Alignments for a candidate for mhpE in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for mhpE in Burkholderia phytofirmans PsJN

Align 4-hydroxy-2-oxovalerate aldolase; HOA; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase; EC 4.1.3.39 (characterized)
to candidate BPHYT_RS07250 BPHYT_RS07250 4-hydroxy-2-oxovalerate aldolase

Query= SwissProt::Q9KWS0
         (343 letters)



>FitnessBrowser__BFirm:BPHYT_RS07250
          Length = 347

 Score =  569 bits (1467), Expect = e-167
 Identities = 283/341 (82%), Positives = 308/341 (90%)

Query: 1   MIDQAKKIYISDVTLRDGMHAIRHRYTLNHVSQIARALDEAGVDSIEVAHGDGLKGSSFN 60
           M D  KKIY+SDVTLRDGMHAIRH+Y+L     IA+ALDEAGVDSIEVAHGDGL GSSFN
Sbjct: 1   MTDSNKKIYVSDVTLRDGMHAIRHQYSLQSAVAIAQALDEAGVDSIEVAHGDGLAGSSFN 60

Query: 61  YGFGAYSDLEWISAAAEAVKQAKIATLLLPGIGTVHDLREAYDAGARVVRVATHCTEADV 120
           YGFGA++DLEWI A A  VK+A++ATLLLPGIGTVHDLR AYDAGARVVR+ATHCTEAD+
Sbjct: 61  YGFGAHTDLEWIEAVAATVKRAQVATLLLPGIGTVHDLRAAYDAGARVVRIATHCTEADI 120

Query: 121 SRQHIEYARGLGMDTVGFLMMSHMQTPVGLAQQAKLMENYGAQCIYVVDSGGAMNMWDIA 180
           S+QHIEYAR LGMDTVGFLMMSHM +P  LA+QAKLME+YGAQC+YVVDSG A+NM D+A
Sbjct: 121 SKQHIEYARSLGMDTVGFLMMSHMTSPEALAKQAKLMESYGAQCVYVVDSGVALNMRDVA 180

Query: 181 ERFKALKDVLDPATQTGMHAHHNLSLGVANSLVALENGCDRVDASLTGMGAGAGNAPLEV 240
           ERF A K VLDPATQTGMHAHHNLSLGVANS+VALE+GCDRVDASLTGMGAGAGNAPLEV
Sbjct: 181 ERFDAFKAVLDPATQTGMHAHHNLSLGVANSIVALEHGCDRVDASLTGMGAGAGNAPLEV 240

Query: 241 FIAAAERMGLNHGCDVKKLINAAEDIVRPLQERPVRVDRETLALGYAGVYSSFLRHAETA 300
           FIAA +RM L HGCDVK+LI+AAEDIVRPLQERPVRVDRETLALGYAGVYSSFLRH E A
Sbjct: 241 FIAAVDRMKLKHGCDVKQLIDAAEDIVRPLQERPVRVDRETLALGYAGVYSSFLRHTEAA 300

Query: 301 AKKYNLSAFDILVELGKRRMIGGQEDMIVDVALDMAKGRVL 341
           A KY LSAFDI+VELGKRRM+GGQEDMIVDVALDM K R L
Sbjct: 301 AAKYGLSAFDIMVELGKRRMVGGQEDMIVDVALDMLKAREL 341


Lambda     K      H
   0.320    0.134    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: 472
Number of extensions: 10
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: 343
Length of database: 347
Length adjustment: 29
Effective length of query: 314
Effective length of database: 318
Effective search space:    99852
Effective search space used:    99852
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 BPHYT_RS07250 BPHYT_RS07250 (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.21504.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     2e-179  581.9  12.3   2.3e-179  581.7  12.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07250  BPHYT_RS07250 4-hydroxy-2-oxoval


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07250  BPHYT_RS07250 4-hydroxy-2-oxovalerate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.7  12.3  2.3e-179  2.3e-179       1     334 []       6     339 ..       6     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 581.7 bits;  conditional E-value: 2.3e-179
                                TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaa 70 
                                              kk++++dvtLrdG+ha+rhq++ ++++aia+aLdeagvd+ievahGdGL+gss+nyGf+a++dle+iea+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07250   6 KKIYVSDVTLRDGMHAIRHQYSLQSAVAIAQALDEAGVDSIEVAHGDGLAGSSFNYGFGAHTDLEWIEAV 75 
                                              689******************************************************************* PP

                                TIGR03217  71 aeavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshma 140
                                              a +vk+a+va+lllPGigtv++l+aa+daG++vvr+athctead+s+qhie+ar lg++tvgfLmmshm+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07250  76 AATVKRAQVATLLLPGIGTVHDLRAAYDAGARVVRIATHCTEADISKQHIEYARSLGMDTVGFLMMSHMT 145
                                              ********************************************************************** PP

                                TIGR03217 141 speklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivav 210
                                              spe+la+qakl+esyGa++vyvvds+ al+++dv++r++a+k++l+p+t++G+hah+nlsl+vansiva+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07250 146 SPEALAKQAKLMESYGAQCVYVVDSGVALNMRDVAERFDAFKAVLDPATQTGMHAHHNLSLGVANSIVAL 215
                                              ********************************************************************** PP

                                TIGR03217 211 eeGatridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlG 280
                                              e+G++r+dasl+g+GagaGnaplev++a++dr+ l++g+d+ +l+daaed+vrPl++rpvrvdre+l+lG
  lcl|FitnessBrowser__BFirm:BPHYT_RS07250 216 EHGCDRVDASLTGMGAGAGNAPLEVFIAAVDRMKLKHGCDVKQLIDAAEDIVRPLQERPVRVDRETLALG 285
                                              ********************************************************************** PP

                                TIGR03217 281 yaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldlaker 334
                                              yaGvyssflrh+e+aa+kyg++a di+velG+r++vgGqedmivdvald++k+r
  lcl|FitnessBrowser__BFirm:BPHYT_RS07250 286 YAGVYSSFLRHTEAAAAKYGLSAFDIMVELGKRRMVGGQEDMIVDVALDMLKAR 339
                                              **************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (347 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.51
//
[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