GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Pedobacter sp. GW460-11-11-14-LB5

Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate CA265_RS11635 CA265_RS11635 3-deoxy-7-phosphoheptulonate synthase

Query= reanno::Pedo557:CA265_RS11635
         (379 letters)



>FitnessBrowser__Pedo557:CA265_RS11635
          Length = 379

 Score =  751 bits (1938), Expect = 0.0
 Identities = 379/379 (100%), Positives = 379/379 (100%)

Query: 1   MKLNLNIQSLNTWLNVNNEPLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRT 60
           MKLNLNIQSLNTWLNVNNEPLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRT
Sbjct: 1   MKLNLNIQSLNTWLNVNNEPLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRT 60

Query: 61  RPGEFEGIGSIGLEWLKRAKAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFT 120
           RPGEFEGIGSIGLEWLKRAKAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFT
Sbjct: 61  RPGEFEGIGSIGLEWLKRAKAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFT 120

Query: 121 VQEIADALKGHDVPVLIKNPVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRN 180
           VQEIADALKGHDVPVLIKNPVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRN
Sbjct: 121 VQEIADALKGHDVPVLIKNPVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRN 180

Query: 181 EPMWELAIQLKTLCPELPIINDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAW 240
           EPMWELAIQLKTLCPELPIINDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAW
Sbjct: 181 EPMWELAIQLKTLCPELPIINDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAW 240

Query: 241 TDAKQQVTPAALAELVDRLTVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIV 300
           TDAKQQVTPAALAELVDRLTVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIV
Sbjct: 241 TDAKQQVTPAALAELVDRLTVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIV 300

Query: 301 EKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIM 360
           EKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIM
Sbjct: 301 EKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIM 360

Query: 361 NAGKAEQGIAAEQHTEVKA 379
           NAGKAEQGIAAEQHTEVKA
Sbjct: 361 NAGKAEQGIAAEQHTEVKA 379


Lambda     K      H
   0.317    0.134    0.389 

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: 620
Number of extensions: 16
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: 379
Length of database: 379
Length adjustment: 30
Effective length of query: 349
Effective length of database: 349
Effective search space:   121801
Effective search space used:   121801
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate CA265_RS11635 CA265_RS11635 (3-deoxy-7-phosphoheptulonate synthase)
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.13273.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    1.1e-21   63.3   0.7    2.8e-21   62.0   0.7    1.7  1  lcl|FitnessBrowser__Pedo557:CA265_RS11635  CA265_RS11635 3-deoxy-7-phosphoh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS11635  CA265_RS11635 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.7   2.8e-21   2.8e-21       1      78 [.     279     356 ..     279     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 2.8e-21
                                       CM_2   1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifr 68 
                                                Rk+Id+iD+ ll+ l eRm+++++i+e+K++n++++l+ +R+++++++  + a++l+ld +++ek+++
  lcl|FitnessBrowser__Pedo557:CA265_RS11635 279 RKSIDKIDDVLLQKLGERMAIVEKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLE 346
                                                99****************************************************************** PP

                                       CM_2  69 eiisesralQ 78 
                                                 ++ es++ Q
  lcl|FitnessBrowser__Pedo557:CA265_RS11635 347 LVHGESIRKQ 356
                                                ********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 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: 10.80
//
[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:

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:

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:

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:

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