Alignments for a candidate for cmutase in Calditerrivibrio nitroreducens DSM 19672

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Calditerrivibrio nitroreducens DSM 19672

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_013450220.1 CALNI_RS00440 prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>NCBI__GCF_000183405.1:WP_013450220.1
          Length = 356

 Score =  311 bits (797), Expect = 2e-89
 Identities = 160/360 (44%), Positives = 228/360 (63%), Gaps = 6/360 (1%)

Query: 5   DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64
           D+L  LR +ID +D  ILDL++ RAR   E+  +K     K++ A  Y P RE  + + +
Sbjct: 2   DRLNELRQQIDEIDNTILDLLNRRARLVIEIGHIK-----KSQNAPLYVPSREKAIYERL 56

Query: 65  MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124
             LN GP  N+ +  +FREI+S+ L+LE+  +VAYLGP+GTF+  AA+KHFG SV   P 
Sbjct: 57  KALNPGPFPNDALRNVFREIISASLSLEEVQKVAYLGPQGTFTHLAAIKHFGLSVKPIPC 116

Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184
            +I EVF +V     ++GVVP+ENS EG VNHTLD F + ++ ICGE+ L + HHL+  +
Sbjct: 117 RSIPEVFEDVEKKRCDYGVVPIENSLEGVVNHTLDMFSQSNLKICGEIFLEVSHHLM-NK 175

Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244
           T K + + R+YSH  ++AQCRKW+  + PNV  V V S A AA+   ++   AAI+ +MA
Sbjct: 176 TGKIEDVKRVYSHPHAIAQCRKWITENIPNVPIVEVESTAKAAEIASTDETIAAISSEMA 235

Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304
              Y L  + + IED   N TRFL+IG+ E  PTG+DKTSI+ S+ ++ G+L   L  F 
Sbjct: 236 ELQYNLKIIYKNIEDMSNNFTRFLVIGNFEPEPTGNDKTSILFSVTHRSGSLFHALKAFA 295

Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKAV 364
              I++T+IE+RPS+   W Y+F++D  GH +   IK  LEK       +K+LGSYPK V
Sbjct: 296 EEEINMTKIESRPSKLKAWEYIFYVDIDGHSKTEKIKKALEKFSENVSFMKILGSYPKGV 355


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: 333
Number of extensions: 11
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: 356
Length adjustment: 29
Effective length of query: 336
Effective length of database: 327
Effective search space:   109872
Effective search space used:   109872
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_013450220.1 CALNI_RS00440 (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.26861.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.8e-28   83.5   0.1    1.4e-27   82.3   0.1    1.6  1  lcl|NCBI__GCF_000183405.1:WP_013450220.1  CALNI_RS00440 prephenate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013450220.1  CALNI_RS00440 prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.1   1.4e-27   1.4e-27       1      79 []       8      85 ..       8      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.4e-27
                                      CM_2  1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlre...gaeelgldpeavekifr 68
                                              R++IdeiD+ +l+Ll++R++l+ ei+++Kk+++ p + p+Re+++ erl++   g+    ++++a++++fr
  lcl|NCBI__GCF_000183405.1:WP_013450220.1  8 RQQIDEIDNTILDLLNRRARLVIEIGHIKKSQNAPLYVPSREKAIYERLKAlnpGP----FPNDALRNVFR 74
                                              9**************************************************97777....*********** PP

                                      CM_2 69 eiisesralQk 79
                                              eiis+s++l++
  lcl|NCBI__GCF_000183405.1:WP_013450220.1 75 EIISASLSLEE 85
                                              *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (356 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: 9.49
//
[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