Alignments for a candidate for cmutase in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Geobacter metallireducens GS-15

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_004513008.1 GMET_RS04315 prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>NCBI__GCF_000012925.1:WP_004513008.1
          Length = 355

 Score =  305 bits (782), Expect = 9e-88
 Identities = 156/357 (43%), Positives = 233/357 (65%), Gaps = 6/357 (1%)

Query: 7   LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66
           L+ LR  ID++D++ILDL++ R+R A EV +VK       E   F+ P RE  + + +  
Sbjct: 4   LQELRRDIDAIDDQILDLLNSRSRLAIEVGKVKAG-----ENRDFHVPSREREIYERLAA 58

Query: 67  LNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAA 126
            N GP  NE +  +FREI+S+ LALE P++VA+LGP+ TF+  A+L+HFG S    P  +
Sbjct: 59  GNSGPFPNEAVRSVFREIISASLALESPMKVAFLGPKATFTHLASLQHFGLSAELVPQKS 118

Query: 127 IDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETT 186
           I  VF EV  G   +GVVPVENSTEG V+HTLD F+E D+ I  E+ L + H LL   T 
Sbjct: 119 IPAVFEEVSKGRSLYGVVPVENSTEGMVSHTLDMFMESDLKINAEILLEVSHDLL-SRTG 177

Query: 187 KTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQ 246
           + + + ++YSH Q++AQCR WLD +   V  V V+S A AA+ V  ++ +AAIA + AA 
Sbjct: 178 RLEDVKKVYSHPQAIAQCRNWLDENLSGVPVVDVASTALAAQIVGEDYTAAAIASEFAAA 237

Query: 247 LYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFHSN 306
           LY L  +  +IED+  N TRFL++G +     GDDKTS++ S++++PG LH +L PF   
Sbjct: 238 LYDLKVVRHRIEDQVNNFTRFLVVGRKMADRCGDDKTSLMFSVKDEPGILHRMLEPFAKR 297

Query: 307 GIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363
           G++L++IE+RP +   W Y+FF+D  GH  DP++ + ++++ +    +K+LGSYP+A
Sbjct: 298 GVNLSKIESRPLKKKAWEYIFFLDLAGHISDPVVSDAVQELKNYCQFVKILGSYPRA 354


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: 312
Number of extensions: 10
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: 355
Length adjustment: 29
Effective length of query: 336
Effective length of database: 326
Effective search space:   109536
Effective search space used:   109536
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_004513008.1 GMET_RS04315 (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.29844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.5e-25   75.6   0.6    3.9e-25   74.3   0.3    1.9  2  lcl|NCBI__GCF_000012925.1:WP_004513008.1  GMET_RS04315 prephenate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_004513008.1  GMET_RS04315 prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.3   3.9e-25   3.9e-25       1      76 []       4      77 ..       4      77 .. 0.98
   2 ?   -3.1   0.0      0.52      0.52      63      75 ..     114     126 ..     109     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 3.9e-25
                                 TIGR01807  1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavari 71
                                              L+elR  iDaiDd+ildLl+ R +la +vg++K    ++  ++ P RE+ +  rl   n Gp ++eav  +
  lcl|NCBI__GCF_000012925.1:WP_004513008.1  4 LQELRRDIDAIDDQILDLLNSRSRLAIEVGKVKAG--ENRDFHVPSREREIYERLAAGNSGPFPNEAVRSV 72
                                              799******************************99..899999**************************** PP

                                 TIGR01807 72 frEim 76
                                              frEi+
  lcl|NCBI__GCF_000012925.1:WP_004513008.1 73 FREII 77
                                              ***97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.52
                                 TIGR01807  63 LdqeavarifrEi 75 
                                               ++q+++ ++f E+
  lcl|NCBI__GCF_000012925.1:WP_004513008.1 114 VPQKSIPAVFEEV 126
                                               6899999***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (76 nodes)
Target sequences:                          1  (355 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: 9.45
//
[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