Aligments for a candidate for cmutase in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Aligments for a candidate for cmutase in Pseudomonas fluorescens FW300-N2C3

Align Monofunctional chorismate mutase; EC 5.4.99.5 (characterized)
to candidate AO356_09710 AO356_09710 chorismate mutase

Query= SwissProt::Q9HU05
         (185 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09710 AO356_09710
           chorismate mutase
          Length = 187

 Score = 90.9 bits (224), Expect = 1e-23
 Identities = 70/177 (39%), Positives = 91/177 (51%), Gaps = 11/177 (6%)

Query: 10  LLALLLLQGPLLQAQPLSPALQQLLSLSSQRLQLADQVAQSKAQSGKAVQDSPREEQQLQ 69
           L A LL       + P   AL  LL+   +RL +ADQVA SK  SGK V+D  RE + + 
Sbjct: 11  LSAALLASTAAAASTPAPEALTPLLNAIGERLAIADQVALSKWDSGKPVEDRQREREVIA 70

Query: 70  MLAGQAGSHGVGAEQVRLLFAAQIEANKLVQYRLLSRPLPDAGQAVDLER------IRSR 123
               QA ++ +  E V   FAAQIEANK+VQY  LS    D G+A DL R      IR +
Sbjct: 71  AAVAQAPAYKLSNETVEAFFAAQIEANKMVQYINLSDWALD-GKAPDLPRPDLVGQIRPQ 129

Query: 124 LNQLNLELLRGYAPALAELRVDDCRPRLNQALQRQVRVDRLDELHAIALSRAAGDLC 180
           L++L   LL+  A   A  R D   P+  Q L      D+   +H +AL RA  +LC
Sbjct: 130 LDRLQKRLLQQLAD-FAPYRTD---PQCPQWLAHATHHDKQHPVHRLALIRATAELC 182


Lambda     K      H
   0.320    0.133    0.374 

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: 88
Number of extensions: 4
Number of successful extensions: 1
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: 185
Length of database: 187
Length adjustment: 20
Effective length of query: 165
Effective length of database: 167
Effective search space:    27555
Effective search space used:    27555
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: 44 (21.6 bits)

Align candidate AO356_09710 AO356_09710 (chorismate mutase)
to HMM TIGR01806 (putative 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/TIGR01806.hmm
# target sequence database:        /tmp/gapView.26081.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01806  [M=114]
Accession:   TIGR01806
Description: CM_mono2: putative 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-37  114.7   0.3    1.7e-37  114.3   0.3    1.2  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09710  AO356_09710 chorismate mutase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09710  AO356_09710 chorismate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.3   1.7e-37   1.7e-37       4     114 .]      29     141 ..      26     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 1.7e-37
                                       TIGR01806   4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfq 66 
                                                     +al  l++++ eRl++ad+Val+K++s++p+eD++re++v++ + aqa++  l+++ ve +f+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09710  29 EALTPLLNAIGERLAIADQVALSKWDSGKPVEDRQREREVIAAAVAQAPAYKLSNETVEAFFA 91 
                                                     5788899******************************************************** PP

                                       TIGR01806  67 aqinAnkaiqyrllsdWk.skaeppvevrdLe.dlRakidqlntelLeal 114
                                                     aqi+Ank++qy  lsdW    ++p  +++dL  ++R+++d l+++lL++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09710  92 AQIEANKMVQYINLSDWAlDGKAPDLPRPDLVgQIRPQLDRLQKRLLQQL 141
                                                     ******************9*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (114 nodes)
Target sequences:                          1  (187 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: 4.49
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 preprint on GapMind for carbon sources, or view the source code, or see 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