Alignments for a candidate for leuC in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfatibacillum aliphaticivorans DSM 15576

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_028313822.1 G491_RS0105155 3-isopropylmalate dehydratase large subunit

Query= reanno::DvH:208495
         (419 letters)



>NCBI__GCF_000429905.1:WP_028313822.1
          Length = 419

 Score =  513 bits (1320), Expect = e-150
 Identities = 249/419 (59%), Positives = 308/419 (73%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  T+A+KIL  H  +     G ++  +V + L NDITAP+AIK FR  GA +VFDKDRV
Sbjct: 1   MGMTIAEKILAAHAGQEEASPGDLINAKVDIALGNDITAPIAIKLFRQSGAAKVFDKDRV 60

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
            LV DHFTP KDI +A QVK+ R+FARE  ++H+YEGGD GVEHALLPE G+VGPGD+V+
Sbjct: 61  VLVPDHFTPTKDINSAMQVKMVRDFAREQELSHWYEGGDSGVEHALLPEKGIVGPGDLVI 120

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
           GADSHTCTYGGLGAFATG+GSTD+A AM  GE W KVP +I+  + G L  +V  KDLIL
Sbjct: 121 GADSHTCTYGGLGAFATGVGSTDLAAAMITGEVWLKVPESIKFVYKGKLRPHVEGKDLIL 180

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
             IG IGVDGALY A+EF G  I+AL +  R+TMANMAIEAGGKAG+ A DA T  Y   
Sbjct: 181 HTIGDIGVDGALYMAMEFTGEVIDALPMAERLTMANMAIEAGGKAGIIAPDATTKEYADG 240

Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300
                   +++D  A Y + + +DVT + P VA PHLP+N +P+S+V DV + QV+IGSC
Sbjct: 241 RVIRKPVFYASDPDAKYAKVIEYDVTDLEPQVAFPHLPENTRPISQVGDVPIHQVIIGSC 300

Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360
           TNGRI D+R AA +L G K  ++VR I++PATP I+RQA+ EGL +TF+ AG ++ P TC
Sbjct: 301 TNGRIEDMRSAARILTGNKADKNVRLIIIPATPQIYRQAMEEGLFDTFLSAGAVISPPTC 360

Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419
           GPCLGGHMGILA GERA+ATTNRNF GRMG +ESEVYL+ PA AAASA+ G I  P  +
Sbjct: 361 GPCLGGHMGILAAGERAVATTNRNFVGRMGHVESEVYLANPAVAAASAIAGKIAGPDDI 419


Lambda     K      H
   0.320    0.136    0.401 

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: 552
Number of extensions: 21
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: 419
Length of database: 419
Length adjustment: 32
Effective length of query: 387
Effective length of database: 387
Effective search space:   149769
Effective search space used:   149769
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: 50 (23.9 bits)

Align candidate WP_028313822.1 G491_RS0105155 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02083 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR02083.hmm
# target sequence database:        /tmp/gapView.16918.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02083  [M=419]
Accession:   TIGR02083
Description: LEU2: 3-isopropylmalate dehydratase, large 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-214  696.6   0.6   6.5e-214  696.4   0.6    1.0  1  lcl|NCBI__GCF_000429905.1:WP_028313822.1  G491_RS0105155 3-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028313822.1  G491_RS0105155 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.4   0.6  6.5e-214  6.5e-214       1     419 []       3     419 .]       3     419 .] 1.00

  Alignments for each domain:
  == domain 1  score: 696.4 bits;  conditional E-value: 6.5e-214
                                 TIGR02083   1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnk 69 
                                               mt+aekila +ag+ee  pg+li ak+d++lgnd+t+p+aik f++ g+ kvfdkd+v+lv+dhftp k
  lcl|NCBI__GCF_000429905.1:WP_028313822.1   3 MTIAEKILAAHAGQEEASPGDLINAKVDIALGNDITAPIAIKLFRQSGAAKVFDKDRVVLVPDHFTPTK 71 
                                               9******************************************************************** PP

                                 TIGR02083  70 dikaaeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvg 138
                                               di +a+qvk++r+fa+e+e+++++e g+ gvehallpekg+v +gdl+igadshtctyg lgafatgvg
  lcl|NCBI__GCF_000429905.1:WP_028313822.1  72 DINSAMQVKMVRDFAREQELSHWYEGGDSGVEHALLPEKGIVGPGDLVIGADSHTCTYGGLGAFATGVG 140
                                               ********************************************************************* PP

                                 TIGR02083 139 stdlavamatgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvd 207
                                               stdla+am+tg++w+kvpe+ikfv+kgkl+++v +kdlil++ig+igvdgaly ++ef+ge+++ l + 
  lcl|NCBI__GCF_000429905.1:WP_028313822.1 141 STDLAAAMITGEVWLKVPESIKFVYKGKLRPHVEGKDLILHTIGDIGVDGALYMAMEFTGEVIDALPMA 209
                                               ********************************************************************* PP

                                 TIGR02083 208 drltianmaieagaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlp 276
                                               +rlt+anmaieag+k+gi+ +d  t ey+ gr +r+   y +d daky +vie+d+ +lepqvafphlp
  lcl|NCBI__GCF_000429905.1:WP_028313822.1 210 ERLTMANMAIEAGGKAGIIAPDATTKEYADGRVIRKPVFYASDPDAKYAKVIEYDVTDLEPQVAFPHLP 278
                                               ********************************************************************* PP

                                 TIGR02083 277 entkeideaekeeikidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkegll 345
                                               ent++i++++  ++ i qv+igsctngr+ed+r aa+il g+k  k+vrlii+pa++++y +a++egl 
  lcl|NCBI__GCF_000429905.1:WP_028313822.1 279 ENTRPISQVG--DVPIHQVIIGSCTNGRIEDMRSAARILTGNKADKNVRLIIIPATPQIYRQAMEEGLF 345
                                               **********..9******************************************************** PP

                                 TIGR02083 346 eifieagavvstptcgpclgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkia 414
                                               ++f+ agav+s+ptcgpclgghmgila+gerav+ttnrnfvgrmgh++sevyla pavaaasai+gkia
  lcl|NCBI__GCF_000429905.1:WP_028313822.1 346 DTFLSAGAVISPPTCGPCLGGHMGILAAGERAVATTNRNFVGRMGHVESEVYLANPAVAAASAIAGKIA 414
                                               ********************************************************************* PP

                                 TIGR02083 415 speev 419
                                                p+++
  lcl|NCBI__GCF_000429905.1:WP_028313822.1 415 GPDDI 419
                                               **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (419 nodes)
Target sequences:                          1  (419 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.01
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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