Alignments for a candidate for cmutase in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Shewanella oneidensis MR-1

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 200537 SO1362 chorismate mutase/prephenate dehydrogenase (NCBI ptt file)

Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER
         (373 letters)



>FitnessBrowser__MR1:200537
          Length = 379

 Score =  426 bits (1096), Expect = e-124
 Identities = 213/369 (57%), Positives = 273/369 (73%), Gaps = 1/369 (0%)

Query: 3   AELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAE 62
           +EL  LR  ID VD+ LL+LL KRL+LVA+VG VK   GLPIY P+REA+MLA RR EA+
Sbjct: 7   SELEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAQ 66

Query: 63  ALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSG 122
            +G+ P LIED+LRR+MRESY +E D GFK +   L  VVIVGG GQ+G LF++ML LSG
Sbjct: 67  TMGIAPQLIEDILRRLMRESYLNEKDVGFKQVKNDLGSVVIVGGKGQLGGLFQQMLRLSG 126

Query: 123 YQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGP 181
           YQV++L++ DW +A  + ADAG+V+V+VPI +T  +I  KL  LP+DCIL DL S+K  P
Sbjct: 127 YQVKVLDKDDWQQAECLFADAGLVLVTVPIAITCDIIREKLTQLPRDCILADLTSIKTEP 186

Query: 182 LQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRIS 241
           +QAML AH GPV+G HPMFGPD GSLAKQVVV C GR+ + YQW LEQI +WGAR+    
Sbjct: 187 MQAMLAAHKGPVVGFHPMFGPDVGSLAKQVVVVCHGREADKYQWLLEQIAIWGARIVEAE 246

Query: 242 AVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQ 301
              HD  M  +QA+RHF+TF YGL+L +E   +E LL  SSPIYRLELAMVGRLFAQ P+
Sbjct: 247 PECHDNAMQLVQAMRHFSTFVYGLNLCKEEADIETLLKFSSPIYRLELAMVGRLFAQSPE 306

Query: 302 LYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSES 361
           LYADII + + +   I  Y   + EA+ELL++GD++ FI+ F+ V  WFGD+A +FQ ES
Sbjct: 307 LYADIIFAQQESQHAIGDYLDNYREALELLKRGDREEFINQFQMVAKWFGDFAPQFQRES 366

Query: 362 RVLLRQAND 370
           R++L+  +D
Sbjct: 367 RMMLQSVSD 375


Lambda     K      H
   0.322    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: 393
Number of extensions: 14
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: 373
Length of database: 379
Length adjustment: 30
Effective length of query: 343
Effective length of database: 349
Effective search space:   119707
Effective search space used:   119707
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 200537 SO1362 (chorismate mutase/prephenate dehydrogenase (NCBI ptt file))
to HMM TIGR01799 (tyrA: 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/TIGR01799.hmm
# target sequence database:        /tmp/gapView.28278.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01799  [M=83]
Accession:   TIGR01799
Description: CM_T: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
      4e-51  157.3   1.4    1.3e-50  155.7   1.2    2.0  2  lcl|FitnessBrowser__MR1:200537  SO1362 chorismate mutase/prephen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200537  SO1362 chorismate mutase/prephenate dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   1.2   1.3e-50   1.3e-50       1      83 []       9      91 ..       9      91 .. 0.99
   2 ?   -2.1   0.0      0.24      0.24      14      49 ..     331     368 ..     320     373 .. 0.60

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 1.3e-50
                       TIGR01799  1 lkdlrdeidevdkellqllakrlelvaqvGkvkhraGlPiyaPereaamlakrreeaeklGiapdliedvlrrlmresyan 81
                                    l++lr+ id+vd++ll+ll+krl+lvaqvG+vkh+aGlPiyaP+reaamlakrreea+++Giap+lied+lrrlmresy+n
  lcl|FitnessBrowser__MR1:200537  9 LEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAQTMGIAPQLIEDILRRLMRESYLN 89
                                    79******************************************************************************* PP

                       TIGR01799 82 en 83
                                    e+
  lcl|FitnessBrowser__MR1:200537 90 EK 91
                                    97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.24
                       TIGR01799  14 ellqllak..rlelvaqvGkvkhraGlPiyaPereaam 49 
                                     e l+ll++  r e++ q   v + +G      +re  m
  lcl|FitnessBrowser__MR1:200537 331 EALELLKRgdREEFINQFQMVAKWFGDFAPQFQRESRM 368
                                     55566653336677777777777776544444566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 nodes)
Target sequences:                          1  (379 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: 13.65
//
[ok]

This GapMind analysis is from Apr 09 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