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.22332.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 5.71
//
[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