GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Shewanella oneidensis MR-1

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 203742 SO4673 threonine 3-dehydrogenase (NCBI ptt file)

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__MR1:203742
          Length = 341

 Score =  624 bits (1608), Expect = 0.0
 Identities = 299/341 (87%), Positives = 319/341 (93%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKALSKLKAE+GIW+ D P PE+GHNDLLIKI+KTAICGTD+HIYNWDEWSQKTIPVPMV
Sbjct: 1   MKALSKLKAEKGIWLVDAPKPEMGHNDLLIKIKKTAICGTDMHIYNWDEWSQKTIPVPMV 60

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

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

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           AV +HVGAR+VVITDVNEYRLELARKMG TRAVNVA+ENL DVM ELGMTEGFDVGLEMS
Sbjct: 181 AVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAQENLKDVMKELGMTEGFDVGLEMS 240

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G P AFR MLDTMNHGG+IAMLGIP  +M+IDW+KVIFKGL IKGIYGREMFETWYKMA+
Sbjct: 241 GVPSAFRAMLDTMNHGGKIAMLGIPGGEMAIDWSKVIFKGLVIKGIYGREMFETWYKMAS 300

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341
           LIQSGLD+SPIITH + IDDFQKGFDAM SGQSGKVILSWD
Sbjct: 301 LIQSGLDISPIITHHYKIDDFQKGFDAMGSGQSGKVILSWD 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: 586
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 203742 SO4673 (threonine 3-dehydrogenase (NCBI ptt file))
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.6480.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.7e-182  589.4   1.6   1.1e-181  589.3   1.6    1.0  1  lcl|FitnessBrowser__MR1:203742  SO4673 threonine 3-dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203742  SO4673 threonine 3-dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  589.3   1.6  1.1e-181  1.1e-181       1     340 []       3     340 ..       3     340 .. 1.00

  Alignments for each domain:
  == domain 1  score: 589.3 bits;  conditional E-value: 1.1e-181
                       TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGeevegvkv 79 
                                     al+k+kae G++l++ p pe+g+n++lik+k+t+icGtd+hiynwdew+qk+i+vp+v+Ghe++Gevv+iG+ev+g+++
  lcl|FitnessBrowser__MR1:203742   3 ALSKLKAEKGIWLVDAPKPEMGHNDLLIKIKKTAICGTDMHIYNWDEWSQKTIPVPMVVGHEYVGEVVDIGQEVRGFNI 81 
                                     89***************************************************************************** PP

                       TIGR00692  80 GdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqeplGnavdtvles 158
                                     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__MR1:203742  82 GDRVSGEGHITCGHCRNCRAGRTHLCRNTSGVGVNREGSFAEYLVIPAFNAFKIPDDISDDLASIFDPFGNAVHTALSF 160
                                     ******************************************************************************* PP

                       TIGR00692 159 dlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlvkvvaeltsgeGvdvvlel 237
                                     dl+Ge+vl++GaGpiG++a+av +++Ga++v+++d+neyrlela+k+Gatr+vnva+e+l +v+ el+++eG+dv+le+
  lcl|FitnessBrowser__MR1:203742 161 DLVGEDVLITGAGPIGIMAAAVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAQENLKDVMKELGMTEGFDVGLEM 239
                                     ******************************************************************************* PP

                       TIGR00692 238 sGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldlapiithkf 316
                                     sG p+a++ +ld++++gG++a+lg+p ++++id++ kvifkgl+ikGi+Gr++fetwyk++ liqs +ld++piith++
  lcl|FitnessBrowser__MR1:203742 240 SGVPSAFRAMLDTMNHGGKIAMLGIPGGEMAIDWS-KVIFKGLVIKGIYGREMFETWYKMASLIQS-GLDISPIITHHY 316
                                     **********************************9.******************************.9*********** PP

                       TIGR00692 317 kldefekgfelmrsGksGkvilil 340
                                     k+d+f+kgf++m sG+sGkvil++
  lcl|FitnessBrowser__MR1:203742 317 KIDDFQKGFDAMGSGQSGKVILSW 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.14
//
[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