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.11765.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.79
//
[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:

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:

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:

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:

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