Alignments for a candidate for tdh in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdh in Maridesulfovibrio zosterae DSM 11974

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_156891687.1 H589_RS0108180 L-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>NCBI__GCF_000425265.1:WP_156891687.1
          Length = 344

 Score =  545 bits (1403), Expect = e-160
 Identities = 246/341 (72%), Positives = 296/341 (86%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL K KA+EGIWM +VPVP+ G ND+L+K++KTAICGTDVHIYNWD+W+Q+TIPVPMV
Sbjct: 4   MKALVKSKAKEGIWMEEVPVPQCGPNDVLVKVKKTAICGTDVHIYNWDKWAQQTIPVPMV 63

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHE+VG +  +G EV+G  +GDRVS EGH+TCGHCRNCR G+ HLCRNTIGVGVNRPGC
Sbjct: 64  VGHEFVGTIESMGSEVQGLDLGDRVSAEGHVTCGHCRNCRAGKRHLCRNTIGVGVNRPGC 123

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAE++ +PA N FK+ ++ISDD+A++ DP GNA HTALSFDLVGEDVL++GAGPIGIMA 
Sbjct: 124 FAEFISVPASNVFKLTESISDDVASVLDPLGNAAHTALSFDLVGEDVLITGAGPIGIMAV 183

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           A+A+H GAR++VITD+N+YRLE+A K+G ++ VNV+KE L+DVMA+L MTEGFDVGLEMS
Sbjct: 184 AIARHAGARHIVITDLNDYRLEIAGKLGASKTVNVSKEKLDDVMADLKMTEGFDVGLEMS 243

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G+P AF+ MLD MNHGG IAMLGI P    IDW KV+FKGL IKGIYGREMFETWYKMA+
Sbjct: 244 GSPAAFKDMLDKMNHGGNIAMLGIMPEGTGIDWNKVVFKGLKIKGIYGREMFETWYKMAS 303

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341
           ++QS LD++P ITH F IDDFQKGFD MRSGQSGKV+L WD
Sbjct: 304 MLQSNLDITPAITHHFKIDDFQKGFDVMRSGQSGKVVLDWD 344


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: 518
Number of extensions: 16
Number of successful extensions: 1
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_156891687.1 H589_RS0108180 (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.1170457.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-168  546.0   2.4   1.7e-168  545.9   2.4    1.0  1  NCBI__GCF_000425265.1:WP_156891687.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_156891687.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.9   2.4  1.7e-168  1.7e-168       1     340 []       6     343 ..       6     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 545.9 bits;  conditional E-value: 1.7e-168
                             TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGee 73 
                                           al+k ka+eG+++ evpvp+ g+n+vl+kvk+t+icGtdvhiynwd+waq++i+vp+v+Ghe++G ++ +G e
  NCBI__GCF_000425265.1:WP_156891687.1   6 ALVKSKAKEGIWMEEVPVPQCGPNDVLVKVKKTAICGTDVHIYNWDKWAQQTIPVPMVVGHEFVGTIESMGSE 78 
                                           799********************************************************************** PP

                             TIGR00692  74 vegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqe 146
                                           v+g+++Gd+vsae+h++cG+c++cr+Gk h+crnt++vGv+++G+fae++ vpa+n+fk  ++i++++a++ +
  NCBI__GCF_000425265.1:WP_156891687.1  79 VQGLDLGDRVSAEGHVTCGHCRNCRAGKRHLCRNTIGVGVNRPGCFAEFISVPASNVFKLTESISDDVASVLD 151
                                           ************************************************************************* PP

                             TIGR00692 147 plGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlv 219
                                           plGna +t+l++dl+Ge+vl++GaGpiG++ava+a++aGa++++++d n+yrle+a k+Ga+++vnv ke+l 
  NCBI__GCF_000425265.1:WP_156891687.1 152 PLGNAAHTALSFDLVGEDVLITGAGPIGIMAVAIARHAGARHIVITDLNDYRLEIAGKLGASKTVNVSKEKLD 224
                                           ************************************************************************* PP

                             TIGR00692 220 kvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfe 292
                                           +v+a+l ++eG+dv+le+sG+p a++++ld +++gG +a+lg+ ++   id++ kv+fkgl ikGi+Gr++fe
  NCBI__GCF_000425265.1:WP_156891687.1 225 DVMADLKMTEGFDVGLEMSGSPAAFKDMLDKMNHGGNIAMLGIMPEGTGIDWN-KVVFKGLKIKGIYGREMFE 296
                                           ****************************************************9.******************* PP

                             TIGR00692 293 twykvsrliqsnkldlapiithkfkldefekgfelmrsGksGkvilil 340
                                           twyk++ ++qs +ld++p ith+fk+d+f+kgf++mrsG+sGkv+l +
  NCBI__GCF_000425265.1:WP_156891687.1 297 TWYKMASMLQS-NLDITPAITHHFKIDDFQKGFDVMRSGQSGKVVLDW 343
                                           ***********.8********************************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: 00:00:00.00
# Mc/sec: 23.55
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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