYFRVAFKPPATIGQEQKTVDYEGNETILAAKGRHDPCVVPRAVPIVESMAALVLADL 351

Query: 362 LLIQKAR 368
            LIQK R
Sbjct: 352 ALIQKMR 358


Lambda     K      H
   0.316    0.133    0.383 

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: 471
Number of extensions: 15
Number of successful extensions: 3
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: 376
Length of database: 359
Length adjustment: 30
Effective length of query: 346
Effective length of database: 329
Effective search space:   113834
Effective search space used:   113834
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_072907971.1 BUB13_RS08745 (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.2695461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-144  466.7   0.4   2.4e-144  466.5   0.4    1.0  1  NCBI__GCF_900142125.1:WP_072907971.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072907971.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.5   0.4  2.4e-144  2.4e-144       1     349 [.       9     357 ..       9     359 .] 0.99

  Alignments for each domain:
  == domain 1  score: 466.5 bits;  conditional E-value: 2.4e-144
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPia 73 
                                           +++ tfGeSH++ +g+++dG+P+ ++l+e+diq +l+rRrpg  +l ++r+E+D+v+ilsGv++G T G+Pi 
  NCBI__GCF_900142125.1:WP_072907971.1   9 FKISTFGESHCAGVGVVVDGVPPRMQLSEADIQVQLDRRRPGGNKLGTERNEADQVQILSGVENGLTLGSPIG 81 
                                           7899********************************************************************* PP

                             TIGR00033  74 llikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieiva 146
                                           +l+kNkd+r+ dy +++++pRP+Hadyty+ KYgi++++gggrsSaReT++rvaaGa+a+k+L e++gieiva
  NCBI__GCF_900142125.1:WP_072907971.1  82 MLVKNKDQRPGDYGSMSQIPRPSHADYTYRAKYGIHASSGGGRSSARETIGRVAAGAIAEKFLLEQYGIEIVA 154
                                           ************************************************************************* PP

                             TIGR00033 147 yvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplf 219
                                           +v+ +g  +++e  + ++++e++d+s vrcpda a+++m eei  a+ d+ds+Ggvv++v +n+p+glGep f
  NCBI__GCF_900142125.1:WP_072907971.1 155 WVSGVGLQQTDEIDMATVTREQVDASDVRCPDAVAAEKMTEEIVAARADKDSIGGVVTCVCRNLPAGLGEPAF 227
                                           ************************************************************************* PP

                             TIGR00033 220 dkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriav 292
                                           d+l+a+la+a+ls++A Kg+eiG+GF+ + +rGs +nD+ v++ +++ + +n+sGG++GGi+nGed ++r+a+
  NCBI__GCF_900142125.1:WP_072907971.1 228 DRLEAKLAHAMLSLPATKGFEIGSGFAGTCQRGSVHNDPYVMKGERLGTLSNRSGGVQGGISNGEDAYFRVAF 300
                                           ************************************************************************* PP

                             TIGR00033 293 KpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekra 349
                                           Kp +ti++++ktvd+e++e++ a+kgRhDpcvvpravp+vE+m alvlad++l +++
  NCBI__GCF_900142125.1:WP_072907971.1 301 KPPATIGQEQKTVDYEGNETILAAKGRHDPCVVPRAVPIVESMAALVLADLALIQKM 357
                                           ***************************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (359 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: 21.00
//
[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