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_2042 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2042
          Length = 519

 Score =  517 bits (1331), Expect = e-151
 Identities = 266/510 (52%), Positives = 361/510 (70%), Gaps = 12/510 (2%)

Query: 14  AEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGL 73
           A+YL+ +L A VY+ A  + L+  + LS RL N +L+KRED+QPV SFKLRGAY  MA L
Sbjct: 8   ADYLKKILTARVYDVAVESALEPAKSLSRRLHNKVLLKREDQQPVFSFKLRGAYNKMAHL 67

Query: 74  TEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGA 133
           T EQ   GVI ASAGNHAQGVA S+ +LG +A++VMPT T  +KVDAV+  GGEV+LHG 
Sbjct: 68  TPEQLQRGVICASAGNHAQGVAMSAHKLGTRAVVVMPTTTPQLKVDAVKTLGGEVVLHGE 127

Query: 134 NFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-----DAHLDRVFVPVG 188
           ++ +A   A  L ++QG T+V PFD P+VIAGQGT+A+E+L+Q        LD VFV +G
Sbjct: 128 SYSDAYEHAARLQKEQGLTFVHPFDDPLVIAGQGTIAMEILRQLQSLGSNQLDAVFVAIG 187

Query: 189 GGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIG 248
           GGGL +GVA  IK + P+IKVI V+  DS  +  +++A   V LP VGLF++G AVK +G
Sbjct: 188 GGGLVSGVANYIKAVRPEIKVIGVQMNDSDAMIQSVNAHQRVTLPDVGLFSDGTAVKLVG 247

Query: 249 DETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGE 308
           +ETFR+ Q  +D+ +TVD+DA+CAA+KD+F D R++ EP+GALA+A +K+Y+A H  +GE
Sbjct: 248 EETFRVAQGLVDEFVTVDTDAVCAAIKDIFVDTRSIVEPAGALAVAAIKQYVATHKTKGE 307

Query: 309 RLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGG-----RS 363
             A IL GAN+NF  LR+V+ER E+GE+REAL AVTIPEE+GSF +FC+++GG     R+
Sbjct: 308 TYAAILCGANMNFDRLRFVAERAEVGEEREALFAVTIPEERGSFRRFCEVVGGLPGGPRN 367

Query: 364 VTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMV 423
           VTEFNYR +DA  A +FVG+  + G  E ++I +     G+  +DL+ DE+AK H+R++V
Sbjct: 368 VTEFNYRISDAAQAHVFVGI-TTNGKGESEKIAKNFGRHGFEALDLTHDELAKEHLRHLV 426

Query: 424 GGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGD 483
           GG  +    ERL  F FPE PGALL+FL+ +   WNISLFHYR+ G DYGR+L   ++  
Sbjct: 427 GGHSALAQDERLMRFTFPERPGALLKFLSLMQPTWNISLFHYRNQGADYGRILVGIQVPP 486

Query: 484 HE-PDFETRLNELGYDCHDETNNPAFRFFL 512
            +   F+  L  LGY   +ET NPA+R FL
Sbjct: 487 EDTATFDAFLATLGYPYVEETLNPAYRLFL 516


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: 700
Number of extensions: 33
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: 519
Length adjustment: 35
Effective length of query: 479
Effective length of database: 484
Effective search space:   231836
Effective search space used:   231836
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 Ac3H11_2042 (Threonine dehydratase biosynthetic (EC 4.3.1.19))
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.13100.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.9e-248  809.6   0.5   5.5e-248  809.4   0.5    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042  Threonine dehydratase biosynthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042  Threonine dehydratase biosynthetic (EC 4.3.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  809.4   0.5  5.5e-248  5.5e-248       1     499 []       9     516 ..       9     516 .. 0.98

  Alignments for each domain:
  == domain 1  score: 809.4 bits;  conditional E-value: 5.5e-248
                                        TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsae 62 
                                                      dyl++il+arvy++ave+ le+a++ls+rl+n+vllkred+qpvfsfklrGaynkma+l++e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042   9 DYLKKILTARVYDVAVESALEPAKSLSRRLHNKVLLKREDQQPVFSFKLRGAYNKMAHLTPE 70 
                                                      89************************************************************ PP

                                        TIGR01124  63 qkakGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydea 124
                                                      q  +Gvi+asaGnhaqGva+sa+klG++av+vmp+ttp++kvdavk+ GgevvlhGe+y++a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042  71 QLQRGVICASAGNHAQGVAMSAHKLGTRAVVVMPTTTPQLKVDAVKTLGGEVVLHGESYSDA 132
                                                      ************************************************************** PP

                                        TIGR01124 125 kakalelaqekgltfiapfddplviaGqGtvalellrqve....edldavfvpvGGGGliaG 182
                                                      +++a +l++e+gltf++pfddplviaGqGt+a+e+lrq +    ++ldavfv++GGGGl++G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042 133 YEHAARLQKEQGLTFVHPFDDPLVIAGQGTIAMEILRQLQslgsNQLDAVFVAIGGGGLVSG 194
                                                      **************************************86444479**************** PP

                                        TIGR01124 183 vaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlcke 244
                                                      va ++k+++peikvigv+ +ds+a+ q+++a +rv+l +vGlf+dG+avk vG+etfr+++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042 195 VANYIKAVRPEIKVIGVQMNDSDAMIQSVNAHQRVTLPDVGLFSDGTAVKLVGEETFRVAQG 256
                                                      ************************************************************** PP

                                        TIGR01124 245 ylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanl 306
                                                      ++d++v+vdtd+vcaaikd+f dtr+++epaGala+a +k+yva+++ +++t +ail+Gan+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042 257 LVDEFVTVDTDAVCAAIKDIFVDTRSIVEPAGALAVAAIKQYVATHKTKGETYAAILCGANM 318
                                                      ************************************************************** PP

                                        TIGR01124 307 nfdrlryvseraelGeqreallavtipeekGsllkfvevlGe.....raitefnyrladdek 363
                                                      nfdrlr+v+erae+Ge+real+avtipee+Gs+++f+ev+G      r++tefnyr++d+ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042 319 NFDRLRFVAERAEVGEEREALFAVTIPEERGSFRRFCEVVGGlpggpRNVTEFNYRISDAAQ 380
                                                      ****************************************75444449************** PP

                                        TIGR01124 364 ahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfe 425
                                                      ah+fvG+ ++ + e +++++++ ++g++ +dlt+delak h+r+lvGG +a +++erl++f+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042 381 AHVFVGITTNGKGESEKIAKNFGRHGFEALDLTHDELAKEHLRHLVGGHSALAQDERLMRFT 442
                                                      ************************************************************** PP

                                        TIGR01124 426 fperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyrye 487
                                                      fperpGallkfl+ +q++wnislfhyrn GadyGr+lvg++vp+e++++f+ fla+lgy y+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042 443 FPERPGALLKFLSLMQPTWNISLFHYRNQGADYGRILVGIQVPPEDTATFDAFLATLGYPYV 504
                                                      ************************************************************** PP

                                        TIGR01124 488 detenpayrlfl 499
                                                      +et npayrlfl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2042 505 EETLNPAYRLFL 516
                                                      ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (519 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: 00:00:00.02
# Mc/sec: 10.60
//
[ok]

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

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Protein sequences (fasta format)
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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