Alignments for a candidate for mhpE in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mhpE in Cupriavidus basilensis 4G11

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate RR42_RS05095 RR42_RS05095 4-hyroxy-2-oxovalerate aldolase

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



>FitnessBrowser__Cup4G11:RR42_RS05095
          Length = 335

 Score =  545 bits (1403), Expect = e-160
 Identities = 269/334 (80%), Positives = 300/334 (89%)

Query: 4   QKLYISDVTLRDGSHAIRHQYTVEQVKQIARALDDAKVDSIEVAHGDGLQGGSFNYGFGA 63
           +K+++SDVTLRDG HAIRHQY++ Q   IARALD A+VDSIEVAHGDGL G SFNYGFGA
Sbjct: 2   KKVHVSDVTLRDGMHAIRHQYSLPQAVAIARALDAARVDSIEVAHGDGLNGSSFNYGFGA 61

Query: 64  HTDLEWIEAAASVVKHAKIATLLLPGIGTVHDLKAVYEAGVRVVRVATHCTEADISRQHI 123
           HTDLEWI A A+ +KHA++ATLLLPGIGT+HDL+A Y+AG R VRVATHCTEADISRQHI
Sbjct: 62  HTDLEWIAAVAAQLKHARVATLLLPGIGTIHDLRAAYDAGARTVRVATHCTEADISRQHI 121

Query: 124 EYARHLGMEAVGFLMMSHMTTPQHLAQQAKLMESYGATVCYVVDSGGALSMNDVRDRFRA 183
           EYAR LGM+ VGFLMMSHMTTP  LAQQA+LMESYGA   YVVDSGGALSM DV +RF A
Sbjct: 122 EYARKLGMDTVGFLMMSHMTTPAALAQQARLMESYGAQCVYVVDSGGALSMRDVAERFDA 181

Query: 184 FKDVLKPETQTGMHAHHNLSLGVANSIVAVENGCDRVDASLAGMGAGAGNAPLEVFIAAA 243
           FK VL P T+TGMHAHHNLSLGVANS+VA+E+GCDRVDASLAGMGAGAGNAPLEVFIAA 
Sbjct: 182 FKQVLDPATETGMHAHHNLSLGVANSMVALEHGCDRVDASLAGMGAGAGNAPLEVFIAAI 241

Query: 244 ERMGWNHGTDLYKLMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEMAASKYG 303
           +R G  HGTDL+ LMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRH+E A+++YG
Sbjct: 242 DRAGIAHGTDLHALMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHAEAASARYG 301

Query: 304 LKTVDILVELGRRRMVGGQEDMIIDVALDLLKQQ 337
           + TVDILVELGRRRMVGGQEDMI+DVALDLL+Q+
Sbjct: 302 IATVDILVELGRRRMVGGQEDMIVDVALDLLRQR 335


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: 482
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: 352
Length of database: 335
Length adjustment: 29
Effective length of query: 323
Effective length of database: 306
Effective search space:    98838
Effective search space used:    98838
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 RR42_RS05095 RR42_RS05095 (4-hyroxy-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.21950.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-179  581.4  12.2   3.1e-179  581.3  12.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05095  RR42_RS05095 4-hyroxy-2-oxovaler


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05095  RR42_RS05095 4-hyroxy-2-oxovalerate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.3  12.2  3.1e-179  3.1e-179       1     334 []       2     335 .]       2     335 .] 0.99

  Alignments for each domain:
  == domain 1  score: 581.3 bits;  conditional E-value: 3.1e-179
                                 TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdleliea 69 
                                               kk++++dvtLrdG+ha+rhq++  +++aia+aLd+a+vd+ievahGdGL+gss+nyGf+a++dle+i+a
  lcl|FitnessBrowser__Cup4G11:RR42_RS05095   2 KKVHVSDVTLRDGMHAIRHQYSLPQAVAIARALDAARVDSIEVAHGDGLNGSSFNYGFGAHTDLEWIAA 70 
                                               689****************************************************************** PP

                                 TIGR03217  70 aaeavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmsh 138
                                               +a ++k+a+va+lllPGigt+++l+aa+daG+++vrvathctead+s+qhie+ar+lg++tvgfLmmsh
  lcl|FitnessBrowser__Cup4G11:RR42_RS05095  71 VAAQLKHARVATLLLPGIGTIHDLRAAYDAGARTVRVATHCTEADISRQHIEYARKLGMDTVGFLMMSH 139
                                               ********************************************************************* PP

                                 TIGR03217 139 maspeklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansi 207
                                               m++p +la+qa+l+esyGa++vyvvds+Gal+++dv++r++a+k++l+p+te+G+hah+nlsl+vans+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05095 140 MTTPAALAQQARLMESYGAQCVYVVDSGGALSMRDVAERFDAFKQVLDPATETGMHAHHNLSLGVANSM 208
                                               ********************************************************************* PP

                                 TIGR03217 208 vaveeGatridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrea 276
                                               va+e+G++r+daslag+GagaGnaplev++a++dr+G+ +g+dl++l+daa+d+vrPl+drpvrvdre+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05095 209 VALEHGCDRVDASLAGMGAGAGNAPLEVFIAAIDRAGIAHGTDLHALMDAADDLVRPLQDRPVRVDRET 277
                                               ********************************************************************* PP

                                 TIGR03217 277 ltlGyaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldlaker 334
                                               l+lGyaGvyssflrhae+a+++yg+ ++dilvelGrr++vgGqedmivdvaldl+++r
  lcl|FitnessBrowser__Cup4G11:RR42_RS05095 278 LALGYAGVYSSFLRHAEAASARYGIATVDILVELGRRRMVGGQEDMIVDVALDLLRQR 335
                                               ******************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (335 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: 10.09
//
[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