Alignments for a candidate for aroC in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Alicycliphilus denitrificans K601

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013518766.1 ALIDE2_RS10590 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000204645.1:WP_013518766.1
          Length = 364

 Score =  461 bits (1186), Expect = e-134
 Identities = 225/359 (62%), Positives = 275/359 (76%), Gaps = 1/359 (0%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNT+G LF VT FGESHG A+GC++DG PPG+ L EAD+Q DLDRRRPGTSR+ TQR 
Sbjct: 1   MSGNTLGTLFCVTNFGESHGPAIGCVIDGCPPGMALCEADIQADLDRRRPGTSRHVTQRN 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD V+ILSGV+EG TTGT I LLI N DQRS+DY  I   FRPGHADY Y  KYGLRD 
Sbjct: 61  EPDAVEILSGVYEGRTTGTPIALLIRNQDQRSKDYGDIAQSFRPGHADYAYWHKYGLRDP 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSAR TA  VAAGA+AKK+LAE +G   R C+ Q+G++P+  ++W  V  NPFF 
Sbjct: 121 RGGGRSSARLTAPTVAAGAVAKKWLAETYGTRFRACMAQLGELPIPFENWEHVPNNPFFA 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P  D + A ++ M AL+K GDS GA++ V A+GVP GLGEP++D+LDADIAHA+M +NAV
Sbjct: 181 PVAD-VQAYEDYMDALRKSGDSCGARLRVQATGVPVGLGEPLYDKLDADIAHAMMGLNAV 239

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  VA RG+ + D +T  GF  N+AGG+LGGIS+GQ I   +A+KPTSSI  
Sbjct: 240 KGVEIGAGFASVAQRGTTHGDSLTPQGFAGNNAGGVLGGISTGQDIEVQLAIKPTSSIIS 299

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
           P  +I+  G   E++T+GRHDPCVGIRA PIAEA+LA+VLMDH LRQRAQ  DV+  +P
Sbjct: 300 PRESIDVHGRSTEVVTRGRHDPCVGIRAAPIAEALLALVLMDHALRQRAQCGDVRQAVP 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: 471
Number of extensions: 15
Number of successful extensions: 2
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: 364
Length adjustment: 29
Effective length of query: 332
Effective length of database: 335
Effective search space:   111220
Effective search space used:   111220
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_013518766.1 ALIDE2_RS10590 (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.16231.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-133  430.9   0.0     2e-133  430.6   0.0    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013518766.1  ALIDE2_RS10590 chorismate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013518766.1  ALIDE2_RS10590 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.6   0.0    2e-133    2e-133       2     350 ..      11     349 ..      10     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 430.6 bits;  conditional E-value: 2e-133
                                 TIGR00033   2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGa 70 
                                                +t fGeSHg+a+g++idG+P+g+ l e+diq +l+rRrpg+sr+ ++r+E D+veilsGv+eG+TtG+
  lcl|NCBI__GCF_000204645.1:WP_013518766.1  11 CVTNFGESHGPAIGCVIDGCPPGMALCEADIQADLDRRRPGTSRHVTQRNEPDAVEILSGVYEGRTTGT 79 
                                               6899***************************************************************** PP

                                 TIGR00033  71 PiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLket 139
                                               Pialli+N+d+rskdy di++++RPgHady+y++KYg++d +gggrsSaR Ta  vaaGavakk+L+et
  lcl|NCBI__GCF_000204645.1:WP_013518766.1  80 PIALLIRNQDQRSKDYGDIAQSFRPGHADYAYWHKYGLRDPRGGGRSSARLTAPTVAAGAVAKKWLAET 148
                                               ********************************************************************* PP

                                 TIGR00033 140 agieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvs 208
                                               +g++  a + +lge+ +++e+      e++ ++p+++p a+  ++ e+++d ++k+gds G+++ v+++
  lcl|NCBI__GCF_000204645.1:WP_013518766.1 149 YGTRFRACMAQLGELPIPFEN-----WEHVPNNPFFAPVAD-VQAYEDYMDALRKSGDSCGARLRVQAT 211
                                               ******************855.....557999999999865.5679*********************** PP

                                 TIGR00033 209 nvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGie 277
                                               +vpvglGepl+dklda +a+a++++nAvKgveiG+GF+++ +rG  + D      + + +  nn GG++
  lcl|NCBI__GCF_000204645.1:WP_013518766.1 212 GVPVGLGEPLYDKLDADIAHAMMGLNAVKGVEIGAGFASVAQRGTTHGDS----LTPQGFAGNNAGGVL 276
                                               *************************************************5....4678899******** PP

                                 TIGR00033 278 GGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladalle 346
                                               GGi++G+di+v+ a+Kp+++i  p++++d++++ +  +t+gRhDpcv +ra+p++Ea++alvl+d++l+
  lcl|NCBI__GCF_000204645.1:WP_013518766.1 277 GGISTGQDIEVQLAIKPTSSIISPRESIDVHGRSTEVVTRGRHDPCVGIRAAPIAEALLALVLMDHALR 345
                                               ********************************************************************* PP

                                 TIGR00033 347 kras 350
                                               +ra+
  lcl|NCBI__GCF_000204645.1:WP_013518766.1 346 QRAQ 349
                                               9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (364 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: 7.95
//
[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