Alignments for a candidate for leuC in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Malonomonas rubra DSM 5091

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_072908947.1 BUB13_RS11705 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_900142125.1:WP_072908947.1
          Length = 469

 Score =  634 bits (1635), Expect = 0.0
 Identities = 310/467 (66%), Positives = 377/467 (80%), Gaps = 1/467 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           MAKTLY+KL+DAH+V++ ++ T LLYIDR L+HEVTSPQAF+GLR  GR  R+     A 
Sbjct: 1   MAKTLYDKLWDAHLVHQDDDGTALLYIDRQLLHEVTSPQAFEGLRLAGRKPRRIDANLAV 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  +       ++R+Q++ L KNCKEFG+ ++ +N P QGIVHV+GPEQG TLP
Sbjct: 61  PDHNVPTDDRSSEIADPVSRLQVETLEKNCKEFGITMFAMNDPRQGIVHVIGPEQGATLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMT+VCGDSHTATHGAFGALAFGIGTSEVEHVLATQ L Q ++KTM IEV G+   G+TA
Sbjct: 121 GMTVVCGDSHTATHGAFGALAFGIGTSEVEHVLATQCLIQKKSKTMLIEVNGELPSGLTA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIG+ G+AGGTG+ VEF G+AIR LSMEGRMT+CNMAIE GA+AGL+A D+ T 
Sbjct: 181 KDIVLAIIGRIGTAGGTGYCVEFGGDAIRALSMEGRMTVCNMAIEAGARAGLIAVDQKTI 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           +YV+GR  AP+G D++ AVA W+ L++D  A FD +V + A +++PQVTWGT+P  V+S+
Sbjct: 241 DYVEGRPFAPQGADWELAVASWRQLKSDPDAEFDKIVRIDARDLNPQVTWGTSPEMVVSI 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
            D +P PA  ADPV++   + AL YMGL+PG P+ ++  D VFIGSCTN RIEDLRA A 
Sbjct: 301 ADRVPSPAEEADPVKQEGMQAALKYMGLEPGTPINQIKPDIVFIGSCTNGRIEDLRAVAA 360

Query: 361 IAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           +AKGRKVA  + QAL+VPGSG VK QAE EGLDKIFI+AGFEWR PGCSMCLAMNNDRL 
Sbjct: 361 VAKGRKVADNIKQALIVPGSGLVKQQAEKEGLDKIFIDAGFEWREPGCSMCLAMNNDRLK 420

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           PGERCASTSNRNFEGRQG+GGRTHLVSPAMAAAAAVTGHF D+R+++
Sbjct: 421 PGERCASTSNRNFEGRQGQGGRTHLVSPAMAAAAAVTGHFVDVRSLE 467


Lambda     K      H
   0.317    0.134    0.396 

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: 781
Number of extensions: 33
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: 466
Length of database: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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: 51 (24.3 bits)

Align candidate WP_072908947.1 BUB13_RS11705 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.7099.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-249  811.6   0.0     1e-248  811.4   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072908947.1  BUB13_RS11705 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072908947.1  BUB13_RS11705 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.4   0.0    1e-248    1e-248       1     465 [.       1     465 [.       1     466 [. 1.00

  Alignments for each domain:
  == domain 1  score: 811.4 bits;  conditional E-value: 1e-248
                                 TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 
                                               maktly+kl+dah+v++++++t llyidr l+hevtspqafeglr agrk rr+d  la  dhn++t+ 
  lcl|NCBI__GCF_900142125.1:WP_072908947.1   1 MAKTLYDKLWDAHLVHQDDDGTALLYIDRQLLHEVTSPQAFEGLRLAGRKPRRIDANLAVPDHNVPTDD 69 
                                               89******************************************************************* PP

                                 TIGR00170  70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138
                                               r  ei + +++lqv++lekn+kefg+ +f +++ +qgivhv+gpe+g tlpg+t+vcgdshtathgafg
  lcl|NCBI__GCF_900142125.1:WP_072908947.1  70 RSSEIADPVSRLQVETLEKNCKEFGITMFAMNDPRQGIVHVIGPEQGATLPGMTVVCGDSHTATHGAFG 138
                                               ********************************************************************* PP

                                 TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207
                                               alafgigtsevehvlatq l+q+++kt+ iev+g+l +g+takdi+laiig+ig+aggtgy vef g+a
  lcl|NCBI__GCF_900142125.1:WP_072908947.1 139 ALAFGIGTSEVEHVLATQCLIQKKSKTMLIEVNGELPSGLTAKDIVLAIIGRIGTAGGTGYCVEFGGDA 207
                                               ********************************************************************* PP

                                 TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276
                                               ir+lsme+rmtvcnmaieaga+aglia d+ t++yv +r++ap+g+++e ava w+ lk+d++a+fdk 
  lcl|NCBI__GCF_900142125.1:WP_072908947.1 208 IRALSMEGRMTVCNMAIEAGARAGLIAVDQKTIDYVEGRPFAPQGADWELAVASWRQLKSDPDAEFDKI 276
                                               ********************************************************************* PP

                                 TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345
                                               v ++a+d+ pqvtwgt+p++v+s+ + vp+p++ adpv++++++ al+y+glepgt++++ik d vfig
  lcl|NCBI__GCF_900142125.1:WP_072908947.1 277 VRIDARDLNPQVTWGTSPEMVVSIADRVPSPAEEADPVKQEGMQAALKYMGLEPGTPINQIKPDIVFIG 345
                                               ********************************************************************* PP

                                 TIGR00170 346 sctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgm 414
                                               sctn+riedlra a+v+kg+kvadn+k+al+vpgsglvk+qaekegldkif++agfewre+gcs+cl+m
  lcl|NCBI__GCF_900142125.1:WP_072908947.1 346 SCTNGRIEDLRAVAAVAKGRKVADNIKQALIVPGSGLVKQQAEKEGLDKIFIDAGFEWREPGCSMCLAM 414
                                               ********************************************************************* PP

                                 TIGR00170 415 nndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                               nnd+l+++ercastsnrnfegrqg+g+rthlvspamaaaaav+g+fvd+r 
  lcl|NCBI__GCF_900142125.1:WP_072908947.1 415 NNDRLKPGERCASTSNRNFEGRQGQGGRTHLVSPAMAAAAAVTGHFVDVRS 465
                                               *************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (469 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.62
//
[ok]

This GapMind analysis is from Apr 10 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