GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvI in Dyella japonica UNC79MFTsu3.2

Align Probable acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized)
to candidate N515DRAFT_0566 N515DRAFT_0566 acetolactate synthase, small subunit

Query= curated2:O28555
         (159 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0566 N515DRAFT_0566
          acetolactate synthase, small subunit
          Length = 82

 Score = 85.5 bits (210), Expect = 2e-22
 Identities = 39/74 (52%), Positives = 58/74 (78%)

Query: 1  MKHTIAVLVENKPGVLARVAGLFRRRGFNIESLTVGTTERDDLSRMTIVVEGDDKVVEQV 60
          MKHT+++L++N+ G L RVAGLF  RGFNI+SLTV  T+   +S++T+V+ G D+ V+Q+
Sbjct: 1  MKHTLSILLQNEAGALVRVAGLFSARGFNIDSLTVAATQDPAVSQLTLVMHGADEAVDQL 60

Query: 61 IKQLNKLIETIKVS 74
          IKQ  KL++ I+VS
Sbjct: 61 IKQTRKLVDVIEVS 74


Lambda     K      H
   0.319    0.137    0.365 

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: 33
Number of extensions: 1
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: 159
Length of database: 82
Length adjustment: 12
Effective length of query: 147
Effective length of database: 70
Effective search space:    10290
Effective search space used:    10290
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: 40 (21.3 bits)
S2: 40 (20.0 bits)

Align candidate N515DRAFT_0566 N515DRAFT_0566 (acetolactate synthase, small subunit)
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (EC 2.2.1.6))

# 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/TIGR00119.hmm
# target sequence database:        /tmp/gapView.12852.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00119  [M=158]
Accession:   TIGR00119
Description: acolac_sm: acetolactate synthase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
      7e-32   96.7   0.1    7.6e-32   96.5   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0566  N515DRAFT_0566 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0566  N515DRAFT_0566 acetolactate synthase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.1   7.6e-32   7.6e-32       1      75 [.       1      75 [.       1      81 [. 0.97

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 7.6e-32
                                    TIGR00119  1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklv 68
                                                 +kh+ls+l++ne+G+L rv+Glf++rgfni+sltv+ t+++ +s++t+v++g d++v+q++kq +klv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0566  1 MKHTLSILLQNEAGALVRVAGLFSARGFNIDSLTVAATQDPAVSQLTLVMHGADEAVDQLIKQTRKLV 68
                                                 79****************************************************************** PP

                                    TIGR00119 69 dvlkvld 75
                                                 dv++v+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0566 69 DVIEVSH 75
                                                 ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (82 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: 2.86
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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