Alignments for a candidate for ilvA in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Burkholderia vietnamiensis G4

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_011882427.1 PLP-dependent threonine dehydratase

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000016205.1:WP_011882427.1
          Length = 507

 Score =  446 bits (1146), Expect = e-129
 Identities = 233/472 (49%), Positives = 312/472 (66%), Gaps = 2/472 (0%)

Query: 12  EGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMA 71
           E   YL ++L APVY+ A  TPL+ + +LS RL + +L+KRED QP  SFK+RGAY +MA
Sbjct: 3   EDFNYLTSILNAPVYDVAVKTPLESLSRLSERLGSRVLLKREDMQPSFSFKVRGAYTLMA 62

Query: 72  GLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLH 131
            L+ E  A GV+TASAGNHAQGVA ++  LG +A + MP  T DIKV AV  +G EV+L+
Sbjct: 63  RLSAEALARGVVTASAGNHAQGVALAAHTLGCRARVFMPHTTPDIKVQAVARYGAEVVLY 122

Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGG 191
           G NFD+A   A+  ++++  T+VPPFDHP VIAGQGT+ +E+LQQ   LD +FVP+GGGG
Sbjct: 123 GDNFDDACDAALADARERDSTFVPPFDHPHVIAGQGTVGMEILQQTTQLDAIFVPIGGGG 182

Query: 192 LAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDET 251
           LAAG+   +K++ PQI++  VE  D+  +  AL+ G PV L  VG F +GVAV+++G  +
Sbjct: 183 LAAGICAYVKRVKPQIRIFGVEPSDADSMYQALEGGAPVRLAHVGRFCDGVAVRQVGAYS 242

Query: 252 FRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLA 311
           F LC++YLD ++ VD+D +CAA+KD+F D R++ EPSGALALAG+K +      +G  L 
Sbjct: 243 FALCRQYLDGVVRVDNDEVCAAIKDVFVDTRSILEPSGALALAGLKAW-QRREQKGGTLV 301

Query: 312 HILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRF 371
            I SGAN+NF  LRY++ER  LGE REA  AV+I E  GSF    + LG   VT F+YR 
Sbjct: 302 AIASGANMNFDQLRYIAERSTLGENREARFAVSIAERPGSFRALIEQLGDCVVTAFDYRR 361

Query: 372 ADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPL 431
           A   +A +FVGVR + G E  ++I+Q L   GY   DL    + + H   +VG       
Sbjct: 362 ATGGDAQVFVGVR-TPGAEGARKIVQDLAAAGYRATDLGGSTLWRTHGHQLVGAEAFRID 420

Query: 432 QERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGD 483
            E+L+   FPE  GALL FL  L   W+ISLFHYR+ G DYGRVL     G+
Sbjct: 421 DEKLFQVMFPERRGALLEFLRKLDDAWDISLFHYRNEGFDYGRVLIGIRCGE 472


Lambda     K      H
   0.321    0.138    0.403 

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: 676
Number of extensions: 34
Number of successful extensions: 4
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: 514
Length of database: 507
Length adjustment: 35
Effective length of query: 479
Effective length of database: 472
Effective search space:   226088
Effective search space used:   226088
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: 52 (24.6 bits)

Align candidate WP_011882427.1 (PLP-dependent threonine dehydratase)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (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/TIGR01124.hmm
# target sequence database:        /tmp/gapView.22897.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01124  [M=499]
Accession:   TIGR01124
Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-205  668.0   0.0   4.7e-205  667.8   0.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011882427.1  PLP-dependent threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011882427.1  PLP-dependent threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.8   0.0  4.7e-205  4.7e-205       1     495 [.       6     498 ..       6     502 .. 0.99

  Alignments for each domain:
  == domain 1  score: 667.8 bits;  conditional E-value: 4.7e-205
                                 TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvi 69 
                                               +yl+ il+a vy++av+tple  ++lserl+ rvllkred+qp fsfk+rGay+ ma+lsae+ a+Gv+
  lcl|NCBI__GCF_000016205.1:WP_011882427.1   6 NYLTSILNAPVYDVAVKTPLESLSRLSERLGSRVLLKREDMQPSFSFKVRGAYTLMARLSAEALARGVV 74 
                                               599****************************************************************** PP

                                 TIGR01124  70 aasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekglt 138
                                               +asaGnhaqGval+a+ lG++a + mp+ttp+ikv+av  +G+evvl+G+n+d+a + al+ a+e++ t
  lcl|NCBI__GCF_000016205.1:WP_011882427.1  75 TASAGNHAQGVALAAHTLGCRARVFMPHTTPDIKVQAVARYGAEVVLYGDNFDDACDAALADARERDST 143
                                               ********************************************************************* PP

                                 TIGR01124 139 fiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaal 207
                                               f++pfd+p viaGqGtv++e+l+q++ +lda+fvp+GGGGl+aG+ a+vk+++p+i++ gve++d++++
  lcl|NCBI__GCF_000016205.1:WP_011882427.1 144 FVPPFDHPHVIAGQGTVGMEILQQTT-QLDAIFVPIGGGGLAAGICAYVKRVKPQIRIFGVEPSDADSM 211
                                               ************************99.9***************************************** PP

                                 TIGR01124 208 kqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaG 276
                                               +qale G +v+l +vG f+dGvav++vG+++f+lc++yld +v+vd devcaaikdvf dtr++lep+G
  lcl|NCBI__GCF_000016205.1:WP_011882427.1 212 YQALEGGAPVRLAHVGRFCDGVAVRQVGAYSFALCRQYLDGVVRVDNDEVCAAIKDVFVDTRSILEPSG 280
                                               ********************************************************************* PP

                                 TIGR01124 277 alalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvev 345
                                               alalaGlk++ + ++ ++ tlvai+sGan+nfd+lry++er+ lGe+rea +av+i e++Gs++ ++e 
  lcl|NCBI__GCF_000016205.1:WP_011882427.1 281 ALALAGLKAWQR-REQKGGTLVAIASGANMNFDQLRYIAERSTLGENREARFAVSIAERPGSFRALIEQ 348
                                               ********9965.567899************************************************** PP

                                 TIGR01124 346 lGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraa 414
                                               lG+  +t f+yr a   +a++fvGv++   e +++++++l  agy+  dl    l ++h   lvG  a 
  lcl|NCBI__GCF_000016205.1:WP_011882427.1 349 LGDCVVTAFDYRRATGGDAQVFVGVRTPGAEGARKIVQDLAAAGYRATDLGGSTLWRTHGHQLVGAEAF 417
                                               ********************************************************************* PP

                                 TIGR01124 415 kvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelg 483
                                               ++++e+l++  fper+Gall+fl +l+ +w+islfhyrn G dyGrvl+g+   +++++++  +l+  +
  lcl|NCBI__GCF_000016205.1:WP_011882427.1 418 RIDDEKLFQVMFPERRGALLEFLRKLDDAWDISLFHYRNEGFDYGRVLIGIRCGEADSARLYGALEATN 486
                                               ********************************************************************* PP

                                 TIGR01124 484 yryedetenpay 495
                                               +++ ++++ + y
  lcl|NCBI__GCF_000016205.1:WP_011882427.1 487 FEFSEQADASPY 498
                                               *****9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (507 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: 00:00:00.03
# Mc/sec: 7.35
//
[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