Alignments for a candidate for cmutase in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Shewanella loihica PV-4

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 5208557 Shew_1068 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)

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



>FitnessBrowser__PV4:5208557
          Length = 384

 Score =  421 bits (1082), Expect = e-122
 Identities = 214/368 (58%), Positives = 268/368 (72%), Gaps = 1/368 (0%)

Query: 4   ELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAEA 63
           EL  LR+ ID VD+ LL+LL KRL+LVA+VG VK   G+PIY P+REASMLA RR EA  
Sbjct: 13  ELEKLREHIDSVDQQLLHLLRKRLDLVAQVGGVKHAAGVPIYAPQREASMLAKRREEAAK 72

Query: 64  LGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSGY 123
           + V P LIED+LRR+MRESY +E D GFK +   L  VVIVGG G++G LF +ML+LSGY
Sbjct: 73  MNVSPQLIEDILRRLMRESYLNEKDVGFKQVKTDLGHVVIVGGQGKLGGLFAQMLSLSGY 132

Query: 124 QVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVI-GKLPPLPKDCILVDLASVKNGPL 182
           QV+ L++ DW +A  I   AGMVIV+VPI +T ++I  KL  LP  CIL DL S+K  PL
Sbjct: 133 QVKSLDKDDWQQADAIFDGAGMVIVTVPISITCELIRDKLTSLPSSCILADLTSIKEKPL 192

Query: 183 QAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRISA 242
           +AML +H GPV+GLHPMFGPD GSLAKQVVV C GR  E Y+W LEQI +WGARL    A
Sbjct: 193 EAMLASHQGPVVGLHPMFGPDVGSLAKQVVVVCHGRGREQYEWLLEQIGIWGARLVEADA 252

Query: 243 VEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQL 302
            +HD+ M  +QA+RHF++F YGL+L  E   ++ LL  SSPIYRLELAMVGRLFAQ P+L
Sbjct: 253 QQHDKAMQLVQAMRHFSSFVYGLNLYREAADIDNLLQFSSPIYRLELAMVGRLFAQSPEL 312

Query: 303 YADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSESR 362
           YADII + + +L  I  Y   + +A+ELL++GD+Q FI  F +V  WFGD+A +FQ ESR
Sbjct: 313 YADIIFAQQESLTAIGDYLDNYAQALELLKRGDRQGFIREFEEVAAWFGDFAPQFQRESR 372

Query: 363 VLLRQAND 370
            +L+  ND
Sbjct: 373 AMLQSVND 380


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: 404
Number of extensions: 16
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: 384
Length adjustment: 30
Effective length of query: 343
Effective length of database: 354
Effective search space:   121422
Effective search space used:   121422
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 5208557 Shew_1068 (bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq))
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.29038.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    1.5e-47  145.9   1.9    4.1e-47  144.5   1.9    1.8  1  lcl|FitnessBrowser__PV4:5208557  Shew_1068 bifunctional chorismat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208557  Shew_1068 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   1.9   4.1e-47   4.1e-47       1      83 []      14      96 ..      14      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 4.1e-47
                        TIGR01799  1 lkdlrdeidevdkellqllakrlelvaqvGkvkhraGlPiyaPereaamlakrreeaeklGiapdliedvlrrlmresya 80
                                     l++lr++id+vd++ll+ll+krl+lvaqvG vkh+aG+PiyaP+rea+mlakrreea k+ ++p+lied+lrrlmresy+
  lcl|FitnessBrowser__PV4:5208557 14 LEKLREHIDSVDQQLLHLLRKRLDLVAQVGGVKHAAGVPIYAPQREASMLAKRREEAAKMNVSPQLIEDILRRLMRESYL 93
                                     799***************************************************************************** PP

                        TIGR01799 81 nen 83
                                     ne+
  lcl|FitnessBrowser__PV4:5208557 94 NEK 96
                                     *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 nodes)
Target sequences:                          1  (384 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: 8.54
//
[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