Alignments for a candidate for aroC in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Desulfobulbus mediterraneus DSM 13871

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_028585259.1 G494_RS0115545 chorismate synthase

Query= SwissProt::P28777
         (376 letters)



>NCBI__GCF_000429965.1:WP_028585259.1
          Length = 361

 Score =  443 bits (1139), Expect = e-129
 Identities = 231/367 (62%), Positives = 277/367 (75%), Gaps = 11/367 (2%)

Query: 2   STFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRRPGQSKLSTPRDEKD 61
           ST G L++V+T+GESHCK VG IVDG PPGM L+EADIQPQL+RRRPGQS L+TPR E D
Sbjct: 3   STLGTLYKVSTFGESHCKGVGAIVDGCPPGMELSEADIQPQLSRRRPGQSDLTTPRQEAD 62

Query: 62  RVEIQSGTEFGKTLGTPIAMMIKNEDQRPHDYSDMDKFPRPSHADFTYSEKYGIKASSGG 121
           +V I SGTEFG+TLGTPI ++I N+DQRP DY +M   PRPSHADFTY  KYGI+ASSGG
Sbjct: 63  QVTIYSGTEFGRTLGTPIMLLIHNKDQRPGDYGEMSTIPRPSHADFTYQLKYGIRASSGG 122

Query: 122 GRASARETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITR 181
           GR+SARETIGRVA+GAIAEK+L QN   EIVA+V+ +G+I+    + DP        I+R
Sbjct: 123 GRSSARETIGRVAAGAIAEKWLQQNYGTEIVAWVSSVGDIE--APAIDP------GRISR 174

Query: 182 EKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAM 241
           ++VDS   IRCP    A LM + + +    KDS GG++TCV RNLP GLGEP FDKL+A 
Sbjct: 175 QEVDST-LIRCPHGPTAELMEQRVAEILEAKDSTGGILTCVCRNLPVGLGEPIFDKLDAC 233

Query: 242 LAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYFEKETNRLRTKTNNSGGVQGGISNG 301
           LA AMLS+PA+KGF+IGSGF G  + GS+HNDPF   ++   L T +NNSGGVQGGISNG
Sbjct: 234 LAQAMLSLPATKGFDIGSGFAGTRMRGSEHNDPFV--RKGAGLGTSSNNSGGVQGGISNG 291

Query: 302 ENIYFSVPFKSVATISQEQKTATYDGEEGILAAKGRHDPAVTPRAIPIVEAMTALVLADA 361
           E I F V FK VATI + Q+T  +DG +  LAAKGRHDP V PRAIPIVE+M ALVL D 
Sbjct: 292 EPIIFRVAFKPVATIGRVQQTVDFDGNQVELAAKGRHDPCVVPRAIPIVESMAALVLMDL 351

Query: 362 LLIQKAR 368
            L Q+AR
Sbjct: 352 ALQQRAR 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: 476
Number of extensions: 19
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: 361
Length adjustment: 30
Effective length of query: 346
Effective length of database: 331
Effective search space:   114526
Effective search space used:   114526
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_028585259.1 G494_RS0115545 (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.23202.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-145  468.7   0.0   5.9e-145  468.5   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028585259.1  G494_RS0115545 chorismate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028585259.1  G494_RS0115545 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.5   0.0  5.9e-145  5.9e-145       2     350 ..      10     358 ..       9     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.5 bits;  conditional E-value: 5.9e-145
                                 TIGR00033   2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGa 70 
                                               ++ tfGeSH+k +gai+dG+P+g+el+e+diq++l+rRrpgqs lt++r+E+D+v+i sG++ G+T G+
  lcl|NCBI__GCF_000429965.1:WP_028585259.1  10 KVSTFGESHCKGVGAIVDGCPPGMELSEADIQPQLSRRRPGQSDLTTPRQEADQVTIYSGTEFGRTLGT 78 
                                               789****************************************************************** PP

                                 TIGR00033  71 PiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLket 139
                                               Pi lli+Nkd+r+ dy +++++pRP+Had+ty+ KYgi++++gggrsSaReT++rvaaGa+a+k+L+++
  lcl|NCBI__GCF_000429965.1:WP_028585259.1  79 PIMLLIHNKDQRPGDYGEMSTIPRPSHADFTYQLKYGIRASSGGGRSSARETIGRVAAGAIAEKWLQQN 147
                                               ********************************************************************* PP

                                 TIGR00033 140 agieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvs 208
                                               +g+eiva+v+++g++e++     +is++++d++ +rcp   +++ me+ + ++ +++ds Gg++++v +
  lcl|NCBI__GCF_000429965.1:WP_028585259.1 148 YGTEIVAWVSSVGDIEAPAIDPGRISRQEVDSTLIRCPHGPTAELMEQRVAEILEAKDSTGGILTCVCR 216
                                               *******************9999********************************************** PP

                                 TIGR00033 209 nvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGie 277
                                               n+pvglGep+fdklda la+a+ls++A Kg++iG+GF+ +++rGse+nD++v +  ++ + +nnsGG++
  lcl|NCBI__GCF_000429965.1:WP_028585259.1 217 NLPVGLGEPIFDKLDACLAQAMLSLPATKGFDIGSGFAGTRMRGSEHNDPFVRKGAGLGTSSNNSGGVQ 285
                                               ********************************************************************* PP

                                 TIGR00033 278 GGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladalle 346
                                               GGi+nGe+i +r+a+Kp++ti++ ++tvd ++++   a+kgRhDpcvvpra+p+vE+m alvl+d++l+
  lcl|NCBI__GCF_000429965.1:WP_028585259.1 286 GGISNGEPIIFRVAFKPVATIGRVQQTVDFDGNQVELAAKGRHDPCVVPRAIPIVESMAALVLMDLALQ 354
                                               ********************************************************************* PP

                                 TIGR00033 347 kras 350
                                               +ra+
  lcl|NCBI__GCF_000429965.1:WP_028585259.1 355 QRAR 358
                                               9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (361 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: 7.58
//
[ok]

This GapMind analysis is from Apr 10 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