Alignments for a candidate for catA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Pseudomonas simiae WCS417

Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate GFF4624 PS417_23660 catechol 1,2-dioxygenase

Query= reanno::WCS417:GFF4624
         (309 letters)



>FitnessBrowser__WCS417:GFF4624
          Length = 309

 Score =  629 bits (1622), Expect = 0.0
 Identities = 309/309 (100%), Positives = 309/309 (100%)

Query: 1   MSIRLSQTAHAQQFLEEASGNLNDGGNPRTKALVYRILRDTVNIIEDLEVTPEEFWKAVN 60
           MSIRLSQTAHAQQFLEEASGNLNDGGNPRTKALVYRILRDTVNIIEDLEVTPEEFWKAVN
Sbjct: 1   MSIRLSQTAHAQQFLEEASGNLNDGGNPRTKALVYRILRDTVNIIEDLEVTPEEFWKAVN 60

Query: 61  YLNELGKHQEAGLLAAGLGLEHYLDLLMDAADEKAGKSGGTPRTIEGPLYVAGAPLSKYE 120
           YLNELGKHQEAGLLAAGLGLEHYLDLLMDAADEKAGKSGGTPRTIEGPLYVAGAPLSKYE
Sbjct: 61  YLNELGKHQEAGLLAAGLGLEHYLDLLMDAADEKAGKSGGTPRTIEGPLYVAGAPLSKYE 120

Query: 121 ARLDDGKDDAVPLFMRGQVRDTEGKPLAGAIVDVWQANTAGTYSWFDPTQSEFNLRRRIE 180
           ARLDDGKDDAVPLFMRGQVRDTEGKPLAGAIVDVWQANTAGTYSWFDPTQSEFNLRRRIE
Sbjct: 121 ARLDDGKDDAVPLFMRGQVRDTEGKPLAGAIVDVWQANTAGTYSWFDPTQSEFNLRRRIE 180

Query: 181 TDAQGNYRFRSIVPSGYGCPPSGPTQQLLDQLGRHGQRPAHIHFFISAPGHRHLTTQINL 240
           TDAQGNYRFRSIVPSGYGCPPSGPTQQLLDQLGRHGQRPAHIHFFISAPGHRHLTTQINL
Sbjct: 181 TDAQGNYRFRSIVPSGYGCPPSGPTQQLLDQLGRHGQRPAHIHFFISAPGHRHLTTQINL 240

Query: 241 SDDPYLHDDFAYATRDELIAQIRFSDDPQLAREFGVEGRFAQIDFDFELQVADAPVEQKR 300
           SDDPYLHDDFAYATRDELIAQIRFSDDPQLAREFGVEGRFAQIDFDFELQVADAPVEQKR
Sbjct: 241 SDDPYLHDDFAYATRDELIAQIRFSDDPQLAREFGVEGRFAQIDFDFELQVADAPVEQKR 300

Query: 301 MQRVRALED 309
           MQRVRALED
Sbjct: 301 MQRVRALED 309


Lambda     K      H
   0.318    0.137    0.408 

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: 506
Number of extensions: 15
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: 309
Length of database: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
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: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate GFF4624 PS417_23660 (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.11450.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.9e-142  458.3   0.0   4.5e-142  458.1   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4624  PS417_23660 catechol 1,2-dioxyge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4624  PS417_23660 catechol 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.1   0.0  4.5e-142  4.5e-142       2     285 .]       8     289 ..       7     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 458.1 bits;  conditional E-value: 4.5e-142
                           TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaGlGleh 76 
                                         t++ q++l++++g+ ++ggn+r+k +v r+l+d+++ iedl++t++efw+av+yln+lG+++e+gllaaGlGleh
  lcl|FitnessBrowser__WCS417:GFF4624   8 TAHAQQFLEEASGNLNDGGNPRTKALVYRILRDTVNIIEDLEVTPEEFWKAVNYLNELGKHQEAGLLAAGLGLEH 82 
                                         56789********************************************************************** PP

                           TIGR02439  77 fldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGkpiagakvevw 151
                                         +ldl++daad+kag +ggtPrtieGPlyvaGap+s+ +arlddg+  d+a +l+++Gqv+d+eGkp+aga+v+vw
  lcl|FitnessBrowser__WCS417:GFF4624  83 YLDLLMDAADEKAGKSGGTPRTIEGPLYVAGAPLSKYEARLDDGK--DDAVPLFMRGQVRDTEGKPLAGAIVDVW 155
                                         ********************************************9..457************************* PP

                           TIGR02439 152 hanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPahvhffvsapg 226
                                         +an+ G+ys+fd++qsefnlrr+i tda+G+yr+rs+vP+Gyg+pp+gptqqll++lGrhG+rPah+hff+sapg
  lcl|FitnessBrowser__WCS417:GFF4624 156 QANTAGTYSWFDPTQSEFNLRRRIETDAQGNYRFRSIVPSGYGCPPSGPTQQLLDQLGRHGQRPAHIHFFISAPG 230
                                         *************************************************************************** PP

                           TIGR02439 227 yrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrfaeiefdlel 285
                                         +r+lttqinl++d+yl+ddfa+atr++l+a++++ +d + a++ gvegrfa+i+fd+el
  lcl|FitnessBrowser__WCS417:GFF4624 231 HRHLTTQINLSDDPYLHDDFAYATRDELIAQIRFSDDPQLAREFGVEGRFAQIDFDFEL 289
                                         *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (309 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.77
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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