Alignments for a candidate for mhpE in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mhpE in Sphingomonas histidinilytica UM2

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_079650119.1 B5X82_RS20940 4-hydroxy-2-oxovalerate aldolase

Query= metacyc::MONOMER-3404
         (345 letters)



>NCBI__GCF_900167915.1:WP_079650119.1
          Length = 345

 Score =  498 bits (1282), Expect = e-146
 Identities = 248/341 (72%), Positives = 285/341 (83%), Gaps = 1/341 (0%)

Query: 1   MTFNPGK-KLYISDVTLRDGSHAIRHQYSIQNVQDIARALDKARVDSIEVTHGDGLQGSS 59
           M+F+  K KLYI DVTLRDG HAIRH Y I +V+ IA+ALD+A VD+IEV HGDGL G+S
Sbjct: 1   MSFDVSKDKLYIQDVTLRDGMHAIRHMYGIDHVRAIAKALDEAGVDAIEVAHGDGLNGAS 60

Query: 60  FNYGFGAHSDLEWIEAAADVIQHARVTVLLVPGIGTVHDLKAAYDAGARSVRVATHCTEA 119
           FNYGFGAH+D EW+EA ADV+  + +T L++PG+GTV +L+ AYD G RSVRVATHCTEA
Sbjct: 61  FNYGFGAHTDWEWLEAVADVLTRSVLTTLILPGVGTVDELRRAYDIGVRSVRVATHCTEA 120

Query: 120 DVSRQHIEYARELGMDTVGFLMMSHMIPAEQLAAQGKLMETYGAQCIYMADSGGAMNMND 179
           DVS+QHI  AR+LGMD  GFLMMSHMI  E LA Q  LME+YGAQC+Y+ DSGGA++M+ 
Sbjct: 121 DVSKQHIGIARDLGMDVSGFLMMSHMIEPEALAQQALLMESYGAQCVYVTDSGGALDMDG 180

Query: 180 IRDRMRAFKAVLNPQTQTGMHAHHNLSLGVANSIIAVEEGCDRIDASLAGMGAGAGNAPL 239
           IR R +A+  VL P+TQ GMHAHHNLSLGVANSI+A +EG  RIDASLAGMGAGAGNAPL
Sbjct: 181 IRARFQAYDRVLRPETQRGMHAHHNLSLGVANSIVAAQEGAVRIDASLAGMGAGAGNAPL 240

Query: 240 EVFIAAAERLGWNHGTDLYTLMDAADDIVRPLQDRPVRVDRETLGLGYAGVYSSFLRHAE 299
           EVFIAA +R GWNHG D+  LMDAA+D+VRPLQDRPVRVDRETL LGYAGVYSSFLRHAE
Sbjct: 241 EVFIAAVDRKGWNHGCDVNALMDAAEDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHAE 300

Query: 300 VAAAKYGLKTLDILVELGRRRMVGGQEDMIVDVALDLLAAR 340
            AAA YGL T  ILVELGRR+MVGGQEDMIVDVALDL+  R
Sbjct: 301 KAAADYGLDTRTILVELGRRKMVGGQEDMIVDVALDLIRER 341


Lambda     K      H
   0.320    0.135    0.389 

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: 467
Number of extensions: 12
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: 345
Length of database: 345
Length adjustment: 29
Effective length of query: 316
Effective length of database: 316
Effective search space:    99856
Effective search space used:    99856
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 WP_079650119.1 B5X82_RS20940 (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.892364.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.2e-178  576.6   8.4   9.5e-178  576.4   8.4    1.0  1  NCBI__GCF_900167915.1:WP_079650119.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079650119.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.4   8.4  9.5e-178  9.5e-178       2     333 ..       9     340 ..       8     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 576.4 bits;  conditional E-value: 9.5e-178
                             TIGR03217   2 kltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeav 74 
                                           kl+i+dvtLrdG+ha+rh++ +++vraia+aLdeagvdaievahGdGL+g+s+nyGf+a++d+e++ea+a+++
  NCBI__GCF_900167915.1:WP_079650119.1   9 KLYIQDVTLRDGMHAIRHMYGIDHVRAIAKALDEAGVDAIEVAHGDGLNGASFNYGFGAHTDWEWLEAVADVL 81 
                                           789********************************************************************** PP

                             TIGR03217  75 kkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklae 147
                                           +++ +++l+lPG+gtv+el++a+d+Gv++vrvathcteadvs+qhi++ar+lg++++gfLmmshm++pe+la+
  NCBI__GCF_900167915.1:WP_079650119.1  82 TRSVLTTLILPGVGTVDELRRAYDIGVRSVRVATHCTEADVSKQHIGIARDLGMDVSGFLMMSHMIEPEALAQ 154
                                           ************************************************************************* PP

                             TIGR03217 148 qakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridas 220
                                           qa l+esyGa++vyv+ds+Gal ++ +++r++a++++l+pet+ G+hah+nlsl+vansiva +eGa ridas
  NCBI__GCF_900167915.1:WP_079650119.1 155 QALLMESYGAQCVYVTDSGGALDMDGIRARFQAYDRVLRPETQRGMHAHHNLSLGVANSIVAAQEGAVRIDAS 227
                                           ************************************************************************* PP

                             TIGR03217 221 laglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhae 293
                                           lag+GagaGnaplev++a++dr G+++g+d+ +l+daaed+vrPl+drpvrvdre+l+lGyaGvyssflrhae
  NCBI__GCF_900167915.1:WP_079650119.1 228 LAGMGAGAGNAPLEVFIAAVDRKGWNHGCDVNALMDAAEDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHAE 300
                                           ************************************************************************* PP

                             TIGR03217 294 raaekygvdardilvelGrrklvgGqedmivdvaldlake 333
                                           +aa+ yg+d+r+ilvelGrrk+vgGqedmivdvaldl++e
  NCBI__GCF_900167915.1:WP_079650119.1 301 KAAADYGLDTRTILVELGRRKMVGGQEDMIVDVALDLIRE 340
                                           *************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (345 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: 00:00:00.00
# Mc/sec: 22.02
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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