Alignments for a candidate for ilvA in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Clostridium kluyveri DSM 555

Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate WP_011988995.1 CKL_RS02105 threonine ammonia-lyase

Query= SwissProt::Q9WYJ1
         (401 letters)



>NCBI__GCF_000016505.1:WP_011988995.1
          Length = 412

 Score =  378 bits (970), Expect = e-109
 Identities = 195/396 (49%), Positives = 273/396 (68%), Gaps = 1/396 (0%)

Query: 2   ITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAH 61
           +TLED+ EA++ +K++   T L YSS  S  +G E+Y+K ENLQ TG+FK+RGA NKI+ 
Sbjct: 14  LTLEDVLEARKRIKDICIDTELIYSSEYSLESGNEVYIKPENLQITGAFKLRGALNKISK 73

Query: 62  LSEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEG 121
           LSE+ +K+G++A+SAGNHAQGVA AA   GI ATIVMP   PL K+  T+N GA+V+L+G
Sbjct: 74  LSEDNKKKGLIASSAGNHAQGVAYAANKLGIKATIVMPETTPLIKVQATKNYGAEVVLKG 133

Query: 122 NIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGL 181
            ++DEAYE A R++++ G  F+HPF+D  V+AGQGTI LEI+E L DV+ +VVP+GGGGL
Sbjct: 134 KVYDEAYEEAKRLEKEKGYTFIHPFDDLDVMAGQGTIALEIIEKLKDVDAIVVPIGGGGL 193

Query: 182 ISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTF 241
           ISG+SVA KS+NP +K+IGVQ +    M  S   G+    E   T+ADG AVK PG LTF
Sbjct: 194 ISGISVAAKSINPNIKIIGVQADGANPMKYSFDTGKLTSAEDIDTIADGAAVKNPGKLTF 253

Query: 242 ELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLDVKGKKVAIVIS 301
           ++VKKYVDE+V V+++++ + +  LLE+ K+VAE  GA+ +AA L+KL  K KKV  +IS
Sbjct: 254 QVVKKYVDEIVTVSDQQLMEDVYILLEKHKLVAEATGAMSLAA-LSKLKFKNKKVVCLIS 312

Query: 302 GGNIDVNMIDRIINKGLVKSGRKVFIETFVMDRPGALKELLGIVAELGANVLSVFHNRSA 361
           GGNIDV  +  ++N GLV  GR       + D PG L ++  I+AE  AN++ + HN+  
Sbjct: 313 GGNIDVVTMSALLNHGLVSRGRIFCFSVKLKDTPGQLLQISKILAEKSANIIKLDHNQFK 372

Query: 362 KEVPIGFAKIELELETVDEKHVEEIERVLIAKGYEV 397
               +    +E+ +ET    H+EEI + L   GY +
Sbjct: 373 AIDRLKHVALEVTVETNGHDHIEEIIKSLNEHGYNI 408


Lambda     K      H
   0.317    0.136    0.367 

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: 368
Number of extensions: 13
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: 401
Length of database: 412
Length adjustment: 31
Effective length of query: 370
Effective length of database: 381
Effective search space:   140970
Effective search space used:   140970
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_011988995.1 CKL_RS02105 (threonine ammonia-lyase)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (EC 4.3.1.19))

# 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/TIGR01127.hmm
# target sequence database:        /tmp/gapView.26114.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-152  494.0  11.3   1.6e-152  493.8  11.3    1.0  1  lcl|NCBI__GCF_000016505.1:WP_011988995.1  CKL_RS02105 threonine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_011988995.1  CKL_RS02105 threonine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.8  11.3  1.6e-152  1.6e-152       1     378 [.      33     408 ..      33     410 .. 0.99

  Alignments for each domain:
  == domain 1  score: 493.8 bits;  conditional E-value: 1.6e-152
                                 TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakv 69 
                                               t l++ss +s + g evy+k enlq+tG+fk+rGalnki+klse++kk+G +a+saGnhaqGva+aa++
  lcl|NCBI__GCF_000016505.1:WP_011988995.1  33 TELIYSSEYSLESGNEVYIKPENLQITGAFKLRGALNKISKLSEDNKKKGLIASSAGNHAQGVAYAANK 101
                                               789****************************************************************** PP

                                 TIGR01127  70 fgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtl 138
                                                gika+ivmPe +pl kv+atk+yGaev+L+G+++Deay+ a++l++e+g++f+h+fdD  v+aGqGt+
  lcl|NCBI__GCF_000016505.1:WP_011988995.1 102 LGIKATIVMPETTPLIKVQATKNYGAEVVLKGKVYDEAYEEAKRLEKEKGYTFIHPFDDLDVMAGQGTI 170
                                               ********************************************************************* PP

                                 TIGR01127 139 gleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvkti 207
                                               +lei+e+l dvd ++vP+GGGGLisG+++a+k++np++k+iGv+a++a+ ++ s++ gk +++e  +ti
  lcl|NCBI__GCF_000016505.1:WP_011988995.1 171 ALEIIEKLKDVDAIVVPIGGGGLISGISVAAKSINPNIKIIGVQADGANPMKYSFDTGKLTSAEDIDTI 239
                                               ********************************************************************* PP

                                 TIGR01127 208 aDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkk 276
                                               aDG avk+pg+ltf++vk++vDe+v+v+++++ + +++Lle++k+vae++Ga+++aa+   k++ k+kk
  lcl|NCBI__GCF_000016505.1:WP_011988995.1 240 ADGAAVKNPGKLTFQVVKKYVDEIVTVSDQQLMEDVYILLEKHKLVAEATGAMSLAALS--KLKFKNKK 306
                                               *********************************************************95..58889999 PP

                                 TIGR01127 277 vavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskei 345
                                               v+ ++sGGnid+  ++ ++++gLv++gr+   ++ lkD+PG+L ++ +++aek ani+k++h++++   
  lcl|NCBI__GCF_000016505.1:WP_011988995.1 307 VVCLISGGNIDVVTMSALLNHGLVSRGRIFCFSVKLKDTPGQLLQISKILAEKSANIIKLDHNQFKAID 375
                                               *****************************************************************9999 PP

                                 TIGR01127 346 algaakvelelevkgkehleellktlrdkgyev 378
                                                l    +e+++e++g++h+ee+ k l+++gy++
  lcl|NCBI__GCF_000016505.1:WP_011988995.1 376 RLKHVALEVTVETNGHDHIEEIIKSLNEHGYNI 408
                                               9999***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (412 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: 8.52
//
[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