Alignments for a candidate for leuC in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Shewanella oneidensis MR-1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 203315 SO4234 3-isopropylmalate dehydratase, large subunit (NCBI ptt file)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__MR1:203315
          Length = 474

 Score =  699 bits (1805), Expect = 0.0
 Identities = 340/461 (73%), Positives = 395/461 (85%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K++DAH+V   E E P++Y+DRHLVHEVTSPQAF GL+  GR +R P KTFATMD
Sbjct: 11  KTLYQKVWDAHIVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRQLRAPEKTFATMD 70

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HN ST++  ++A   MARIQ++ L +NCK+FGV LYD++HP QGIVHVMGPE G+TLPG 
Sbjct: 71  HNTSTRSASLDALSPMARIQVETLAQNCKDFGVLLYDIHHPNQGIVHVMGPELGITLPGT 130

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
            IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL+Q +AKTMKIEV+G+   G+TAKD
Sbjct: 131 VIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAKTMKIEVRGQVTDGVTAKD 190

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           IVLAIIGK G  GGTG+VVEFCGEAI  LSMEGRMT+CNMAIEMGAKAG+VAPD+TTF+Y
Sbjct: 191 IVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGMVAPDQTTFDY 250

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           ++GR  APKG+D+  AVA WKTL+TD GA FD  V L A +I+PQ+TWGTNPGQV++++ 
Sbjct: 251 LEGREFAPKGEDWAQAVAEWKTLKTDVGAEFDATVVLDAADIAPQLTWGTNPGQVVAIDA 310

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +P+PA   +P  R+S EKAL Y+GL  G P+TEVAI+KVFIGSCTNSRIEDLR+AA+ A
Sbjct: 311 PVPNPADEVNPTIRSSMEKALDYIGLTAGTPMTEVAINKVFIGSCTNSRIEDLRSAAKHA 370

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           KGRKVA GV A+VVPGSG VKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMN+DRL  G+
Sbjct: 371 KGRKVAAGVTAIVVPGSGQVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNDDRLEAGD 430

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           RCASTSNRNFEGRQGRG RTHLVSPAMAAAAA+ GHF DIR
Sbjct: 431 RCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDIR 471


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: 783
Number of extensions: 14
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: 466
Length of database: 474
Length adjustment: 33
Effective length of query: 433
Effective length of database: 441
Effective search space:   190953
Effective search space used:   190953
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 203315 SO4234 (3-isopropylmalate dehydratase, large subunit (NCBI ptt file))
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.1274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-256  836.4   1.8     3e-256  836.2   1.8    1.0  1  lcl|FitnessBrowser__MR1:203315  SO4234 3-isopropylmalate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203315  SO4234 3-isopropylmalate dehydratase, large subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  836.2   1.8    3e-256    3e-256       2     465 ..      10     472 ..       9     473 .. 1.00

  Alignments for each domain:
  == domain 1  score: 836.2 bits;  conditional E-value: 3e-256
                       TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikeekak 80 
                                     +ktly+k++dah+v   e+e++++y+drhlvhevtspqaf gl++agr++r ++kt+at+dhn st+s  ++++  +a+
  lcl|FitnessBrowser__MR1:203315  10 PKTLYQKVWDAHIVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRQLRAPEKTFATMDHNTSTRSASLDALSPMAR 88 
                                     8****************************************************************************** PP

                       TIGR00170  81 lqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlatqtlk 159
                                     +qv++l +n+k+fgv l+d+++ +qgivhv+gpe g+tlpg+ ivcgdshtathgafgalafgigtsevehvlatqtl+
  lcl|FitnessBrowser__MR1:203315  89 IQVETLAQNCKDFGVLLYDIHHPNQGIVHVMGPELGITLPGTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLR 167
                                     ******************************************************************************* PP

                       TIGR00170 160 qaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliapdet 238
                                     q +akt+kiev+g++++g+takdi+laiigkig+ ggtgyvvef+geai++lsme+rmtvcnmaie+gakag++apd+t
  lcl|FitnessBrowser__MR1:203315 168 QLKAKTMKIEVRGQVTDGVTAKDIVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGMVAPDQT 246
                                     ******************************************************************************* PP

                       TIGR00170 239 tfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpveka 317
                                     tf+y+ +r++apkg+++ +ava+wktlktd ga+fd +v+l+a di+pq+twgtnpgqv++++  vp+p++  +p  ++
  lcl|FitnessBrowser__MR1:203315 247 TFDYLEGREFAPKGEDWAQAVAEWKTLKTDVGAEFDATVVLDAADIAPQLTWGTNPGQVVAIDAPVPNPADEVNPTIRS 325
                                     ******************************************************************************* PP

                       TIGR00170 318 saekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkif 396
                                     s+ekal+y+gl++gt++++++++kvfigsctnsriedlr+aa+ +kg+kva +v  a+vvpgsg+vk+qae+egldkif
  lcl|FitnessBrowser__MR1:203315 326 SMEKALDYIGLTAGTPMTEVAINKVFIGSCTNSRIEDLRSAAKHAKGRKVAAGVT-AIVVPGSGQVKAQAEAEGLDKIF 403
                                     ******************************************************9.*********************** PP

                       TIGR00170 397 leagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                     +eagfewr +gcs+cl+mn+d+l++++rcastsnrnfegrqg+g+rthlvspamaaaaa+ag+fvdir+
  lcl|FitnessBrowser__MR1:203315 404 IEAGFEWRLPGCSMCLAMNDDRLEAGDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDIRK 472
                                     *******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (474 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: 9.60
//
[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