Alignments for a candidate for tdcB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Dinoroseobacter shibae DFL-12

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 3610092 Dshi_3473 threonine dehydratase (RefSeq)

Query= BRENDA::Q04513
         (436 letters)



>FitnessBrowser__Dino:3610092
          Length = 413

 Score =  306 bits (785), Expect = 6e-88
 Identities = 176/414 (42%), Positives = 240/414 (57%), Gaps = 7/414 (1%)

Query: 23  AADIQTAQARISSVIAPTPLQYCPRLSEETGAEIYLKREDLQDVRSYKIRGALNSGAQLT 82
           A +   A + +  +   TPLQ    LSE  GAEI+LKREDL  VRSYKIRGA N+ ++  
Sbjct: 5   ADNAHRAASAMRPLFPATPLQMNIHLSERYGAEIWLKREDLSPVRSYKIRGAFNAISKRV 64

Query: 83  QEQRDAGIVAASAGNHAQGVAYVCKSLGVQGRIYVPVQTPKQKRDRIMVHGGEFVSLVVT 142
            E +      ASAGNHAQGVAY C+  GV G I++PV TP+QK D+  + GG  + + + 
Sbjct: 65  AEGQTQ-FACASAGNHAQGVAYACQHFGVHGVIFMPVTTPRQKIDKTRIFGGTAIDIELV 123

Query: 143 GNNFDEASAAAHEDAERTGATLIEPFDARNTVIGQGTVAAEILSQLTSMGKSADHVMVPV 202
           G+ FD+  AAA        AT + PFD  + + GQ TVA E+L QL       D V++PV
Sbjct: 124 GDYFDDTLAAAQRYCTEASATFLSPFDDADVIEGQSTVAVELLEQLEG---PPDMVILPV 180

Query: 203 GGGGLLAGVVSYMADMAPRTAIVGIEPAGAASMQAALHNGGPITLETVDPFVDGAAVKRV 262
           GGGGL +G+  Y      +  +  +EP GA S+  AL  G P TL  VD FVDGAAV R+
Sbjct: 181 GGGGLSSGMKRYFEVCGVQVDLRLVEPCGARSLAKALETGAPQTLSKVDNFVDGAAVARI 240

Query: 263 GDLNYTIVEKNQGRVHMMSATEGAVCTEMLDLYQNEGIIAEPAGALSIAGLKEM-SFAPG 321
           G   + I+ ++    H++ A E  +C  ML++   EGI+ EPAGAL++  L  +     G
Sbjct: 241 GARPFEIL-RDVPPDHVLGAPEDRICHTMLEMLNVEGIVLEPAGALAVDVLDTLRDSITG 299

Query: 322 SVVVCIISGGNNDVLRYAEIAERSLVHRGLKHYFLVNFPQKPGQLRHFLEDILGPDDDIT 381
             VVC+ SGGN D  R  E+ ERSL + GLK YF++  PQ+PG L+ FL   LGPDDDI 
Sbjct: 300 KRVVCVTSGGNFDFERLPEVKERSLRYAGLKKYFILRLPQRPGALKEFL-GFLGPDDDIA 358

Query: 382 LFEYLKRNNRETGTALVGIHLSEASGLDSLLERMEESAIDSRRLEPGTPEYEYL 435
            FEYLK++ R  G+ L+GI   +A   + L  R++ +    R +       E+L
Sbjct: 359 RFEYLKKSARNFGSVLIGIETKDAGAFEQLFARLDAAGFPFRDITEDALLAEFL 412


Lambda     K      H
   0.316    0.133    0.373 

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: 442
Number of extensions: 24
Number of successful extensions: 7
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: 436
Length of database: 413
Length adjustment: 32
Effective length of query: 404
Effective length of database: 381
Effective search space:   153924
Effective search space used:   153924
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate 3610092 Dshi_3473 (threonine dehydratase (RefSeq))
to HMM TIGR02079 (ilvA: threonine dehydratase (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/TIGR02079.hmm
# target sequence database:        /tmp/gapView.17604.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02079  [M=410]
Accession:   TIGR02079
Description: THD1: threonine dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.7e-166  538.0   0.0   7.6e-166  537.9   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610092  Dshi_3473 threonine dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610092  Dshi_3473 threonine dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.9   0.0  7.6e-166  7.6e-166       4     410 .]       9     413 .]       6     413 .] 0.97

  Alignments for each domain:
  == domain 1  score: 537.9 bits;  conditional E-value: 7.6e-166
                         TIGR02079   4 ekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynkl.kqlsdeelekgvvcasaGnhaqGv 79 
                                       ++a+  +++++  tPlq+n +lse+y+aei+lkredl+ vrsyk+rGa+n++ k++++   +  + casaGnhaqGv
  lcl|FitnessBrowser__Dino:3610092   9 HRAASAMRPLFPATPLQMNIHLSERYGAEIWLKREDLSPVRSYKIRGAFNAIsKRVAEG--QTQFACASAGNHAQGV 83 
                                       689999**********************************************4455544..45699*********** PP

                         TIGR02079  80 ayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekegktlipPfddkdiieGqgt 156
                                       ayac+++gv+g++fmPvttP+qk+dk+++fGg  i++ lvGd fd++ aaa++ + +  +t++ Pfdd d+ieGq+t
  lcl|FitnessBrowser__Dino:3610092  84 AYACQHFGVHGVIFMPVTTPRQKIDKTRIFGGTAIDIELVGDYFDDTLAAAQRYCTEASATFLSPFDDADVIEGQST 160
                                       ***************************************************************************** PP

                         TIGR02079 157 vaveileqleeekidlvlvpvGGGGlisGvtsylkekskktkiigvePeGapslkaslkagevvtldkidkfvdGaa 233
                                       vave+leqle + +d+v++pvGGGGl+sG+  y++    + ++  veP Ga sl ++l++g + tl k+d+fvdGaa
  lcl|FitnessBrowser__Dino:3610092 161 VAVELLEQLEGP-PDMVILPVGGGGLSSGMKRYFEVCGVQVDLRLVEPCGARSLAKALETGAPQTLSKVDNFVDGAA 236
                                       **********98.**************************************************************** PP

                         TIGR02079 234 vkrvGdlnfkalkkvvd.evtlveegavcstildlynkegivaePaGalsiaaleelseeikgktvvcvvsGgnndi 309
                                       v+r+G   f++l++v   +v   +e+++c t+l+++n egiv+ePaGal++  l++l++ i+gk vvcv sGgn+d+
  lcl|FitnessBrowser__Dino:3610092 237 VARIGARPFEILRDVPPdHVLGAPEDRICHTMLEMLNVEGIVLEPAGALAVDVLDTLRDSITGKRVVCVTSGGNFDF 313
                                       ***************865999******************************************************** PP

                         TIGR02079 310 erleeikersllyeGlkhyflvkfpqraGalreflndvlGPndditkfeyvkksnretGevliGielsdkedfeGll 386
                                       erl+e+kersl+y Glk+yf++++pqr+Gal+efl   lGP+ddi++fey+kks+r++G+vliGie++d+  fe l+
  lcl|FitnessBrowser__Dino:3610092 314 ERLPEVKERSLRYAGLKKYFILRLPQRPGALKEFLG-FLGPDDDIARFEYLKKSARNFGSVLIGIETKDAGAFEQLF 389
                                       ***********************************9.**************************************** PP

                         TIGR02079 387 erlkaadieyeainenetlyellv 410
                                       +rl+aa+  +++i+e+  l e+l+
  lcl|FitnessBrowser__Dino:3610092 390 ARLDAAGFPFRDITEDALLAEFLI 413
                                       *****************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (410 nodes)
Target sequences:                          1  (413 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.11
//
[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