Alignments for a candidate for tdcB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Burkholderia phytofirmans PsJN

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate BPHYT_RS03145 BPHYT_RS03145 threonine dehydratase

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__BFirm:BPHYT_RS03145
          Length = 507

 Score =  525 bits (1352), Expect = e-153
 Identities = 268/504 (53%), Positives = 359/504 (71%), Gaps = 6/504 (1%)

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

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

Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGG 190
           G ++ +A   A++L +++  T+V PFD P VIAGQGT+A+E+L Q    +  +FVP+GGG
Sbjct: 125 GESYSDAYEHAVKLQKERDLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGG 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 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERL 310
           TFRLC EYLDD++ V++DA+CAA+KD+F+D R+V EP+G+LA+AG K+Y     I  + L
Sbjct: 245 TFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQYAEREGIENQTL 304

Query: 311 AHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYR 370
             I SGAN+NF  +R+V+ER E+GE REA+ AVTIPEE+GSF +FC+L+G RSVTEFNYR
Sbjct: 305 IAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSVTEFNYR 364

Query: 371 FADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHP 430
            ADA +A IFVGV++ R   E  +I       G++ VDL+ DE++K H+RYMVGGR    
Sbjct: 365 IADANSAHIFVGVQI-RNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLA 423

Query: 431 LQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPD-FE 489
             ERL+ FEFPE PGAL++FL+++   WNISLFHYR+ G DY  +L   ++ D E + F 
Sbjct: 424 HDERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFN 483

Query: 490 TRLNELGYDCHDETNNPAFRFFLA 513
             L  LGY   +ET NP +R FLA
Sbjct: 484 KFLATLGYPNWEETQNPVYRLFLA 507


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: 650
Number of extensions: 27
Number of successful extensions: 6
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 BPHYT_RS03145 BPHYT_RS03145 (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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.22958.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.8e-251  820.9   0.4     2e-251  820.8   0.4    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS03145  BPHYT_RS03145 threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS03145  BPHYT_RS03145 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.8   0.4    2e-251    2e-251       1     499 []       5     506 ..       5     506 .. 1.00

  Alignments for each domain:
  == domain 1  score: 820.8 bits;  conditional E-value: 2e-251
                                TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 
                                              dyl++ l+arvy++a et le+a +ls+rl+n v+lkred+qpvfsfk+rGaynkma++sae+  +Gvi+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145   5 DYLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHISAEALERGVIT 74 
                                              89******************************************************************** PP

                                TIGR01124  71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakalelaqekgl 137
                                              asaGnhaqGvalsa+++Gvka+iv+p ttp++kvdav+a+Gg   evv  Ge+y++a+++a++l++e++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145  75 ASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGptvEVVQFGESYSDAYEHAVKLQKERDL 144
                                              *****************************************877789*********************** PP

                                TIGR01124 138 tfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaal 207
                                              tf++pfddp viaGqGtva+e+l+q++ +++a+fvp+GGGGl+aGvaa+vk ++peikvigv+++ds+a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 145 TFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGGLAAGVAAYVKSVRPEIKVIGVQTDDSCAM 214
                                              ********************************************************************** PP

                                TIGR01124 208 kqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277
                                              +++l+aGerv+l++vGlf+dG+avk vG+etfrlc eyldd++lv+td++caaikdvf+dtr+vlepaG+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 215 AASLKAGERVTLNEVGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGS 284
                                              ********************************************************************** PP

                                TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlG 347
                                              la+aG k+y++++gie++tl+ai+sGan+nfdr+r+v+erae+Ge rea++avtipee+Gs+++f+e++G
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 285 LAVAGAKQYAEREGIENQTLIAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVG 354
                                              ********************************************************************** PP

                                TIGR01124 348 eraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakve 417
                                               r++tefnyr+ad+++ahifvGvq+++++e ++++  +e +g+++vdlt del+k h+ry+vGGr+  ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 355 TRSVTEFNYRIADANSAHIFVGVQIRNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLAH 424
                                              ********************************************************************** PP

                                TIGR01124 418 nerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyrye 487
                                              +erl++fefperpGal+kfl+++ ++wnislfhyrn Gady  +lvg++vpd+e+e+f++fla+lgy  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 425 DERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFNKFLATLGYPNW 494
                                              ********************************************************************** PP

                                TIGR01124 488 detenpayrlfl 499
                                              +et+np+yrlfl
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 495 EETQNPVYRLFL 506
                                              ***********8 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.30
//
[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