Alignments for a candidate for tdh in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdh in Burkholderia phytofirmans PsJN

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate BPHYT_RS34650 BPHYT_RS34650 l-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__BFirm:BPHYT_RS34650
          Length = 343

 Score =  559 bits (1441), Expect = e-164
 Identities = 262/340 (77%), Positives = 302/340 (88%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL+KL+   G+ +TDV  PE+GHND++I+I +TAICGTD+HI+ WD+W+QKTIPVPM 
Sbjct: 1   MKALAKLERAPGLTLTDVKKPEVGHNDVMIRITRTAICGTDIHIWKWDDWAQKTIPVPMH 60

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHEYVGE+V +GQEV+GF IGDRVSGEGHITCG CRNCR GR HLCRNT+GVGVNR G 
Sbjct: 61  VGHEYVGEIVEMGQEVRGFAIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNREGA 120

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAEYLVIPAFNAFKIP  ISDDLAAIFDPFGNA HTALSF+LVGEDVL++GAGPIGIMA 
Sbjct: 121 FAEYLVIPAFNAFKIPPEISDDLAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAV 180

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           A+AKHVGARNVVITDVN+YRLELARKMG TRAVNV++E+L DVMA+L MTEGFDVGLEMS
Sbjct: 181 AIAKHVGARNVVITDVNDYRLELARKMGATRAVNVSRESLRDVMADLHMTEGFDVGLEMS 240

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G P AF +ML+ MNHGG+IA+LGIPP+  +IDWT+VIFKGL IKGIYGREMFETWYKM A
Sbjct: 241 GVPSAFTSMLEAMNHGGKIALLGIPPAQTAIDWTQVIFKGLEIKGIYGREMFETWYKMVA 300

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340
           ++QSGLDLSPI+TH F +DD+Q+ F  M SG+SGKVIL W
Sbjct: 301 MLQSGLDLSPILTHHFKVDDYQEAFATMLSGESGKVILDW 340


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: 524
Number of extensions: 13
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: 343
Length adjustment: 29
Effective length of query: 312
Effective length of database: 314
Effective search space:    97968
Effective search space used:    97968
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 BPHYT_RS34650 BPHYT_RS34650 (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.10834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.2e-167  542.2   0.4   2.5e-167  542.1   0.4    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS34650  BPHYT_RS34650 l-threonine 3-dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS34650  BPHYT_RS34650 l-threonine 3-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.1   0.4  2.5e-167  2.5e-167       1     340 []       3     340 ..       3     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 542.1 bits;  conditional E-value: 2.5e-167
                                TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgi 70 
                                              al+k++ + G +lt+v+ pe+g+n+v+i++ +t+icGtd+hi++wd+waqk+i+vp+ +Ghe++Ge+v++
  lcl|FitnessBrowser__BFirm:BPHYT_RS34650   3 ALAKLERAPGLTLTDVKKPEVGHNDVMIRITRTAICGTDIHIWKWDDWAQKTIPVPMHVGHEYVGEIVEM 72 
                                              7999****************************************************************** PP

                                TIGR00692  71 GeevegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpe 140
                                              G+ev+g+ +Gd+vs+e+hi+cG c++cr+G+ h+crnt++vGv+++G+faey+v+pa+n+fk+p +i+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS34650  73 GQEVRGFAIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNREGAFAEYLVIPAFNAFKIPPEISDD 142
                                              ********************************************************************** PP

                                TIGR00692 141 laaiqeplGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrv 210
                                              laai++p+Gna +t+l+++l+Ge+vl++GaGpiG++ava+ak++Ga++v+++d+n+yrlela+k+Gatr+
  lcl|FitnessBrowser__BFirm:BPHYT_RS34650 143 LAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAVAIAKHVGARNVVITDVNDYRLELARKMGATRA 212
                                              ********************************************************************** PP

                                TIGR00692 211 vnvakedlvkvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgl 280
                                              vnv +e l +v+a+l ++eG+dv+le+sG p+a++ +l+a+++gG++allg+p+++ +id+t +vifkgl
  lcl|FitnessBrowser__BFirm:BPHYT_RS34650 213 VNVSRESLRDVMADLHMTEGFDVGLEMSGVPSAFTSMLEAMNHGGKIALLGIPPAQTAIDWT-QVIFKGL 281
                                              **************************************************************.9****** PP

                                TIGR00692 281 tikGitGrklfetwykvsrliqsnkldlapiithkfkldefekgfelmrsGksGkvilil 340
                                               ikGi+Gr++fetwyk+ +++qs +ldl+pi+th+fk+d+++++f  m sG+sGkvil +
  lcl|FitnessBrowser__BFirm:BPHYT_RS34650 282 EIKGIYGREMFETWYKMVAMLQS-GLDLSPILTHHFKVDDYQEAFATMLSGESGKVILDW 340
                                              ***********************.9********************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (343 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: 8.89
//
[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