Alignments for a candidate for tdh in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdh in Shewanella amazonensis SB2B

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 6935882 Sama_0097 L-threonine 3-dehydrogenase (RefSeq)

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__SB2B:6935882
          Length = 341

 Score =  632 bits (1630), Expect = 0.0
 Identities = 302/341 (88%), Positives = 320/341 (93%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL+KLK EEGIWM D P PE+GHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV
Sbjct: 1   MKALAKLKPEEGIWMVDAPKPEMGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHEYVGEVVGIGQEV+GFKIGDRVSGEGHITCGHCRNCR GRTHLCRNT GVGVNR G 
Sbjct: 61  VGHEYVGEVVGIGQEVRGFKIGDRVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNREGS 120

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAEYLVIPAFNAFKIPD+ISDDLAAIFDPFGNAVHTALSFDLVGEDVL++GAGPIGIMAA
Sbjct: 121 FAEYLVIPAFNAFKIPDDISDDLAAIFDPFGNAVHTALSFDLVGEDVLITGAGPIGIMAA 180

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           AV +HVGAR+VVITDVNEYRLELARKMG TRAVNVAKENL DVM +LGMTEGFDVGLEMS
Sbjct: 181 AVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAKENLKDVMKDLGMTEGFDVGLEMS 240

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G P AF  MLDTMNHGG+IAMLGIP  +M+IDW+KVIFKGL IKGIYGREMFETWYKMA+
Sbjct: 241 GVPAAFHAMLDTMNHGGKIAMLGIPGGEMAIDWSKVIFKGLIIKGIYGREMFETWYKMAS 300

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341
           L+QSGLDLSPI+TH F +DDFQ+GFDAMRSGQSGKVILSWD
Sbjct: 301 LLQSGLDLSPIVTHHFKVDDFQQGFDAMRSGQSGKVILSWD 341


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: 591
Number of extensions: 17
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: 341
Length adjustment: 29
Effective length of query: 312
Effective length of database: 312
Effective search space:    97344
Effective search space used:    97344
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 6935882 Sama_0097 (L-threonine 3-dehydrogenase (RefSeq))
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.27435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.5e-183  594.6   1.3   2.9e-183  594.5   1.3    1.0  1  lcl|FitnessBrowser__SB2B:6935882  Sama_0097 L-threonine 3-dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6935882  Sama_0097 L-threonine 3-dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.5   1.3  2.9e-183  2.9e-183       1     340 []       3     340 ..       3     340 .. 1.00

  Alignments for each domain:
  == domain 1  score: 594.5 bits;  conditional E-value: 2.9e-183
                         TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGeevegv 77 
                                       al+k+k+eeG+++++ p pe+g+n++lik+++t+icGtdvhiynwdew+qk+i+vp+v+Ghe++GevvgiG+ev+g+
  lcl|FitnessBrowser__SB2B:6935882   3 ALAKLKPEEGIWMVDAPKPEMGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVGIGQEVRGF 79 
                                       799************************************************************************** PP

                         TIGR00692  78 kvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqeplGnavdt 154
                                       k+Gd+vs+e+hi+cG+c++cr+G++h+crnt++vGv+++G faey+v+pa+n+fk+p+di+++laai++p+Gnav+t
  lcl|FitnessBrowser__SB2B:6935882  80 KIGDRVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNREGSFAEYLVIPAFNAFKIPDDISDDLAAIFDPFGNAVHT 156
                                       ***************************************************************************** PP

                         TIGR00692 155 vlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlvkvvaeltsgeGv 231
                                       +l++dl+Ge+vl++GaGpiG++a+av +++Ga++v+++d+neyrlela+k+Gatr+vnvake+l +v+ +l+++eG+
  lcl|FitnessBrowser__SB2B:6935882 157 ALSFDLVGEDVLITGAGPIGIMAAAVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAKENLKDVMKDLGMTEGF 233
                                       ***************************************************************************** PP

                         TIGR00692 232 dvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldl 308
                                       dv+le+sG p a++ +ld++++gG++a+lg+p ++++id++ kvifkgl+ikGi+Gr++fetwyk++ l+qs +ldl
  lcl|FitnessBrowser__SB2B:6935882 234 DVGLEMSGVPAAFHAMLDTMNHGGKIAMLGIPGGEMAIDWS-KVIFKGLIIKGIYGREMFETWYKMASLLQS-GLDL 308
                                       ****************************************9.******************************.9*** PP

                         TIGR00692 309 apiithkfkldefekgfelmrsGksGkvilil 340
                                       +pi+th+fk+d+f++gf++mrsG+sGkvil++
  lcl|FitnessBrowser__SB2B:6935882 309 SPIVTHHFKVDDFQQGFDAMRSGQSGKVILSW 340
                                       ******************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (341 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.95
//
[ok]

This GapMind analysis is from Sep 17 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 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