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.17440.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.33
//
[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:

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:

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:

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:

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