Alignments for a candidate for cmutase in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Thiomicrospira cyclica ALM1

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_013835368.1 THICY_RS04225 prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>NCBI__GCF_000214825.1:WP_013835368.1
          Length = 364

 Score =  323 bits (828), Expect = 4e-93
 Identities = 175/364 (48%), Positives = 238/364 (65%), Gaps = 3/364 (0%)

Query: 2   SEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVL 61
           +EA+QL+ +R +ID++DE I  LI++RA CA +VA +KT       EAVFYRPEREA VL
Sbjct: 3   TEAEQLQQIRQQIDAIDEHIQALITQRALCANQVADIKTQGG--RVEAVFYRPEREAQVL 60

Query: 62  KHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVIS 121
           + +   N   L +++MARLFREIMS CLALEQPLRVAYLGPEG+++ AA LK FG     
Sbjct: 61  RAVKARNTSVLSDDDMARLFREIMSVCLALEQPLRVAYLGPEGSYTHAAVLKQFGSFAQP 120

Query: 122 KPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLL 181
            P++ I++VF+ V    V++GVVP+ENSTEGAV  T D  +     + GEVEL IHH LL
Sbjct: 121 VPVSTIEDVFKVVDTQQVDYGVVPLENSTEGAVTTTQDCLICTQATVTGEVELPIHHCLL 180

Query: 182 VGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAG 241
            G++     IT++ +H Q+L QCR WL  + P V+  AV SNA AA+  + + + AAIA 
Sbjct: 181 -GQSKNLQGITKVLAHPQALGQCRTWLRNNLPGVKLEAVDSNALAAQMAQEQADVAAIAS 239

Query: 242 DMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLM 301
           + AA LY L  L   IED   N+T+F +IG     P+G+DKT++I+S+ N+ GAL  +L 
Sbjct: 240 EQAASLYQLHILKSHIEDAQNNTTKFWVIGRHAPTPSGEDKTAMILSLANEAGALLRILE 299

Query: 302 PFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361
            F    I +TRI +RP+   KW Y+F+ID  GH QDP +   L ++   A   K+LGSYP
Sbjct: 300 SFAKRNISMTRIVSRPASDQKWDYMFYIDITGHQQDPAVAEALAEVQANARFFKLLGSYP 359

Query: 362 KAVL 365
            + L
Sbjct: 360 VSPL 363


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: 331
Number of extensions: 8
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: 365
Length of database: 364
Length adjustment: 29
Effective length of query: 336
Effective length of database: 335
Effective search space:   112560
Effective search space used:   112560
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_013835368.1 THICY_RS04225 (prephenate dehydratase)
to HMM TIGR01807 (pheA: chorismate mutase (EC 5.4.99.5))

# 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/TIGR01807.hmm
# target sequence database:        /tmp/gapView.28809.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01807  [M=76]
Accession:   TIGR01807
Description: CM_P2: chorismate mutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.3e-28   85.4   0.7    2.8e-28   84.3   0.7    1.6  1  lcl|NCBI__GCF_000214825.1:WP_013835368.1  THICY_RS04225 prephenate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013835368.1  THICY_RS04225 prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.7   2.8e-28   2.8e-28       1      76 []       8      84 ..       8      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 2.8e-28
                                 TIGR01807  1 LkelRnkiDaiDdrildLlseRaklakavgelKkks.aseaviYRPeREaavlrrlkelnkGpLdqeavar 70
                                              L+++R++iDaiD++i  L+++Ra +a++v+++K+++   eav+YRPeREa+vlr +k +n+  L ++++ar
  lcl|NCBI__GCF_000214825.1:WP_013835368.1  8 LQQIRQQIDAIDEHIQALITQRALCANQVADIKTQGgRVEAVFYRPEREAQVLRAVKARNTSVLSDDDMAR 78
                                              7899******************************99678******************************** PP

                                 TIGR01807 71 ifrEim 76
                                              +frEim
  lcl|NCBI__GCF_000214825.1:WP_013835368.1 79 LFREIM 84
                                              *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (76 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.83
//
[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