Alignments for a candidate for cmutase in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Sulfurihydrogenibium subterraneum DSM 15120

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate WP_028950188.1 Q385_RS0102700 prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>NCBI__GCF_000619805.1:WP_028950188.1
          Length = 360

 Score =  309 bits (792), Expect = 7e-89
 Identities = 158/363 (43%), Positives = 235/363 (64%), Gaps = 6/363 (1%)

Query: 1   MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60
           M    +L+ +R  ID++D+ IL L+++RA  A++V  +K     K      + P RE  +
Sbjct: 1   MDYQKELQKIRKEIDNIDQTILQLLNKRALLAKQVGEIK-----KKNNLPIFVPTREKEI 55

Query: 61  LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120
            + + +LN GPL N+ +  +FREI+S+C ++E+ ++VAYLGP+ TF+  A+LK+FG SV 
Sbjct: 56  FERLEKLNTGPLSNDVIKHIFREIISACRSVEENIKVAYLGPKATFTHQASLKYFGSSVE 115

Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180
             P++ I +VF E+    VN+GVVPVEN+ EG VN+TLD FL++D+ I GEV L I  HL
Sbjct: 116 HIPVSTIKDVFEEIAKKKVNYGVVPVENTIEGVVNYTLDMFLDYDLKIIGEVILEISLHL 175

Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240
           +       + I RIYSH  ++A+CR WL  + PN + + V S A AA+  + ++ SAAIA
Sbjct: 176 M-SINPNINEIQRIYSHKFAIAECRDWLQKNMPNAQIIEVESTAKAAEMARDDYESAAIA 234

Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300
            + AA +YGL  L  KI+    N TRFLIIG++   PTG DKT+ I S++N+ GAL++ L
Sbjct: 235 SESAATVYGLHILERKIDKHLYNYTRFLIIGNEIPQPTGKDKTTFIFSVKNQVGALYKAL 294

Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360
            PF+ N I++T+IE+RPS+   W Y+FF D  GH +D  +   L+++ +     KVLGSY
Sbjct: 295 EPFYKNQINMTKIESRPSKKEAWDYIFFTDIEGHIEDEKVSKTLQELKNNVPFFKVLGSY 354

Query: 361 PKA 363
           PKA
Sbjct: 355 PKA 357


Lambda     K      H
   0.319    0.133    0.390 

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: 304
Number of extensions: 12
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: 365
Length of database: 360
Length adjustment: 29
Effective length of query: 336
Effective length of database: 331
Effective search space:   111216
Effective search space used:   111216
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_028950188.1 Q385_RS0102700 (prephenate dehydratase)
to HMM PF01817 (CM_2)

# 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/PF01817.25.hmm
# target sequence database:        /tmp/gapView.19462.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CM_2  [M=79]
Accession:   PF01817.25
Description: Chorismate mutase type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.9e-30   89.8   1.2    2.6e-29   87.8   0.7    2.2  2  lcl|NCBI__GCF_000619805.1:WP_028950188.1  Q385_RS0102700 prephenate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028950188.1  Q385_RS0102700 prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.7   2.6e-29   2.6e-29       1      78 [.      11      87 ..      11      88 .. 0.97
   2 ?   -0.6   0.0     0.097     0.097      56      74 ..     115     133 ..     105     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 2.6e-29
                                      CM_2  1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlre...gaeelgldpeavekifr 68
                                              RkeId+iD+ +l+Ll++R+ lak+++e+Kk+n+lp++ p Re+e++erl++   g+    l+++++++ifr
  lcl|NCBI__GCF_000619805.1:WP_028950188.1 11 RKEIDNIDQTILQLLNKRALLAKQVGEIKKKNNLPIFVPTREKEIFERLEKlntGP----LSNDVIKHIFR 77
                                              9**************************************************87777....*********** PP

                                      CM_2 69 eiisesralQ 78
                                              eiis++r+++
  lcl|NCBI__GCF_000619805.1:WP_028950188.1 78 EIISACRSVE 87
                                              *******998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.097
                                      CM_2  56 lgldpeavekifreiises 74 
                                               ++++ ++++++f+ei +  
  lcl|NCBI__GCF_000619805.1:WP_028950188.1 115 EHIPVSTIKDVFEEIAKKK 133
                                               46888999*****998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (360 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.23
//
[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