Alignments for a candidate for ilvH in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvH in Marinobacter adhaerens HP15

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate GFF544 HP15_532 acetolactate synthase 3 regulatory subunit

Query= BRENDA::P00894
         (163 letters)



>FitnessBrowser__Marino:GFF544
          Length = 173

 Score =  207 bits (527), Expect = 7e-59
 Identities = 101/162 (62%), Positives = 137/162 (84%), Gaps = 1/162 (0%)

Query: 1   MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60
           MRRI+SVLLENE GALSRV+GLFSQR YNIE+LTVAPT+D TLSR+T+ T G +KV+EQI
Sbjct: 11  MRRIISVLLENEPGALSRVVGLFSQRNYNIETLTVAPTEDETLSRLTVTTTGSDKVIEQI 70

Query: 61  EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120
            KQL+KL++V+++ +L +GAH+ERE+MLVK++A+G  R E+KR  +IFRGQI+DVT S+Y
Sbjct: 71  TKQLNKLIEVVKLVDLTEGAHIERELMLVKLKATGSQRAEIKRTVDIFRGQIVDVTSSVY 130

Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDKIM 162
           TVQLAG S KLD F+ ++   + ++EV RSGV G++RG+K++
Sbjct: 131 TVQLAGDSEKLDGFIQAV-GTSGVLEVVRSGVSGIARGEKVL 171


Lambda     K      H
   0.318    0.136    0.360 

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: 140
Number of extensions: 5
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: 163
Length of database: 173
Length adjustment: 18
Effective length of query: 145
Effective length of database: 155
Effective search space:    22475
Effective search space used:    22475
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 (21.7 bits)
S2: 43 (21.2 bits)

Align candidate GFF544 HP15_532 (acetolactate synthase 3 regulatory 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.24177.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
      4e-66  207.9   4.7    4.6e-66  207.8   4.7    1.0  1  lcl|FitnessBrowser__Marino:GFF544  HP15_532 acetolactate synthase 3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF544  HP15_532 acetolactate synthase 3 regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.8   4.7   4.6e-66   4.6e-66       1     158 []      11     168 ..      11     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: 207.8 bits;  conditional E-value: 4.6e-66
                          TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldl 76 
                                        +++++svl+enepG+Lsrv+Glf++r++nie+ltv+ te+++lsr+t++++g dkv+eqi+kql+kl++v+k +dl
  lcl|FitnessBrowser__Marino:GFF544  11 MRRIISVLLENEPGALSRVVGLFSQRNYNIETLTVAPTEDETLSRLTVTTTGSDKVIEQITKQLNKLIEVVKLVDL 86 
                                        69************************************************************************** PP

                          TIGR00119  77 teseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlv 152
                                        te ++++rel+lvk++a+g++r+eik++++ifrg++vDv+ + ++v+l+g+++k++ f++++   g++ev+rsG+ 
  lcl|FitnessBrowser__Marino:GFF544  87 TEGAHIERELMLVKLKATGSQRAEIKRTVDIFRGQIVDVTSSVYTVQLAGDSEKLDGFIQAVGTSGVLEVVRSGVS 162
                                        **************************************************************************** PP

                          TIGR00119 153 alsrge 158
                                        +++rge
  lcl|FitnessBrowser__Marino:GFF544 163 GIARGE 168
                                        ****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (173 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: 4.63
//
[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