Alignments for a candidate for catA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Cupriavidus basilensis 4G11

Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate RR42_RS23505 RR42_RS23505 catechol 1,2-dioxygenase

Query= BRENDA::Q9F103
         (306 letters)



>FitnessBrowser__Cup4G11:RR42_RS23505
          Length = 304

 Score =  402 bits (1032), Expect = e-117
 Identities = 198/306 (64%), Positives = 234/306 (76%), Gaps = 2/306 (0%)

Query: 1   MNRQQIDALVKQMNVDTAKGPVDERIQQVVVRLLGDLFQAIEDLDIQPSEVWKGLEYLTD 60
           M   +I+ALVK   +DTA G  D R+Q VVVRL  DLF+AIEDLD+  SEVWKG+EY  +
Sbjct: 1   MTHPEIEALVKAFILDTASGKADARVQSVVVRLTTDLFKAIEDLDLSASEVWKGIEYFAE 60

Query: 61  AGQANELGLLAAGLGLEHYLDLRADEADAKAGITGGTPRTIEGPLYVAGAPESVGFARMD 120
           AG   ELGLLAAGLGLE +LD+RADEA+AKAG+ GGTPRTIEGPLYVAGAP S GFAR+D
Sbjct: 61  AGP--ELGLLAAGLGLERFLDIRADEAEAKAGLAGGTPRTIEGPLYVAGAPASEGFARLD 118

Query: 121 DGSESDKVDTLIIEGTVTDTEGNIIEGAKVEVWHANSLGNYSFFDKSQSDFNLRRTILTD 180
           DGSE  + + L ++GTV DT G  + GA VEVWHAN LGNYSFFDK+QSDFNLRRTI TD
Sbjct: 119 DGSEDGQGEVLFMQGTVFDTSGKPLPGASVEVWHANLLGNYSFFDKTQSDFNLRRTITTD 178

Query: 181 VNGKYVALTTMPVGYGCPPEGTTQALLNKLGRHGNRPSHVHYFVSAPGYRKLTTQFNIEG 240
             G+Y   + +P+GYGCPP+GTTQ LL+ LGRHG RP+H+H+FVSAPG+RKLTTQ NI+G
Sbjct: 179 SEGRYQFRSIVPMGYGCPPQGTTQRLLDLLGRHGRRPAHIHFFVSAPGHRKLTTQINIDG 238

Query: 241 DEYLWDDFAFATRDGLVATATDVTDEAEIARRELDKPFKHITFNVELVKEAEAAPSSEVE 300
           DEYLWDDFAFA+R+GLV     V     +A   LDKPF  I F+  L  +  AAP  EVE
Sbjct: 239 DEYLWDDFAFASREGLVPALRHVESPRALAEHGLDKPFASIDFDFRLYADCAAAPVPEVE 298

Query: 301 RRRASA 306
           R RA+A
Sbjct: 299 RTRAAA 304


Lambda     K      H
   0.315    0.134    0.387 

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: 331
Number of extensions: 3
Number of successful extensions: 2
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: 306
Length of database: 304
Length adjustment: 27
Effective length of query: 279
Effective length of database: 277
Effective search space:    77283
Effective search space used:    77283
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS23505 RR42_RS23505 (catechol 1,2-dioxygenase)
to HMM TIGR02439 (catA: catechol 1,2-dioxygenase (EC 1.13.11.1))

# 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/TIGR02439.hmm
# target sequence database:        /tmp/gapView.24516.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02439  [M=285]
Accession:   TIGR02439
Description: catechol_proteo: catechol 1,2-dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-136  440.3   0.0   1.3e-136  440.1   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS23505  RR42_RS23505 catechol 1,2-dioxyg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS23505  RR42_RS23505 catechol 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.1   0.0  1.3e-136  1.3e-136       3     285 .]       4     285 ..       2     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 440.1 bits;  conditional E-value: 1.3e-136
                                 TIGR02439   3 kevqallkkvagleqeg.gnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaa 70 
                                               +e++al+k+   ++++g ++ar++ +v+r+ +dlfkaiedld++++e+w+++ey++++G   elgllaa
  lcl|FitnessBrowser__Cup4G11:RR42_RS23505   4 PEIEALVKAFILDTASGkADARVQSVVVRLTTDLFKAIEDLDLSASEVWKGIEYFAEAGP--ELGLLAA 70 
                                               699*****99887777669***************************************95..8****** PP

                                 TIGR02439  71 GlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldae 139
                                               GlGle+fld+r+d+a+akagl ggtPrtieGPlyvaGap seGfarlddgsed ++e+l+++G+v+d+ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS23505  71 GLGLERFLDIRADEAEAKAGLAGGTPRTIEGPLYVAGAPASEGFARLDDGSEDGQGEVLFMQGTVFDTS 139
                                               ********************************************************************* PP

                                 TIGR02439 140 GkpiagakvevwhanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnll 208
                                               Gkp++ga vevwhan  Gnysffdk+qs+fnlrrti+td+eG+y++rs+vP+Gyg+ppqg+tq+ll+ll
  lcl|FitnessBrowser__Cup4G11:RR42_RS23505 140 GKPLPGASVEVWHANLLGNYSFFDKTQSDFNLRRTITTDSEGRYQFRSIVPMGYGCPPQGTTQRLLDLL 208
                                               ********************************************************************* PP

                                 TIGR02439 209 GrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrfa 277
                                               GrhG+rPah+hffvsapg+rklttqin++gd+yl+ddfafa+reglv+++++ve   a +++g++++fa
  lcl|FitnessBrowser__Cup4G11:RR42_RS23505 209 GRHGRRPAHIHFFVSAPGHRKLTTQINIDGDEYLWDDFAFASREGLVPALRHVESPRALAEHGLDKPFA 277
                                               ********************************************************************* PP

                                 TIGR02439 278 eiefdlel 285
                                               +i+fd++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS23505 278 SIDFDFRL 285
                                               *****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (304 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: 7.82
//
[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