Alignments for a candidate for tdh in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdh in Shewanella loihica PV-4

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 5211294 Shew_3710 L-threonine 3-dehydrogenase (RefSeq)

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__PV4:5211294
          Length = 341

 Score =  622 bits (1605), Expect = 0.0
 Identities = 298/341 (87%), Positives = 318/341 (93%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKALSKLK EEGIWM D P PE+GHNDLLIKIRKTAICGTDVHIYNWDEWSQ TIPVPMV
Sbjct: 1   MKALSKLKPEEGIWMVDAPKPEVGHNDLLIKIRKTAICGTDVHIYNWDEWSQNTIPVPMV 60

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHEYVGEVV IGQEV+GF+IGDRVSGEGHITCGHCRNCR GRTHLCRNT GVGVNR G 
Sbjct: 61  VGHEYVGEVVEIGQEVRGFQIGDRVSGEGHITCGHCRNCRAGRTHLCRNTSGVGVNREGA 120

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAEYLVIPAFNAFKIPD+ISDDLA+IFDPFGNAVHTALSFDLVGEDVL++GAGPIGIMAA
Sbjct: 121 FAEYLVIPAFNAFKIPDDISDDLASIFDPFGNAVHTALSFDLVGEDVLITGAGPIGIMAA 180

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           AV +HVGAR+VVITDVNEYRLELA+KMG TRAVNVAKE L DVM +LGMTEGFDVGLEMS
Sbjct: 181 AVCRHVGARHVVITDVNEYRLELAKKMGATRAVNVAKEKLEDVMQDLGMTEGFDVGLEMS 240

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G P AF +MLDTMNHGG+IAMLGIP  DM+IDW+KVIFKGL IKGIYGREMFETWYKMA+
Sbjct: 241 GVPAAFHSMLDTMNHGGKIAMLGIPGGDMAIDWSKVIFKGLIIKGIYGREMFETWYKMAS 300

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341
           LIQSGLD+SPIITH +++DDFQ GFDAMRSGQSGKVILSWD
Sbjct: 301 LIQSGLDISPIITHHYNVDDFQAGFDAMRSGQSGKVILSWD 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: 575
Number of extensions: 18
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 5211294 Shew_3710 (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.4185.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.4e-182  590.9   1.5   3.8e-182  590.8   1.5    1.0  1  lcl|FitnessBrowser__PV4:5211294  Shew_3710 L-threonine 3-dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211294  Shew_3710 L-threonine 3-dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.8   1.5  3.8e-182  3.8e-182       1     340 []       3     340 ..       3     340 .. 1.00

  Alignments for each domain:
  == domain 1  score: 590.8 bits;  conditional E-value: 3.8e-182
                        TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGeevegvk 78 
                                      al+k+k+eeG+++++ p pe+g+n++lik+++t+icGtdvhiynwdew+q++i+vp+v+Ghe++Gevv+iG+ev+g++
  lcl|FitnessBrowser__PV4:5211294   3 ALSKLKPEEGIWMVDAPKPEVGHNDLLIKIRKTAICGTDVHIYNWDEWSQNTIPVPMVVGHEYVGEVVEIGQEVRGFQ 80 
                                      89**************************************************************************** PP

                        TIGR00692  79 vGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqeplGnavdtvl 156
                                      +Gd+vs+e+hi+cG+c++cr+G++h+crnt +vGv+++G+faey+v+pa+n+fk+p+di+++la+i++p+Gnav+t+l
  lcl|FitnessBrowser__PV4:5211294  81 IGDRVSGEGHITCGHCRNCRAGRTHLCRNTSGVGVNREGAFAEYLVIPAFNAFKIPDDISDDLASIFDPFGNAVHTAL 158
                                      ****************************************************************************** PP

                        TIGR00692 157 esdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlvkvvaeltsgeGvdvv 234
                                      ++dl+Ge+vl++GaGpiG++a+av +++Ga++v+++d+neyrlelakk+Gatr+vnvake+l +v+++l+++eG+dv+
  lcl|FitnessBrowser__PV4:5211294 159 SFDLVGEDVLITGAGPIGIMAAAVCRHVGARHVVITDVNEYRLELAKKMGATRAVNVAKEKLEDVMQDLGMTEGFDVG 236
                                      ****************************************************************************** PP

                        TIGR00692 235 lelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldlapii 312
                                      le+sG p a++ +ld++++gG++a+lg+p ++++id++ kvifkgl+ikGi+Gr++fetwyk++ liqs +ld++pii
  lcl|FitnessBrowser__PV4:5211294 237 LEMSGVPAAFHSMLDTMNHGGKIAMLGIPGGDMAIDWS-KVIFKGLIIKGIYGREMFETWYKMASLIQS-GLDISPII 312
                                      *************************************9.******************************.9******* PP

                        TIGR00692 313 thkfkldefekgfelmrsGksGkvilil 340
                                      th++++d+f+ gf++mrsG+sGkvil++
  lcl|FitnessBrowser__PV4:5211294 313 THHYNVDDFQAGFDAMRSGQSGKVILSW 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 10.19
//
[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