Alignments for a candidate for ilvA in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Polaromonas naphthalenivorans CJ2

Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate WP_011799546.1 PNAP_RS00550 threonine ammonia-lyase

Query= reanno::Caulo:CCNA_03750
         (400 letters)



>NCBI__GCF_000015505.1:WP_011799546.1
          Length = 400

 Score =  405 bits (1041), Expect = e-117
 Identities = 201/393 (51%), Positives = 278/393 (70%)

Query: 3   LDLAAIQAAAGRLQGQIERTPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKLML 62
           L L  I+ AA RL G +  TPC  S+TLS++TGA++++KFENLQ+TA++KERGA NKL  
Sbjct: 2   LSLTVIEQAAQRLHGHLLDTPCVESRTLSQLTGAQIYLKFENLQYTASFKERGACNKLAQ 61

Query: 63  LSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIVMPKTTPFVKVQHTRDFGATVVIEG 122
           L+E+E+QRGVIA SAGNHAQG+AYH  RLG+   IVMP+ TP VK++ TR FGA VV+ G
Sbjct: 62  LTESERQRGVIAMSAGNHAQGVAYHAQRLGIRAVIVMPRFTPGVKIERTRGFGAEVVLHG 121

Query: 123 ETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPVPIGGGGL 182
           +T D + AHA  L + + L FVHP+DD  I+AGQGT+ LEML   P+LE+L + +GGGGL
Sbjct: 122 DTLDASRAHAMGLAEREKLVFVHPYDDEAIVAGQGTVGLEMLHAVPELEVLVIAVGGGGL 181

Query: 183 ISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRGVAAHCGGQTIAEGVAVKQVGELTYGV 242
           I+GVATAAKALKP I IIG + + +P+    ++G     G  TIA+G+AV   G +   +
Sbjct: 182 IAGVATAAKALKPGIEIIGVQTSRFPAMVNAIKGTHHPQGTSTIADGIAVGTPGVIAQAI 241

Query: 243 VRPLLDDVLLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLILCG 302
           +   +DD+LL++E  +EQA+ +   +EKT+ EGAGAA LAALL YP RF G+K GL+LCG
Sbjct: 242 IAEKVDDLLLVDEGDIEQAMVMLLEIEKTLVEGAGAAGLAALLKYPARFAGRKVGLVLCG 301

Query: 303 GNIDTRLLASVLTRELVRAQRLASLRIIGDDRPGLLSTVASVIGAMGANIIEVNHNRLAL 362
           GNID  LLA+++ R +VRA RLA +R+   D PG L+ + + +   GANI EV+H R   
Sbjct: 302 GNIDPLLLAAIIERGMVRAGRLARIRVSARDIPGSLAKITATVADAGANIEEVHHQRAFT 361

Query: 363 DVPAKGAEFDITIETRDAQHTQEVMEALRESGY 395
            + A+  E ++ ++TR   H  +V++ALR +G+
Sbjct: 362 MLAAQNVEIELVLQTRGRPHIAQVLQALRTAGF 394


Lambda     K      H
   0.319    0.136    0.390 

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: 364
Number of extensions: 9
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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_011799546.1 PNAP_RS00550 (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.4914.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-135  437.1   5.6   3.1e-135  437.0   5.6    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011799546.1  PNAP_RS00550 threonine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011799546.1  PNAP_RS00550 threonine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.0   5.6  3.1e-135  3.1e-135       1     378 [.      21     396 ..      21     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 437.0 bits;  conditional E-value: 3.1e-135
                                 TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakv 69 
                                               tp   s tls++tga++ylk enlq t sfk rGa nk+a+l+e e++rGv+a saGnhaqGva+ a++
  lcl|NCBI__GCF_000015505.1:WP_011799546.1  21 TPCVESRTLSQLTGAQIYLKFENLQYTASFKERGACNKLAQLTESERQRGVIAMSAGNHAQGVAYHAQR 89 
                                               78999**************************************************************** PP

                                 TIGR01127  70 fgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtl 138
                                                gi+a+ivmP+++p  k++ t+++Gaev+LhG+++D + ++a  lae+e +vfvh++dDe ++aGqGt+
  lcl|NCBI__GCF_000015505.1:WP_011799546.1  90 LGIRAVIVMPRFTPGVKIERTRGFGAEVVLHGDTLDASRAHAMGLAEREKLVFVHPYDDEAIVAGQGTV 158
                                               ********************************************************************* PP

                                 TIGR01127 139 gleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvkti 207
                                               gle+l+ +p+++++++ vGGGGLi+Gva+a+k l+p++ +iGv++   p++v+++k    ++ + ++ti
  lcl|NCBI__GCF_000015505.1:WP_011799546.1 159 GLEMLHAVPELEVLVIAVGGGGLIAGVATAAKALKPGIEIIGVQTSRFPAMVNAIKGT--HHPQGTSTI 225
                                               ******************************************************9865..4567899** PP

                                 TIGR01127 208 aDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkk 276
                                               aDGiav +pg ++  i+ e vD+++ vde +i +a+++Lle +k+++egaGa+g+aa+l+      g+k
  lcl|NCBI__GCF_000015505.1:WP_011799546.1 226 ADGIAVGTPGVIAQAIIAEKVDDLLLVDEGDIEQAMVMLLEIEKTLVEGAGAAGLAALLKYPARFAGRK 294
                                               ********************************************************************* PP

                                 TIGR01127 277 vavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskei 345
                                               v++v++GGnid+ ll  iie+g+v+ gr+++i++   D+PG+L k+++++a+++ani +++h+r  + +
  lcl|NCBI__GCF_000015505.1:WP_011799546.1 295 VGLVLCGGNIDPLLLAAIIERGMVRAGRLARIRVSARDIPGSLAKITATVADAGANIEEVHHQRAFTML 363
                                               ********************************************************************* PP

                                 TIGR01127 346 algaakvelelevkgkehleellktlrdkgyev 378
                                               a    ++el l+++g+ h+ ++l+ lr  g+e 
  lcl|NCBI__GCF_000015505.1:WP_011799546.1 364 AAQNVEIELVLQTRGRPHIAQVLQALRTAGFEA 396
                                               *******************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (400 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.93
//
[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