Alignments for a candidate for mhpE in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for mhpE in Klebsiella michiganensis M5al

Align 4-hydroxy-2-oxovalerate aldolase; EC 4.1.3.39 (characterized)
to candidate BWI76_RS16900 BWI76_RS16900 4-hydroxy-2-oxovalerate aldolase

Query= CharProtDB::CH_002284
         (337 letters)



>FitnessBrowser__Koxy:BWI76_RS16900
          Length = 338

 Score =  607 bits (1565), Expect = e-178
 Identities = 307/337 (91%), Positives = 316/337 (93%)

Query: 1   MNGKKLYISDVTLRDGMHAIRHQYSLENVRQIAKALDDARVDSIEVAHGDGLQGSSFNYG 60
           MNGKKLYISDVTLRDGMHAIRHQYSL+NVRQIA+ALD A VDSIEVAHGDGLQGSSFNYG
Sbjct: 1   MNGKKLYISDVTLRDGMHAIRHQYSLDNVRQIARALDSAGVDSIEVAHGDGLQGSSFNYG 60

Query: 61  FGAHSDLEWIEAAADVVKHAKIATLLLPGIGTIHDLKNAWQAGARVVRVATHCTEADVSA 120
           FGAHSDLEWIEAAA+ V  AKIATLLLPGIGT+HDLKNA+QAGARVVRVATHCTEADVSA
Sbjct: 61  FGAHSDLEWIEAAAESVSQAKIATLLLPGIGTLHDLKNAYQAGARVVRVATHCTEADVSA 120

Query: 121 QHIQYARELGMDTVGFLMMSHMTTPENLAKQAKLMEGYGATCIYVVDSGGAMNMSDIRDR 180
           QHI +ARELGMDTVGFLMMSHMT PE LA+QA  ME YGATCIYVVDSGGAMNM DIRDR
Sbjct: 121 QHIAFARELGMDTVGFLMMSHMTAPEQLAQQALKMESYGATCIYVVDSGGAMNMRDIRDR 180

Query: 181 FRALKAELKPETQTGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240
           FRALKA LKPET TGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI
Sbjct: 181 FRALKAVLKPETATGMHAHHNLSLGVANSIAAVEEGCDRIDASLAGMGAGAGNAPLEVFI 240

Query: 241 AAADKLGWQHGTDLYALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHCETAAA 300
           AAADKLGW HGTDLYALM+AAD+LVRPLQDRPVRVDRETLALGYAGVYSSFLRH E AA 
Sbjct: 241 AAADKLGWNHGTDLYALMNAADELVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEAAAG 300

Query: 301 RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLRNNK 337
           RYGLSAVDILVELGKRRMVGGQEDMIVDVALDL   K
Sbjct: 301 RYGLSAVDILVELGKRRMVGGQEDMIVDVALDLLKRK 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: 494
Number of extensions: 9
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: 338
Length adjustment: 28
Effective length of query: 309
Effective length of database: 310
Effective search space:    95790
Effective search space used:    95790
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 BWI76_RS16900 BWI76_RS16900 (4-hydroxy-2-oxovalerate aldolase)
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.17427.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.7e-183  593.5   8.1   6.6e-183  593.3   8.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS16900  BWI76_RS16900 4-hydroxy-2-oxoval


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS16900  BWI76_RS16900 4-hydroxy-2-oxovalerate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  593.3   8.1  6.6e-183  6.6e-183       1     333 [.       4     336 ..       4     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 593.3 bits;  conditional E-value: 6.6e-183
                               TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaa 71 
                                             kkl+i+dvtLrdG+ha+rhq++ ++vr+ia+aLd+agvd+ievahGdGL+gss+nyGf+a+sdle+ieaaa
  lcl|FitnessBrowser__Koxy:BWI76_RS16900   4 KKLYISDVTLRDGMHAIRHQYSLDNVRQIARALDSAGVDSIEVAHGDGLQGSSFNYGFGAHSDLEWIEAAA 74 
                                             689******************************************************************** PP

                               TIGR03217  72 eavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmasp 142
                                             e+v +ak+a+lllPGigt+++lk+a++aG++vvrvathcteadvs+qhi++arelg++tvgfLmmshm+ p
  lcl|FitnessBrowser__Koxy:BWI76_RS16900  75 ESVSQAKIATLLLPGIGTLHDLKNAYQAGARVVRVATHCTEADVSAQHIAFARELGMDTVGFLMMSHMTAP 145
                                             *********************************************************************** PP

                               TIGR03217 143 eklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeG 213
                                             e+la+qa ++esyGa+++yvvds+Ga++++d++dr++alk++lkpet +G+hah+nlsl+vansi+aveeG
  lcl|FitnessBrowser__Koxy:BWI76_RS16900 146 EQLAQQALKMESYGATCIYVVDSGGAMNMRDIRDRFRALKAVLKPETATGMHAHHNLSLGVANSIAAVEEG 216
                                             *********************************************************************** PP

                               TIGR03217 214 atridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGv 284
                                             ++ridaslag+GagaGnaplev++a++d+lG+++g+dl++l++aa+++vrPl+drpvrvdre+l+lGyaGv
  lcl|FitnessBrowser__Koxy:BWI76_RS16900 217 CDRIDASLAGMGAGAGNAPLEVFIAAADKLGWNHGTDLYALMNAADELVRPLQDRPVRVDRETLALGYAGV 287
                                             *********************************************************************** PP

                               TIGR03217 285 yssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldlake 333
                                             yssflrh+e+aa +yg++a+dilvelG+r++vgGqedmivdvaldl+k+
  lcl|FitnessBrowser__Koxy:BWI76_RS16900 288 YSSFLRHSEAAAGRYGLSAVDILVELGKRRMVGGQEDMIVDVALDLLKR 336
                                             **********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (338 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: 9.56
//
[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