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 L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate H281DRAFT_01167 H281DRAFT_01167 threonine ammonia-lyase, biosynthetic, long form

Query= curated2:P53607
         (507 letters)



>FitnessBrowser__Burk376:H281DRAFT_01167
          Length = 281

 Score =  481 bits (1237), Expect = e-140
 Identities = 239/280 (85%), Positives = 257/280 (91%)

Query: 228 EVGLFADGTAVKLVGEETFRLCKEYLDGVVTVDTDALCAAIKDVFQDTRSVLEPSGALAV 287
           EVGLF+DGTAVKLVGEETFRLC EYLD V+ V+TDALCAAIKDVFQDTRSVLEP+G+LAV
Sbjct: 2   EVGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAV 61

Query: 288 AGAKLYAEREGIENQTLVAVTSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFK 347
           AGAK YAEREG+ENQTL+A+TSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSF+
Sbjct: 62  AGAKQYAEREGVENQTLIAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFR 121

Query: 348 RFCSLVGDRNVTEFNYRIADAQSAHIFVGVQIRRRGESADIAANFESHGFKTADLTHDEL 407
           RFC LVG R+VTEFNYRIA A+SAHIFVGVQIR R ESA IA  FE+H F T DLT DEL
Sbjct: 122 RFCELVGTRSVTEFNYRIAQAESAHIFVGVQIRNRSESAQIAGAFEAHNFATVDLTFDEL 181

Query: 408 SKEHIRYMVGGRSPLALDERLFRFEFPERPGALMKFLSSMAPDWNISLFHYRNQGADYSS 467
           SK+HIRYMVGGRSPLA DERLFRFEFPERPGALMKFLSSMAPDWNISLFHYRNQGADYSS
Sbjct: 182 SKQHIRYMVGGRSPLAHDERLFRFEFPERPGALMKFLSSMAPDWNISLFHYRNQGADYSS 241

Query: 468 ILVGLQVPQADHAEFERFLAALGYPYVEESANPAYRLFLS 507
           ILVG+QVPQ D+AEFERFLA LGYP+ EE+ N  YRLFL+
Sbjct: 242 ILVGIQVPQTDNAEFERFLATLGYPHWEETHNSVYRLFLA 281


Lambda     K      H
   0.320    0.135    0.388 

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: 452
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: 507
Length of database: 281
Length adjustment: 30
Effective length of query: 477
Effective length of database: 251
Effective search space:   119727
Effective search space used:   119727
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 candidate H281DRAFT_01167 H281DRAFT_01167 (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.31652.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.2e-138  447.0   0.2   4.6e-138  446.8   0.2    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01167  H281DRAFT_01167 threonine ammoni


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01167  H281DRAFT_01167 threonine ammonia-lyase, biosynthetic, long form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.8   0.2  4.6e-138  4.6e-138     220     499 .]       1     280 [.       1     280 [. 1.00

  Alignments for each domain:
  == domain 1  score: 446.8 bits;  conditional E-value: 4.6e-138
                                    TIGR01124 220 dqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkk 285
                                                  ++vGlf+dG+avk vG+etfrlc eyldd++lv+td++caaikdvf+dtr+vlepaG+la+aG k+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01167   1 NEVGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQ 66 
                                                  58**************************************************************** PP

                                    TIGR01124 286 yvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGerai 351
                                                  y++++g+e++tl+ai+sGan+nfdr+r+v+erae+Ge rea++avtipee+Gs+++f+e++G r++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01167  67 YAEREGVENQTLIAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSV 132
                                                  ****************************************************************** PP

                                    TIGR01124 352 tefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakve 417
                                                  tefnyr+a++e+ahifvGvq+++++e ++++  +e +++++vdlt del+k h+ry+vGGr+  ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01167 133 TEFNYRIAQAESAHIFVGVQIRNRSESAQIAGAFEAHNFATVDLTFDELSKQHIRYMVGGRSPLAH 198
                                                  ****************************************************************** PP

                                    TIGR01124 418 nerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelg 483
                                                  +erl++fefperpGal+kfl+++ ++wnislfhyrn Gady  +lvg++vp+++++efe fla+lg
  lcl|FitnessBrowser__Burk376:H281DRAFT_01167 199 DERLFRFEFPERPGALMKFLSSMAPDWNISLFHYRNQGADYSSILVGIQVPQTDNAEFERFLATLG 264
                                                  ****************************************************************** PP

                                    TIGR01124 484 yryedetenpayrlfl 499
                                                  y  ++et+n++yrlfl
  lcl|FitnessBrowser__Burk376:H281DRAFT_01167 265 YPHWEETHNSVYRLFL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.04
# Mc/sec: 3.16
//
[ok]

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

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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

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