Alignments for a candidate for ilvA in Salinicoccus carnicancri Crm

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Salinicoccus carnicancri Crm

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_169315527.1 C792_RS0105325 threonine ammonia-lyase

Query= SwissProt::Q9WYJ1
         (401 letters)



>NCBI__GCF_000330705.1:WP_169315527.1
          Length = 342

 Score =  297 bits (761), Expect = 3e-85
 Identities = 148/308 (48%), Positives = 215/308 (69%), Gaps = 1/308 (0%)

Query: 7   IKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLSEEE 66
           + +A + L  VVH+T +  S+  +  TG  IY KMEN QKTG+FK RGA  K+  LS +E
Sbjct: 17  VHDAWKRLDPVVHQTPIRTSATTNLRTGKNIYFKMENQQKTGAFKFRGASYKLMRLSPKE 76

Query: 67  RKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGNIFDE 126
             RGV+ ASAGNHAQG+ALAA   G+ ATI M    P +K+  TR  GA+V+L G  F E
Sbjct: 77  LDRGVITASAGNHAQGLALAAYKLGVKATIYMAEATPEAKVEATRGYGAEVVLTGESFQE 136

Query: 127 AYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGGLISGVS 186
           A+EA+L+ QE+ GA +VHPF+D  ++AGQGTI LE++E +  ++ +VVP+GGGGLISG++
Sbjct: 137 AFEASLKQQERCGATYVHPFDDYDIMAGQGTIALELLEQVNTIDTIVVPIGGGGLISGIA 196

Query: 187 VAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTFELVKK 246
           V  KS+NP++KVIGVQ +  P+M  +  RG  ++++   T+A+GIAVK+PG+ T  L+  
Sbjct: 197 VGAKSVNPDIKVIGVQAKAAPAMHTAYHRGVVKKLDKVSTIAEGIAVKQPGENTLPLINN 256

Query: 247 YVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVLNKLD-VKGKKVAIVISGGNI 305
           YVD+++ V+EEEIADAI+ +LE+ K + EGAGA   A +L+  D +  +   +++SGGN 
Sbjct: 257 YVDDIITVSEEEIADAIVNMLERGKSLVEGAGAAAFAGLLSHNDQIDSRHCGVIVSGGNF 316

Query: 306 DVNMIDRI 313
           D++ +  I
Sbjct: 317 DISRMAEI 324


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: 303
Number of extensions: 12
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: 342
Length adjustment: 30
Effective length of query: 371
Effective length of database: 312
Effective search space:   115752
Effective search space used:   115752
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: 49 (23.5 bits)

Align candidate WP_169315527.1 C792_RS0105325 (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.634403.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-120  386.3   5.0   9.1e-120  386.0   5.0    1.0  1  NCBI__GCF_000330705.1:WP_169315527.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_169315527.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.0   5.0  9.1e-120  9.1e-120       1     294 [.      31     324 ..      31     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 386.0 bits;  conditional E-value: 9.1e-120
                             TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgik 73 
                                           tp+  s+t    tg ++y+k+en qktG+fk rGa +k+ +ls +e +rGv++asaGnhaqG alaa + g+k
  NCBI__GCF_000330705.1:WP_169315527.1  31 TPIRTSATTNLRTGKNIYFKMENQQKTGAFKFRGASYKLMRLSPKELDRGVITASAGNHAQGLALAAYKLGVK 103
                                           89999999999************************************************************** PP

                             TIGR01127  74 akivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledl 146
                                           a+i m e +p +kv+at++yGaev+L G++f ea++++ + +e+ g+++vh+fdD  ++aGqGt++le+le++
  NCBI__GCF_000330705.1:WP_169315527.1 104 ATIYMAEATPEAKVEATRGYGAEVVLTGESFQEAFEASLKQQERCGATYVHPFDDYDIMAGQGTIALELLEQV 176
                                           ************************************************************************* PP

                             TIGR01127 147 pdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdl 219
                                            ++dt++vP+GGGGLisG+a+ +k++np++kviGv+a+aap++  ++++g +k+ ++v+tia+Giavk+pg+ 
  NCBI__GCF_000330705.1:WP_169315527.1 177 NTIDTIVVPIGGGGLISGIAVGAKSVNPDIKVIGVQAKAAPAMHTAYHRGVVKKLDKVSTIAEGIAVKQPGEN 249
                                           ************************************************************************* PP

                             TIGR01127 220 tfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkkvavvvsGGnidlnlle 292
                                           t ++++++vD++++v+eeeia+ai+ +ler k ++egaGa++ a +l++  + + ++ +v+vsGGn d+  + 
  NCBI__GCF_000330705.1:WP_169315527.1 250 TLPLINNYVDDIITVSEEEIADAIVNMLERGKSLVEGAGAAAFAGLLSHNDQIDSRHCGVIVSGGNFDISRMA 322
                                           ************************************************99999999*************9998 PP

                             TIGR01127 293 ki 294
                                           +i
  NCBI__GCF_000330705.1:WP_169315527.1 323 EI 324
                                           87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (342 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: 00:00:00.00
# Mc/sec: 13.18
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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