Alignments for a candidate for tdh in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdh in Dyella japonica UNC79MFTsu3.2

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0039
          Length = 344

 Score =  476 bits (1224), Expect = e-139
 Identities = 221/340 (65%), Positives = 267/340 (78%), Gaps = 1/340 (0%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL K   E+GIWM +VPVPE+G N++LIK+ KTAICGTD+HIY WDEWSQ+TI   + 
Sbjct: 5   MKALVKRLPEQGIWMEEVPVPEVGPNEVLIKMEKTAICGTDLHIYKWDEWSQRTIKPGLT 64

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           +GHE+VG +V IG  V G+K+GDRVS EGHI CGHCRNCR GR HLC NT+G+GVNR G 
Sbjct: 65  IGHEFVGRIVDIGPGVTGYKVGDRVSAEGHIVCGHCRNCRAGRQHLCPNTVGIGVNRNGA 124

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAEY+ +PA N + IPD I  +LAA FDP+GNA H AL FDL+GEDVL++GAGPIGI+AA
Sbjct: 125 FAEYMTMPASNLWPIPDQIPSELAAFFDPYGNAAHCALEFDLIGEDVLITGAGPIGIIAA 184

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
            +AKHVGARNVV+TDVN+YRL+LA  MG TR VNVA ++L DV+ +L + EGFDVGLEMS
Sbjct: 185 GIAKHVGARNVVVTDVNDYRLKLAADMGATRVVNVANQSLRDVVKDLHI-EGFDVGLEMS 243

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G P AF  MLD M HGG+IA+LGI P    IDW KVIFKGL ++GIYGR M+ETWYKM  
Sbjct: 244 GNPRAFNDMLDCMYHGGKIALLGIMPRGAGIDWDKVIFKGLTLQGIYGRRMYETWYKMTQ 303

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340
           ++ SG  L  ++TH+  IDDFQKGFD M +G  GKV+ SW
Sbjct: 304 MVLSGFPLQKVLTHQIHIDDFQKGFDLMDAGHCGKVVCSW 343


Lambda     K      H
   0.322    0.140    0.433 

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: 481
Number of extensions: 12
Number of successful extensions: 2
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: 341
Length of database: 344
Length adjustment: 29
Effective length of query: 312
Effective length of database: 315
Effective search space:    98280
Effective search space used:    98280
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate N515DRAFT_0039 N515DRAFT_0039 (L-threonine 3-dehydrogenase)
to HMM TIGR00692 (tdh: L-threonine 3-dehydrogenase (EC 1.1.1.103))

# 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/TIGR00692.hmm
# target sequence database:        /tmp/gapView.28540.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00692  [M=340]
Accession:   TIGR00692
Description: tdh: L-threonine 3-dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.1e-154  499.0   0.3   3.5e-154  498.8   0.3    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0039  N515DRAFT_0039 L-threonine 3-deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0039  N515DRAFT_0039 L-threonine 3-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.8   0.3  3.5e-154  3.5e-154       1     340 []       7     343 ..       7     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 498.8 bits;  conditional E-value: 3.5e-154
                                    TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGe 66 
                                                  al+k+ +e+G+++ evpvpe+g+nevlik+++t+icGtd+hiy+wdew+q++ik+   +Ghe++G 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0039   7 ALVKRLPEQGIWMEEVPVPEVGPNEVLIKMEKTAICGTDLHIYKWDEWSQRTIKPGLTIGHEFVGR 72 
                                                  79999************************************************************* PP

                                    TIGR00692  67 vvgiGeevegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifk 132
                                                  +v+iG++v g kvGd+vsae+hivcG+c++cr+G++h+c nt+++Gv+++G+faey+ +pa+n++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0039  73 IVDIGPGVTGYKVGDRVSAEGHIVCGHCRNCRAGRQHLCPNTVGIGVNRNGAFAEYMTMPASNLWP 138
                                                  ****************************************************************** PP

                                    TIGR00692 133 npkdidpelaaiqeplGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyr 198
                                                  +p++i+ elaa ++p+Gna + +le+dl Ge+vl++GaGpiG++a+ +ak++Ga++v+v+d+n+yr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 139 IPDQIPSELAAFFDPYGNAAHCALEFDLIGEDVLITGAGPIGIIAAGIAKHVGARNVVVTDVNDYR 204
                                                  ****************************************************************** PP

                                    TIGR00692 199 lelakkvGatrvvnvakedlvkvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpe 264
                                                  l+la  +Gatrvvnva++ l +vv +l   eG+dv+le+sG+p+a++++ld + +gG++allg+ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 205 LKLAADMGATRVVNVANQSLRDVVKDLH-IEGFDVGLEMSGNPRAFNDMLDCMYHGGKIALLGIMP 269
                                                  **************************96.69*********************************** PP

                                    TIGR00692 265 skvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldlapiithkfkldefekgfelmrs 330
                                                      id+  kvifkglt++Gi+Gr+++etwyk+++++ s ++ l+ ++th+ ++d+f+kgf+lm +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 270 RGAGIDWD-KVIFKGLTLQGIYGRRMYETWYKMTQMVLS-GFPLQKVLTHQIHIDDFQKGFDLMDA 333
                                                  *******9.******************************.89************************ PP

                                    TIGR00692 331 GksGkvilil 340
                                                  G++Gkv+ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 334 GHCGKVVCSW 343
                                                  ******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (344 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: 7.22
//
[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