Alignments for a candidate for tdh in Neiella marina J221

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdh in Neiella marina J221

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_087507677.1 CBE68_RS18265 L-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>NCBI__GCF_002165625.1:WP_087507677.1
          Length = 344

 Score =  588 bits (1516), Expect = e-173
 Identities = 275/340 (80%), Positives = 312/340 (91%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL+KLKAE GIWMT+VPVPELGHNDLLIKI KTAICGTD+HIY WD+WSQ+TIPVPMV
Sbjct: 1   MKALAKLKAEPGIWMTEVPVPELGHNDLLIKIHKTAICGTDLHIYKWDQWSQQTIPVPMV 60

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHEY GEVV IGQEV+GF+IGDRVSGEGHITCGHCRNCR GR HLCRNT GVGVNRPGC
Sbjct: 61  VGHEYAGEVVAIGQEVRGFEIGDRVSGEGHITCGHCRNCRAGRRHLCRNTTGVGVNRPGC 120

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAEYLVIPA+NAFK+ D+ISDDLAAIFDPFGNAVHTALSFDLVGEDVL++GAGPIGIMAA
Sbjct: 121 FAEYLVIPAYNAFKLADDISDDLAAIFDPFGNAVHTALSFDLVGEDVLITGAGPIGIMAA 180

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           AVA+H GAR+VVITDVN YRL+LAR+MG +RAV+V++++L++VM ELGMTEGFDVG+EMS
Sbjct: 181 AVARHSGARHVVITDVNRYRLDLARQMGASRAVDVSQQSLDEVMTELGMTEGFDVGMEMS 240

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G P AF  +L  MNHGG++A+LGIPPS M IDW +VIFKGL IKGIYGREMFETWYKMA+
Sbjct: 241 GVPAAFCDLLAKMNHGGKVALLGIPPSSMPIDWNQVIFKGLTIKGIYGREMFETWYKMAS 300

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340
           L+QSGLDLSP++TH + +DDFQ+GFDAM SGQ GKVIL W
Sbjct: 301 LVQSGLDLSPMLTHHYKVDDFQQGFDAMLSGQCGKVILDW 340


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: 550
Number of extensions: 20
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: 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 WP_087507677.1 CBE68_RS18265 (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.2453844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-175  567.6   0.1   4.8e-175  567.4   0.1    1.0  1  NCBI__GCF_002165625.1:WP_087507677.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002165625.1:WP_087507677.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.4   0.1  4.8e-175  4.8e-175       1     340 []       3     340 ..       3     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 567.4 bits;  conditional E-value: 4.8e-175
                             TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGee 73 
                                           al+k+kae G+++tevpvpelg+n++lik+++t+icGtd+hiy+wd+w+q++i+vp+v+Ghe+aGevv iG+e
  NCBI__GCF_002165625.1:WP_087507677.1   3 ALAKLKAEPGIWMTEVPVPELGHNDLLIKIHKTAICGTDLHIYKWDQWSQQTIPVPMVVGHEYAGEVVAIGQE 75 
                                           799********************************************************************** PP

                             TIGR00692  74 vegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqe 146
                                           v+g+++Gd+vs+e+hi+cG+c++cr+G+ h+crnt++vGv+++G+faey+v+pa n+fk  +di+++laai++
  NCBI__GCF_002165625.1:WP_087507677.1  76 VRGFEIGDRVSGEGHITCGHCRNCRAGRRHLCRNTTGVGVNRPGCFAEYLVIPAYNAFKLADDISDDLAAIFD 148
                                           ************************************************************************* PP

                             TIGR00692 147 plGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlv 219
                                           p+Gnav+t+l++dl+Ge+vl++GaGpiG++a+ava+++Ga++v+++d+n yrl+la+++Ga+r+v+v ++ l 
  NCBI__GCF_002165625.1:WP_087507677.1 149 PFGNAVHTALSFDLVGEDVLITGAGPIGIMAAAVARHSGARHVVITDVNRYRLDLARQMGASRAVDVSQQSLD 221
                                           ************************************************************************* PP

                             TIGR00692 220 kvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfe 292
                                           +v++el+++eG+dv++e+sG p a+ + l+ +++gG+vallg+p+s++ id++ +vifkgltikGi+Gr++fe
  NCBI__GCF_002165625.1:WP_087507677.1 222 EVMTELGMTEGFDVGMEMSGVPAAFCDLLAKMNHGGKVALLGIPPSSMPIDWN-QVIFKGLTIKGIYGREMFE 293
                                           ****************************************************9.9****************** PP

                             TIGR00692 293 twykvsrliqsnkldlapiithkfkldefekgfelmrsGksGkvilil 340
                                           twyk++ l+qs +ldl+p++th++k+d+f++gf++m sG++Gkvil +
  NCBI__GCF_002165625.1:WP_087507677.1 294 TWYKMASLVQS-GLDLSPMLTHHYKVDDFQQGFDAMLSGQCGKVILDW 340
                                           ***********.9********************************965 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.85
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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