Alignments for a candidate for xylE in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylE in Pseudomonas benzenivorans DSM 8628

Align catechol 2,3-dioxygenase (EC 1.13.11.2) (characterized)
to candidate WP_090439188.1 BLS63_RS02475 catechol 2,3-dioxygenase

Query= BRENDA::E7DDG2
         (307 letters)



>NCBI__GCF_900100495.1:WP_090439188.1
          Length = 307

 Score =  620 bits (1600), Expect = 0.0
 Identities = 296/307 (96%), Positives = 302/307 (98%)

Query: 1   MKKGVMRPGHVQLRVLNLESALAHYRDLLGLIEMDRDEQGRVYLKAWTEVDKFSVVLREA 60
           MKKGVMRPGHVQLRVLNLESALAHYRDLLGLIEMDRDEQGRVYLKAWTEVDKFSVVLREA
Sbjct: 1   MKKGVMRPGHVQLRVLNLESALAHYRDLLGLIEMDRDEQGRVYLKAWTEVDKFSVVLREA 60

Query: 61  DQPGMDFMGFKVIDEDCLNRLTQDLLNYGCLIETIPAGELKGCGRRVRFQTPSGHFFELY 120
           DQPGMDFMGFKVIDEDCLNRLTQDLLNYGCLIETIPAGELKGCGRRVRFQ PSGHFFELY
Sbjct: 61  DQPGMDFMGFKVIDEDCLNRLTQDLLNYGCLIETIPAGELKGCGRRVRFQAPSGHFFELY 120

Query: 121 ADKEYTGKWGLEEINPEAWPRNLKGMRAVRFDHCLLYGDELQATYALFTEVLGFYLAEQV 180
           ADKEYTGKWGLEEINPEAWPRNLKGMRAVRFDHCLLYGDELQATYALFTEVLGFYLAEQV
Sbjct: 121 ADKEYTGKWGLEEINPEAWPRNLKGMRAVRFDHCLLYGDELQATYALFTEVLGFYLAEQV 180

Query: 181 IDDDGTRVAQFLSLSTKAHDVAFIHCPEKGKFHHVSFFLETWEDVLRAADLISMTDTSID 240
           +DD+GTR+AQFLSLSTKAHDVAFI   EKG+FHH SFFLETWEDVLRAADLISMTDTSID
Sbjct: 181 VDDNGTRIAQFLSLSTKAHDVAFIQHTEKGRFHHASFFLETWEDVLRAADLISMTDTSID 240

Query: 241 IGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYQDHKPVTWLAKDLGKAIFYHDRVLNE 300
           IGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYQDHKPVTWLAKDLGKAIFYHDRVLNE
Sbjct: 241 IGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYQDHKPVTWLAKDLGKAIFYHDRVLNE 300

Query: 301 RFMTVLS 307
           RF+TVL+
Sbjct: 301 RFLTVLT 307


Lambda     K      H
   0.324    0.141    0.444 

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: 307
Length of database: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_090439188.1 BLS63_RS02475 (catechol 2,3-dioxygenase)
to HMM TIGR03211 (catechol 2,3 dioxygenase (EC 1.13.11.2))

# 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/TIGR03211.hmm
# target sequence database:        /tmp/gapView.17511.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03211  [M=303]
Accession:   TIGR03211
Description: catechol_2_3: catechol 2,3 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-135  435.9   0.0   4.4e-135  435.7   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090439188.1  BLS63_RS02475 catechol 2,3-dioxy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090439188.1  BLS63_RS02475 catechol 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.7   0.0  4.4e-135  4.4e-135       1     303 []       4     307 .]       4     307 .] 0.99

  Alignments for each domain:
  == domain 1  score: 435.7 bits;  conditional E-value: 4.4e-135
                                 TIGR03211   1 gvlrlghvelrvldleealkfykdvlGleetgrdeq.svYlkawdewdkysvilteadkagldhvafkv 68 
                                               gv+r+ghv+lrvl+le+al +y+d+lGl e++rdeq +vYlkaw+e+dk+sv+l+ead++g+d+++fkv
  lcl|NCBI__GCF_900100495.1:WP_090439188.1   4 GVMRPGHVQLRVLNLESALAHYRDLLGLIEMDRDEQgRVYLKAWTEVDKFSVVLREADQPGMDFMGFKV 72 
                                               69******************************************************************* PP

                                 TIGR03211  69 eseadLeklekkleaaGveverieagedlevGeavrfelPsgheleLyaekelvg.ekkgklnpdpwkk 136
                                                +e+ L++l+++l ++G+ +e+i+age++++G++vrf++Psgh +eLya+ke++g +  +++np++w++
  lcl|NCBI__GCF_900100495.1:WP_090439188.1  73 IDEDCLNRLTQDLLNYGCLIETIPAGELKGCGRRVRFQAPSGHFFELYADKEYTGkWGLEEINPEAWPR 141
                                               *****************************************************886899********** PP

                                 TIGR03211 137 elkGvaakrldHvlllaedveenvklltevLgfkltEqvvaedgkeqlaaflsvsnkahdiafvkdpek 205
                                               +lkG++a r+dH+ll++++++++ +l+tevLgf+l+Eqvv+++g++ +a+fls+s+kahd+af++++ek
  lcl|NCBI__GCF_900100495.1:WP_090439188.1 142 NLKGMRAVRFDHCLLYGDELQATYALFTEVLGFYLAEQVVDDNGTR-IAQFLSLSTKAHDVAFIQHTEK 209
                                               *****************************************99996.********************** PP

                                 TIGR03211 206 gklhHvsflldswedvlkaaDvlskndvkidvgptrHgitrgqtiYvfdPsGnrvElfaggylaypdwe 274
                                               g++hH+sf+l++wedvl+aaD++s++d++id+gptrHg+t+g+tiY+fdPsGnr+E+f+gg ++y d++
  lcl|NCBI__GCF_900100495.1:WP_090439188.1 210 GRFHHASFFLETWEDVLRAADLISMTDTSIDIGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYQDHK 278
                                               ********************************************************************* PP

                                 TIGR03211 275 pitWtedelgrgifyherklnesfltvlt 303
                                               p+tW +++lg++ifyh+r+lne+fltvlt
  lcl|NCBI__GCF_900100495.1:WP_090439188.1 279 PVTWLAKDLGKAIFYHDRVLNERFLTVLT 307
                                               **************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (303 nodes)
Target sequences:                          1  (307 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.26
//
[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 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