Alignments for a candidate for mhpE in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mhpE in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate H281DRAFT_01666 H281DRAFT_01666 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39)

Query= metacyc::MONOMER-11384
         (352 letters)



>FitnessBrowser__Burk376:H281DRAFT_01666
          Length = 351

 Score =  580 bits (1496), Expect = e-170
 Identities = 282/341 (82%), Positives = 313/341 (91%)

Query: 4   QKLYISDVTLRDGSHAIRHQYTVEQVKQIARALDDAKVDSIEVAHGDGLQGGSFNYGFGA 63
           +KLYISDVTLRDGSHA+RHQY++  V+ IARALD+A VDSIEVAHGDG++G SFNYGFGA
Sbjct: 6   KKLYISDVTLRDGSHAVRHQYSIANVRAIARALDEAGVDSIEVAHGDGIEGSSFNYGFGA 65

Query: 64  HTDLEWIEAAASVVKHAKIATLLLPGIGTVHDLKAVYEAGVRVVRVATHCTEADISRQHI 123
           H+D+EWI AAA  VK AKIATLL+PGIGT+HDL+  Y+AG RVVRVATHCTEAD+SRQH+
Sbjct: 66  HSDVEWIAAAAESVKTAKIATLLIPGIGTIHDLRNAYDAGARVVRVATHCTEADVSRQHL 125

Query: 124 EYARHLGMEAVGFLMMSHMTTPQHLAQQAKLMESYGATVCYVVDSGGALSMNDVRDRFRA 183
           E+AR LGM++VGFLMMSHMTTPQ LA QAKLME YGAT  YVVDSGGAL M D+RDRFRA
Sbjct: 126 EFARELGMDSVGFLMMSHMTTPQKLAMQAKLMERYGATCVYVVDSGGALGMADIRDRFRA 185

Query: 184 FKDVLKPETQTGMHAHHNLSLGVANSIVAVENGCDRVDASLAGMGAGAGNAPLEVFIAAA 243
           FKD+L PETQTGMHAHHNLSLGVANS+VAVE GCDR+DASLAGMGAGAGNAPLEVFIAAA
Sbjct: 186 FKDILNPETQTGMHAHHNLSLGVANSLVAVEEGCDRIDASLAGMGAGAGNAPLEVFIAAA 245

Query: 244 ERMGWNHGTDLYKLMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEMAASKYG 303
           +R+GWNHG DLY+LMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRH+E+AASKYG
Sbjct: 246 QRLGWNHGCDLYRLMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHAELAASKYG 305

Query: 304 LKTVDILVELGRRRMVGGQEDMIIDVALDLLKQQEHERIRS 344
           LKTVDILVELGRR+MVGGQEDMI+DVALDLL    H+R RS
Sbjct: 306 LKTVDILVELGRRKMVGGQEDMIVDVALDLLSHGAHKRDRS 346


Lambda     K      H
   0.319    0.133    0.383 

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: 516
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: 352
Length of database: 351
Length adjustment: 29
Effective length of query: 323
Effective length of database: 322
Effective search space:   104006
Effective search space used:   104006
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 H281DRAFT_01666 H281DRAFT_01666 (4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))
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.2511.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.2e-182  591.0   6.9   3.7e-182  590.8   6.9    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01666  H281DRAFT_01666 4-hydroxy-2-oxov


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01666  H281DRAFT_01666 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.8   6.9  3.7e-182  3.7e-182       1     332 [.       6     337 ..       6     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 590.8 bits;  conditional E-value: 3.7e-182
                                    TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlel 66 
                                                  kkl+i+dvtLrdGshavrhq+++ +vraia+aLdeagvd+ievahGdG++gss+nyGf+a+sd+e+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01666   6 KKLYISDVTLRDGSHAVRHQYSIANVRAIARALDEAGVDSIEVAHGDGIEGSSFNYGFGAHSDVEW 71 
                                                  689*************************************************************** PP

                                    TIGR03217  67 ieaaaeavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvg 132
                                                  i+aaae+vk ak+a+ll+PGigt+++l++a+daG++vvrvathcteadvs+qh+e+arelg+++vg
  lcl|FitnessBrowser__Burk376:H281DRAFT_01666  72 IAAAAESVKTAKIATLLIPGIGTIHDLRNAYDAGARVVRVATHCTEADVSRQHLEFARELGMDSVG 137
                                                  ****************************************************************** PP

                                    TIGR03217 133 fLmmshmaspeklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahen 198
                                                  fLmmshm++p+kla qakl+e yGa++vyvvds+Gal ++d++dr++a+k+ l+pet++G+hah+n
  lcl|FitnessBrowser__Burk376:H281DRAFT_01666 138 FLMMSHMTTPQKLAMQAKLMERYGATCVYVVDSGGALGMADIRDRFRAFKDILNPETQTGMHAHHN 203
                                                  ****************************************************************** PP

                                    TIGR03217 199 lslavansivaveeGatridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrP 264
                                                  lsl+vans+vaveeG++ridaslag+GagaGnaplev++a+++rlG+++g+dl++l+daa+d+vrP
  lcl|FitnessBrowser__Burk376:H281DRAFT_01666 204 LSLGVANSLVAVEEGCDRIDASLAGMGAGAGNAPLEVFIAAAQRLGWNHGCDLYRLMDAADDLVRP 269
                                                  ****************************************************************** PP

                                    TIGR03217 265 lldrpvrvdrealtlGyaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldl 330
                                                  l+drpvrvdre+l+lGyaGvyssflrhae aa+kyg++++dilvelGrrk+vgGqedmivdvaldl
  lcl|FitnessBrowser__Burk376:H281DRAFT_01666 270 LQDRPVRVDRETLALGYAGVYSSFLRHAELAASKYGLKTVDILVELGRRKMVGGQEDMIVDVALDL 335
                                                  *****************************************************************9 PP

                                    TIGR03217 331 ak 332
                                                  ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01666 336 LS 337
                                                  86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (351 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: 7.84
//
[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