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_05256 H281DRAFT_05256 threonine ammonia-lyase, biosynthetic, long form

Query= CharProtDB::CH_024588
         (329 letters)



>FitnessBrowser__Burk376:H281DRAFT_05256
          Length = 341

 Score =  196 bits (498), Expect = 7e-55
 Identities = 109/281 (38%), Positives = 167/281 (59%), Gaps = 8/281 (2%)

Query: 18  KQRLAGRIY----KTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTDAE 73
           K+ L  R+Y    +T + R+   S R +  ++LK E+ Q   SFK+RGA+NK++ +    
Sbjct: 46  KKTLTARVYDVARETELERAPQLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHIPAEA 105

Query: 74  KRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDY---SAEVVLHGDN 130
             +GV+  SAGNHAQGV+LS A +G+   +V+P   P+ KV A   +   + EVV  G++
Sbjct: 106 LTRGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQFGES 165

Query: 131 FNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYD-VDNVIVPIGGGGLI 189
           ++D      ++ E  G  F+ P+DDP VIAGQGT+ +EI+      +  + VPIGGGGL 
Sbjct: 166 YSDAYGHAVQLQEERGLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGGLA 225

Query: 190 AGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNLTYE 249
           AG+A  +KS+ P I+VIGVQ+++   MAAS  +GE  T    G  +DG  V   G  T+ 
Sbjct: 226 AGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEETFR 285

Query: 250 IVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACA 290
           +  E +DD++LV+ D +  ++  + Q  + V E AG+LA A
Sbjct: 286 LCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVA 326


Lambda     K      H
   0.318    0.136    0.386 

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: 215
Number of extensions: 8
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: 329
Length of database: 341
Length adjustment: 28
Effective length of query: 301
Effective length of database: 313
Effective search space:    94213
Effective search space used:    94213
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate H281DRAFT_05256 H281DRAFT_05256 (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.5228.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.3e-148  481.6   2.1   1.5e-148  481.4   2.2    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05256  H281DRAFT_05256 threonine ammoni


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05256  H281DRAFT_05256 threonine ammonia-lyase, biosynthetic, long form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.4   2.2  1.5e-148  1.5e-148       1     296 [.      43     341 .]      43     341 .] 0.99

  Alignments for each domain:
  == domain 1  score: 481.4 bits;  conditional E-value: 1.5e-148
                                    TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkak 66 
                                                  dyl++ l+arvy++a et le+a +ls+rl+n v+lkred+qpvfsfk+rGaynkma+++ae+ ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05256  43 DYLKKTLTARVYDVARETELERAPQLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHIPAEALTR 108
                                                  89**************************************************************** PP

                                    TIGR01124  67 GviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakal 129
                                                  Gvi+asaGnhaqGvalsa+++Gvka+iv+p ttp++kvdav+a+Gg   evv  Ge+y++a+ +a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05256 109 GVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGptvEVVQFGESYSDAYGHAV 174
                                                  *********************************************877789*************** PP

                                    TIGR01124 130 elaqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeik 195
                                                  +l++e+gltf++pfddp viaGqGtva+e+l+q++ +++a+fvp+GGGGl+aGvaa+vk ++peik
  lcl|FitnessBrowser__Burk376:H281DRAFT_05256 175 QLQEERGLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGGLAAGVAAYVKSVRPEIK 240
                                                  ****************************************************************** PP

                                    TIGR01124 196 vigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaai 261
                                                  vigv+++ds+a++++l+aGerv+l++vGlf+dG+avk vG+etfrlc eyldd++lv+td++caai
  lcl|FitnessBrowser__Burk376:H281DRAFT_05256 241 VIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAI 306
                                                  ****************************************************************** PP

                                    TIGR01124 262 kdvfedtravlepaGalalaGlkkyvakkgiedkt 296
                                                  kdvf+dtr+vlepaG+la+aG k+y++++g+e++t
  lcl|FitnessBrowser__Burk376:H281DRAFT_05256 307 KDVFQDTRSVLEPAGSLAVAGAKQYAEREGVENQT 341
                                                  ********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (341 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.95
//
[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