Alignments for a candidate for tdh in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdh in Klebsiella michiganensis M5al

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate BWI76_RS27250 BWI76_RS27250 L-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__Koxy:BWI76_RS27250
          Length = 341

 Score =  681 bits (1757), Expect = 0.0
 Identities = 328/341 (96%), Positives = 337/341 (98%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKALSKLKAEEGIWMTDVP PE+GHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV
Sbjct: 1   MKALSKLKAEEGIWMTDVPEPEVGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHEYVGEVVGIGQEV+GFK+GDRVSGEGHITCGHCRNCR GRTHLCRNT GVGVNRPGC
Sbjct: 61  VGHEYVGEVVGIGQEVRGFKLGDRVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNRPGC 120

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAEYLVIPAFNAFKIPDNISDDLA+IFDPFGNAVHTALSFDLVGEDVLVSGAGPIG+MAA
Sbjct: 121 FAEYLVIPAFNAFKIPDNISDDLASIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGVMAA 180

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           AVAKHVGARNVVITDVNEYRLELARKMG+TRAVNV+KENLNDVMAELGMTEGFDVGLEMS
Sbjct: 181 AVAKHVGARNVVITDVNEYRLELARKMGVTRAVNVSKENLNDVMAELGMTEGFDVGLEMS 240

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           GAPPAFRTMLDT+NHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA
Sbjct: 241 GAPPAFRTMLDTINHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341
           LIQSGLDLSPIITHRF IDDFQ+GFDAMRSGQSGKVILSWD
Sbjct: 301 LIQSGLDLSPIITHRFGIDDFQQGFDAMRSGQSGKVILSWD 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: 631
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 BWI76_RS27250 BWI76_RS27250 (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.15425.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.1e-191  622.1   0.3   1.3e-191  621.9   0.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27250  BWI76_RS27250 L-threonine 3-dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27250  BWI76_RS27250 L-threonine 3-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.9   0.3  1.3e-191  1.3e-191       1     340 []       3     340 ..       3     340 .. 1.00

  Alignments for each domain:
  == domain 1  score: 621.9 bits;  conditional E-value: 1.3e-191
                               TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiG 71 
                                             al+k+kaeeG+++t+vp pe+g+n++lik+++t+icGtdvhiynwdew+qk+i+vp+v+Ghe++GevvgiG
  lcl|FitnessBrowser__Koxy:BWI76_RS27250   3 ALSKLKAEEGIWMTDVPEPEVGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVGIG 73 
                                             89********************************************************************* PP

                               TIGR00692  72 eevegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpela 142
                                             +ev+g+k+Gd+vs+e+hi+cG+c++cr+G++h+crnt++vGv+++G+faey+v+pa+n+fk+p++i+++la
  lcl|FitnessBrowser__Koxy:BWI76_RS27250  74 QEVRGFKLGDRVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNRPGCFAEYLVIPAFNAFKIPDNISDDLA 144
                                             *********************************************************************** PP

                               TIGR00692 143 aiqeplGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnv 213
                                             +i++p+Gnav+t+l++dl+Ge+vlvsGaGpiG++a+avak++Ga++v+++d+neyrlela+k+G+tr+vnv
  lcl|FitnessBrowser__Koxy:BWI76_RS27250 145 SIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGVMAAAVAKHVGARNVVITDVNEYRLELARKMGVTRAVNV 215
                                             *********************************************************************** PP

                               TIGR00692 214 akedlvkvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikG 284
                                              ke+l++v+ael+++eG+dv+le+sGap+a++++ld++++gGr+a+lg+p+s+++id+t kvifkgl+ikG
  lcl|FitnessBrowser__Koxy:BWI76_RS27250 216 SKENLNDVMAELGMTEGFDVGLEMSGAPPAFRTMLDTINHGGRIAMLGIPPSDMSIDWT-KVIFKGLFIKG 285
                                             ***********************************************************.*********** PP

                               TIGR00692 285 itGrklfetwykvsrliqsnkldlapiithkfkldefekgfelmrsGksGkvilil 340
                                             i+Gr++fetwyk+++liqs +ldl+piith+f +d+f++gf++mrsG+sGkvil++
  lcl|FitnessBrowser__Koxy:BWI76_RS27250 286 IYGREMFETWYKMAALIQS-GLDLSPIITHRFGIDDFQQGFDAMRSGQSGKVILSW 340
                                             *******************.9*********************************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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.07
//
[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