Aligments for a candidate for mhpE in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for mhpE in Escherichia coli BW25113

Align 4-hydroxy-2-oxovalerate aldolase; EC 4.1.3.39 (characterized)
to candidate 14490 b0352 4-hydroxy-2-ketovalerate aldolase (NCBI)

Query= CharProtDB::CH_002284
         (337 letters)



>lcl|FitnessBrowser__Keio:14490 b0352 4-hydroxy-2-ketovalerate
           aldolase (NCBI)
          Length = 337

 Score =  671 bits (1732), Expect = 0.0
 Identities = 337/337 (100%), Positives = 337/337 (100%)

Query: 1   MNGKKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYG 60
           MNGKKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYG
Sbjct: 1   MNGKKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYG 60

Query: 61  FGAHSDLEWIEAAADVVKHAKIATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSA 120
           FGAHSDLEWIEAAADVVKHAKIATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSA
Sbjct: 61  FGAHSDLEWIEAAADVVKHAKIATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSA 120

Query: 121 QHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGATCIYVVDSGGAMNMSDIRDR 180
           QHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGATCIYVVDSGGAMNMSDIRDR
Sbjct: 121 QHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGATCIYVVDSGGAMNMSDIRDR 180

Query: 181 FRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240
           FRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI
Sbjct: 181 FRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240

Query: 241 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAA 300
           AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAA
Sbjct: 241 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAA 300

Query: 301 RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLRNNK 337
           RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLRNNK
Sbjct: 301 RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLRNNK 337


Lambda     K      H
   0.319    0.134    0.391 

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: 560
Number of extensions: 15
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: 337
Length of database: 337
Length adjustment: 28
Effective length of query: 309
Effective length of database: 309
Effective search space:    95481
Effective search space used:    95481
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 14490 b0352 (4-hydroxy-2-ketovalerate aldolase (NCBI))
to HMM TIGR03217 (dmpG: 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))

# 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/TIGR03217.hmm
# target sequence database:        /tmp/gapView.14084.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03217  [M=334]
Accession:   TIGR03217
Description: 4OH_2_O_val_ald: 4-hydroxy-2-oxovalerate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     3e-185  601.0   7.4   3.4e-185  600.8   7.4    1.0  1  lcl|FitnessBrowser__Keio:14490  b0352 4-hydroxy-2-ketovalerate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14490  b0352 4-hydroxy-2-ketovalerate aldolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.8   7.4  3.4e-185  3.4e-185       1     333 [.       4     336 ..       4     337 .] 0.99

  Alignments for each domain:
  == domain 1  score: 600.8 bits;  conditional E-value: 3.4e-185
                       TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeavkkakv 79 
                                     kkl+i+dvtLrdG+ha+rhq++ e+vr+ia+aLd+a+vd+ievahGdGL+gss+nyGf+a+sdle+ieaaa++vk+ak+
  lcl|FitnessBrowser__Keio:14490   4 KKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYGFGAHSDLEWIEAAADVVKHAKI 82 
                                     689**************************************************************************** PP

                       TIGR03217  80 avlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklaeqakllesyGad 158
                                     a+lllPGigt+++lk+a +aG++vvrvathcteadvs+qhi++arelg++tvgfLmmshm++pe+la+qakl+e yGa+
  lcl|FitnessBrowser__Keio:14490  83 ATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSAQHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGAT 161
                                     ******************************************************************************* PP

                       TIGR03217 159 vvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridaslaglGagaGnaplevlv 237
                                     ++yvvds+Ga++++d++dr++alk++lkpet++G+hah+nlsl+vansi+aveeG++ridaslag+GagaGnaplev++
  lcl|FitnessBrowser__Keio:14490 162 CIYVVDSGGAMNMSDIRDRFRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240
                                     ******************************************************************************* PP

                       TIGR03217 238 avldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhaeraaekygvdardilvelGrrklv 316
                                     a++d+lG+++g+dl++l+daa+d+vrPl+drpvrvdre+l+lGyaGvyssflrh+e+aa++yg++a+dilvelG+r++v
  lcl|FitnessBrowser__Keio:14490 241 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAARYGLSAVDILVELGKRRMV 319
                                     ******************************************************************************* PP

                       TIGR03217 317 gGqedmivdvaldlake 333
                                     gGqedmivdvaldl ++
  lcl|FitnessBrowser__Keio:14490 320 GGQEDMIVDVALDLRNN 336
                                     **************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (337 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.82
//
[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, or view the source code.

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