Alignments for a candidate for ilvA in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Hydrogenophaga taeniospiralis NBRC 102512

Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate WP_068170236.1 HTA01S_RS10060 threonine ammonia-lyase

Query= reanno::Korea:Ga0059261_3694
         (420 letters)



>NCBI__GCF_001592305.1:WP_068170236.1
          Length = 399

 Score =  424 bits (1091), Expect = e-123
 Identities = 214/394 (54%), Positives = 283/394 (71%)

Query: 24  DVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALNTLLQLDDA 83
           D++AAA R+ G V+ TP + S+TLS LTG  V+LKFENLQ+TA++KERGA N L+QL   
Sbjct: 6   DIEAAAQRLTGQVLDTPCVESRTLSQLTGCQVFLKFENLQYTASFKERGACNKLVQLTPE 65

Query: 84  ARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKSTPTVKVMQTESHGATIILEGETFD 143
            RA+GV+A SAGNHAQG+AYH  RLG+   IVMP+ TP VKV +T   GA ++L G+T D
Sbjct: 66  ERARGVVAMSAGNHAQGVAYHAQRLGLRAVIVMPRFTPGVKVERTRGFGAEVVLHGDTLD 125

Query: 144 EAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEMLADAPAIDTLIVPIGGGGLISGA 203
           EA AHAR+L A+ G  FVHP+DD  IIAGQGTV LEML   P +D L+V IGGGGLI+G 
Sbjct: 126 EARAHARELSANEGLVFVHPYDDEAIIAGQGTVALEMLRVQPDLDCLVVAIGGGGLIAGM 185

Query: 204 LTVAKAADKPIEVVGVQAELFPSMFNRFTGAHEPIGGDTLAEGIAVKEPGGLTAQIVEAL 263
            T AKA    IEV+GVQ E FPSM+N   G H P+G  T+AEGIAV  PG +T  IV   
Sbjct: 186 ATAAKAIRPGIEVIGVQTERFPSMYNAIKGTHLPMGVSTIAEGIAVASPGQITQAIVRNQ 245

Query: 264 VDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMTQPERFRGKTVGVILTGGNID 323
           VD+++LV E  +E+A+ +LL+IEKT+VEGAG+AGLAAL+  P+RF GK VG++L+GGNID
Sbjct: 246 VDDLLLVDEGDIEQAIVMLLEIEKTLVEGAGSAGLAALLKHPQRFAGKKVGLVLSGGNID 305

Query: 324 TRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVARIFQEQTVNILELSHQRIFTNLPA 383
             LLA+++ R + R+GRLAR+++  +D PG L ++  I  E   NI E+ HQR FT L A
Sbjct: 306 PLLLASIIERGMVRAGRLARIQVNARDVPGNLARITAIVAEAGANIDEVHHQRAFTLLAA 365

Query: 384 KGLSLDVECETRDRAHLERLISALQEAGYEVRLI 417
           + +++++  +TR R H+  +I  LQ  G+E  L+
Sbjct: 366 QNVAVELVLQTRGREHIAEVIRQLQAHGFEAALV 399


Lambda     K      H
   0.319    0.135    0.374 

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: 430
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: 420
Length of database: 399
Length adjustment: 31
Effective length of query: 389
Effective length of database: 368
Effective search space:   143152
Effective search space used:   143152
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_068170236.1 HTA01S_RS10060 (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.6997.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-136  439.7   3.5   5.1e-136  439.5   3.5    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068170236.1  HTA01S_RS10060 threonine ammonia


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068170236.1  HTA01S_RS10060 threonine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.5   3.5  5.1e-136  5.1e-136       1     377 [.      21     395 ..      21     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 439.5 bits;  conditional E-value: 5.1e-136
                                 TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakv 69 
                                               tp   s tls++tg +v+lk enlq t sfk rGa nk+ +l+ ee+ rGvva saGnhaqGva+ a++
  lcl|NCBI__GCF_001592305.1:WP_068170236.1  21 TPCVESRTLSQLTGCQVFLKFENLQYTASFKERGACNKLVQLTPEERARGVVAMSAGNHAQGVAYHAQR 89 
                                               78999**************************************************************** PP

                                 TIGR01127  70 fgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtl 138
                                                g++a+ivmP+++p  kv+ t+++Gaev+LhG+++Dea ++a+el ++eg+vfvh++dDe +iaGqGt+
  lcl|NCBI__GCF_001592305.1:WP_068170236.1  90 LGLRAVIVMPRFTPGVKVERTRGFGAEVVLHGDTLDEARAHARELSANEGLVFVHPYDDEAIIAGQGTV 158
                                               ********************************************************************* PP

                                 TIGR01127 139 gleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvkti 207
                                               +le+l   pd+d ++v +GGGGLi+G+a+a+k + p++ viGv++e  ps+++++k  +      v+ti
  lcl|NCBI__GCF_001592305.1:WP_068170236.1 159 ALEMLRVQPDLDCLVVAIGGGGLIAGMATAAKAIRPGIEVIGVQTERFPSMYNAIKGTHL--PMGVSTI 225
                                               ******************************************************987665..46899** PP

                                 TIGR01127 208 aDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkk 276
                                               a+Giav +pg++t  iv++ vD+++ vde +i +ai++Lle +k+++egaG++g+aa+l++     gkk
  lcl|NCBI__GCF_001592305.1:WP_068170236.1 226 AEGIAVASPGQITQAIVRNQVDDLLLVDEGDIEQAIVMLLEIEKTLVEGAGSAGLAALLKHPQRFAGKK 294
                                               ************************************************************9999***** PP

                                 TIGR01127 277 vavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskei 345
                                               v++v+sGGnid+ ll  iie+g+v+ gr+++i++   D PG+L ++++++ae++ani +++h+r  + +
  lcl|NCBI__GCF_001592305.1:WP_068170236.1 295 VGLVLSGGNIDPLLLASIIERGMVRAGRLARIQVNARDVPGNLARITAIVAEAGANIDEVHHQRAFTLL 363
                                               ********************************************************************* PP

                                 TIGR01127 346 algaakvelelevkgkehleellktlrdkgye 377
                                               a     vel l+++g+eh+ e+ ++l+++g+e
  lcl|NCBI__GCF_001592305.1:WP_068170236.1 364 AAQNVAVELVLQTRGREHIAEVIRQLQAHGFE 395
                                               *******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (399 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: 10.76
//
[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