Alignments for a candidate for tdcB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Acidovorax sp. GW101-3H11

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Ac3H11_4836 Threonine dehydratase (EC 4.3.1.19)

Query= BRENDA::Q74FW6
         (402 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4836
          Length = 399

 Score =  294 bits (752), Expect = 4e-84
 Identities = 170/396 (42%), Positives = 242/396 (61%), Gaps = 4/396 (1%)

Query: 1   MLPYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMT 60
           ML    I++A  RL+ +V  T  + S   S+ +G  ++ K ENLQ T +FK RGA N +T
Sbjct: 1   MLTLQDIRDAATRLQGQVLDTPCVESKTLSQIVGAQVFLKFENLQFTASFKERGACNRLT 60

Query: 61  SQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLT 120
               +  A+GV+  SAGNHAQGVA+ A  LG+ + + MP  TP  KV  TR +GAEVVL 
Sbjct: 61  LLSEDERARGVVAMSAGNHAQGVAYHAQRLGLRAVIVMPRFTPAVKVERTRGFGAEVVLH 120

Query: 121 GRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGG 180
           G   +EA   A    + +   FVHP+DD  V AGQGT+GLE+LQ +PD+  +++ +GGGG
Sbjct: 121 GDTLEEARQHAYALADAQRLTFVHPYDDEGVAAGQGTLGLEMLQAVPDLDTLVIAVGGGG 180

Query: 181 LIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNT 240
           LI+G+ATA +   P + ++GV+T   P+   +++     Q   T T+A+GIAV  PG  T
Sbjct: 181 LISGVATAAKAIKPGIEVVGVQTTRFPAMVNAVKGTHHPQ--GTSTIAEGIAVGTPGKIT 238

Query: 241 FPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTV-C 299
             I++ LVD++VLV+E +I  A++ LLE  K LVEGAGA  LAAL+ R      GK V  
Sbjct: 239 QEIVKRLVDDLVLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALV-RYPERFQGKRVGL 297

Query: 300 VLSGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHD 359
           VL GGNID   ++ ++ERG+V +GR  ++KV   D+PG LAR+   +A+A ANI  + H 
Sbjct: 298 VLCGGNIDPLLLAAIIERGMVRSGRLARIKVSARDVPGVLARITATVADAGANIGEVHHQ 357

Query: 360 RRSKSLPIGKTEVLIELETRGFEHIQEVISHLQGVG 395
           R    L     E+ + L+TR   H+ EV+  L+  G
Sbjct: 358 RAFTLLAAQNVEIELVLQTRSKAHVAEVLEQLRTAG 393


Lambda     K      H
   0.319    0.137    0.383 

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: 366
Number of extensions: 13
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: 402
Length of database: 399
Length adjustment: 31
Effective length of query: 371
Effective length of database: 368
Effective search space:   136528
Effective search space used:   136528
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 Ac3H11_4836 (Threonine dehydratase (EC 4.3.1.19))
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (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/TIGR01127.hmm
# target sequence database:        /tmp/gapView.5186.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-lyase
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-134  434.5   5.3     2e-134  434.3   5.3    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836  Threonine dehydratase (EC 4.3.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836  Threonine dehydratase (EC 4.3.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.3   5.3    2e-134    2e-134       1     377 [.      21     395 ..      21     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 434.3 bits;  conditional E-value: 2e-134
                                        TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqG 62 
                                                      tp   s+tls+i+ga+v+lk enlq t sfk rGa n+++ lse+e+ rGvva saGnhaqG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836  21 TPCVESKTLSQIVGAQVFLKFENLQFTASFKERGACNRLTLLSEDERARGVVAMSAGNHAQG 82 
                                                      78999********************************************************* PP

                                        TIGR01127  63 valaakvfgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvh 124
                                                      va+ a++ g++a+ivmP+++p  kv+ t+++Gaev+LhG++++ea ++a  la+++ ++fvh
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836  83 VAYHAQRLGLRAVIVMPRFTPAVKVERTRGFGAEVVLHGDTLEEARQHAYALADAQRLTFVH 144
                                                      ************************************************************** PP

                                        TIGR01127 125 afdDefviaGqGtlgleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaa 186
                                                      ++dDe v aGqGtlgle+l+ +pd+dt+++ vGGGGLisGva+a+k ++p++ v+Gv++   
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836 145 PYDDEGVAAGQGTLGLEMLQAVPDLDTLVIAVGGGGLISGVATAAKAIKPGIEVVGVQTTRF 206
                                                      ************************************************************** PP

                                        TIGR01127 187 pslveslkegkikavesvktiaDGiavkkpgdltfeivkelvDevvavdeeeiakaillLle 248
                                                      p++v+++k    ++ + ++tia+Giav +pg++t eivk lvD++v vde +i +a+l+Lle
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836 207 PAMVNAVKGT--HHPQGTSTIAEGIAVGTPGKITQEIVKRLVDDLVLVDEGDIEQAVLMLLE 266
                                                      *****99765..4567899******************************************* PP

                                        TIGR01127 249 rakivaegaGavgvaavleekvdvkgkkvavvvsGGnidlnllekiiekgLvksgrkvkiet 310
                                                       +k+++egaGa+g+aa++      +gk+v++v++GGnid+ ll  iie+g+v+sgr+++i++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836 267 IEKTLVEGAGAAGLAALVRYPERFQGKRVGLVLCGGNIDPLLLAAIIERGMVRSGRLARIKV 328
                                                      *******************8888*************************************** PP

                                        TIGR01127 311 vlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehleellktlr 372
                                                         D PG L ++++++a+++ani +++h+r  + +a    ++el l+++ k h+ e+l++lr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836 329 SARDVPGVLARITATVADAGANIGEVHHQRAFTLLAAQNVEIELVLQTRSKAHVAEVLEQLR 390
                                                      ************************************************************** PP

                                        TIGR01127 373 dkgye 377
                                                        g e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4836 391 TAGME 395
                                                      99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (399 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.55
//
[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