Alignments for a candidate for tdcB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Paraburkholderia bryophila 376MFSha3.1

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate H281DRAFT_01887 H281DRAFT_01887 threonine ammonia-lyase, biosynthetic, long form

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__Burk376:H281DRAFT_01887
          Length = 281

 Score =  303 bits (775), Expect = 7e-87
 Identities = 149/280 (53%), Positives = 203/280 (72%), Gaps = 2/280 (0%)

Query: 235 VGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALA 294
           VGLF++G AVK +G+ETFRLC EYLDD++ V++DA+CAA+KD+F+D R+V EP+G+LA+A
Sbjct: 3   VGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVA 62

Query: 295 GMKKYIALHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLK 354
           G K+Y     I  + L  I SGAN+NF  +R+V+ER E+GE REA+ AVTIPEE+GSF +
Sbjct: 63  GAKQYAEREGIENQTLIAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRR 122

Query: 355 FCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEM 414
           FC+L+G RSVTEFNYR A A++A IFVGV++ R   E  +I        ++ VDL+ DE+
Sbjct: 123 FCELVGTRSVTEFNYRIAQAESAHIFVGVQI-RNRSESAQIAGAFEAHNFATVDLTFDEL 181

Query: 415 AKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGR 474
           +K H+RYMVGGR      ERL+ FEFPE PGAL++FL+++   WNISLFHYR+ G DY  
Sbjct: 182 SKQHIRYMVGGRSPLAHDERLFRFEFPERPGALMKFLSSMAPDWNISLFHYRNQGADYSS 241

Query: 475 VLAAFELGDHE-PDFETRLNELGYDCHDETNNPAFRFFLA 513
           +L   ++   +  +FE  L  LGY   +ET+NP +R FLA
Sbjct: 242 ILVGIQVPQTDNAEFERFLATLGYPHWEETHNPVYRLFLA 281


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: 375
Number of extensions: 17
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: 281
Length adjustment: 30
Effective length of query: 484
Effective length of database: 251
Effective search space:   121484
Effective search space used:   121484
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 threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate H281DRAFT_04606 H281DRAFT_04606 threonine ammonia-lyase, biosynthetic, long form

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__Burk376:H281DRAFT_04606
          Length = 260

 Score =  271 bits (694), Expect = 2e-77
 Identities = 138/256 (53%), Positives = 185/256 (72%), Gaps = 4/256 (1%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +YL+  L A VY+ A+ T L++  +LS+RL N + +KRED QPV SFK+RGAY  MA + 
Sbjct: 5   DYLKKTLTARVYDVARETELERAPQLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHIP 64

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGG---EVLLH 131
            E    GVITASAGNHAQGVA S+AR+GVKA+IV+P  T  +KVDAVR  GG   EV+  
Sbjct: 65  AEALTRGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQF 124

Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELL-QQDAHLDRVFVPVGGG 190
           G ++ +A   A++L +++G T+V PFD P VIAGQGT+A+E+L Q    +  +FVP+GGG
Sbjct: 125 GESYSDAYGHAVQLQEERGLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGG 184

Query: 191 GLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250
           GLAAGVA  +K + P+IKVI V+ +DS  + A+L AG  V L  VGLF++G AVK +G+E
Sbjct: 185 GLAAGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEE 244

Query: 251 TFRLCQEYLDDIITVD 266
           TFRLC EYLDD++ V+
Sbjct: 245 TFRLCSEYLDDVLLVN 260


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: 330
Number of extensions: 11
Number of successful extensions: 3
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: 260
Length adjustment: 29
Effective length of query: 485
Effective length of database: 231
Effective search space:   112035
Effective search space used:   112035
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: 49 (23.5 bits)

Align candidate H281DRAFT_01887 H281DRAFT_01887 (threonine ammonia-lyase, biosynthetic, long form)
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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.5359.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     1e-138  449.0   0.1   1.1e-138  448.8   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01887  H281DRAFT_01887 threonine ammoni


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01887  H281DRAFT_01887 threonine ammonia-lyase, biosynthetic, long form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.8   0.1  1.1e-138  1.1e-138     220     499 .]       1     280 [.       1     280 [. 1.00

  Alignments for each domain:
  == domain 1  score: 448.8 bits;  conditional E-value: 1.1e-138
                                    TIGR01124 220 dqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkk 285
                                                  ++vGlf+dG+avk vG+etfrlc eyldd++lv+td++caaikdvf+dtr+vlepaG+la+aG k+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01887   1 NEVGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQ 66 
                                                  58**************************************************************** PP

                                    TIGR01124 286 yvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGerai 351
                                                  y++++gie++tl+ai+sGan+nfdr+r+v+erae+Ge rea++avtipee+Gs+++f+e++G r++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01887  67 YAEREGIENQTLIAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSV 132
                                                  ****************************************************************** PP

                                    TIGR01124 352 tefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakve 417
                                                  tefnyr+a++e+ahifvGvq+++++e ++++  +e +++++vdlt del+k h+ry+vGGr+  ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01887 133 TEFNYRIAQAESAHIFVGVQIRNRSESAQIAGAFEAHNFATVDLTFDELSKQHIRYMVGGRSPLAH 198
                                                  ****************************************************************** PP

                                    TIGR01124 418 nerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelg 483
                                                  +erl++fefperpGal+kfl+++ ++wnislfhyrn Gady  +lvg++vp+++++efe fla+lg
  lcl|FitnessBrowser__Burk376:H281DRAFT_01887 199 DERLFRFEFPERPGALMKFLSSMAPDWNISLFHYRNQGADYSSILVGIQVPQTDNAEFERFLATLG 264
                                                  ****************************************************************** PP

                                    TIGR01124 484 yryedetenpayrlfl 499
                                                  y  ++et+np+yrlfl
  lcl|FitnessBrowser__Burk376:H281DRAFT_01887 265 YPHWEETHNPVYRLFL 280
                                                  ***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (281 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: 00:00:00.01
# Mc/sec: 8.37
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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

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 catabolism of small carbon sources