Alignments for a candidate for catA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Pseudomonas fluorescens FW300-N2E3

Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate AO353_23525 AO353_23525 catechol 1,2-dioxygenase

Query= reanno::pseudo3_N2E3:AO353_23525
         (309 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_23525
          Length = 309

 Score =  627 bits (1617), Expect = 0.0
 Identities = 309/309 (100%), Positives = 309/309 (100%)

Query: 1   MNAKISHTASAQKFLEEASGLLNDAGNPRAKALIYRILRDSVNIIEDLEVTPEEFWKAVN 60
           MNAKISHTASAQKFLEEASGLLNDAGNPRAKALIYRILRDSVNIIEDLEVTPEEFWKAVN
Sbjct: 1   MNAKISHTASAQKFLEEASGLLNDAGNPRAKALIYRILRDSVNIIEDLEVTPEEFWKAVN 60

Query: 61  YLNELGARQEAGLLVAGLGLEHYLDLLMDAEDAQAGKTGGTPRTIEGPLYVAGAPLSNGE 120
           YLNELGARQEAGLLVAGLGLEHYLDLLMDAEDAQAGKTGGTPRTIEGPLYVAGAPLSNGE
Sbjct: 61  YLNELGARQEAGLLVAGLGLEHYLDLLMDAEDAQAGKTGGTPRTIEGPLYVAGAPLSNGE 120

Query: 121 ARLDDGVDPGVVLFMQGQVKNTDGKPLAGAVVDVWHANTGGTYSYFDGSQSEFNLRRRIV 180
           ARLDDGVDPGVVLFMQGQVKNTDGKPLAGAVVDVWHANTGGTYSYFDGSQSEFNLRRRIV
Sbjct: 121 ARLDDGVDPGVVLFMQGQVKNTDGKPLAGAVVDVWHANTGGTYSYFDGSQSEFNLRRRIV 180

Query: 181 TDAEGRYRFRSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHIHFFISADDHRHLTTQINL 240
           TDAEGRYRFRSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHIHFFISADDHRHLTTQINL
Sbjct: 181 TDAEGRYRFRSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHIHFFISADDHRHLTTQINL 240

Query: 241 DGDKYLHDDFAYATRDELIAKITFSDDQQRAREHGVSGRFAEIEFDFTLQSSAQPEEQHR 300
           DGDKYLHDDFAYATRDELIAKITFSDDQQRAREHGVSGRFAEIEFDFTLQSSAQPEEQHR
Sbjct: 241 DGDKYLHDDFAYATRDELIAKITFSDDQQRAREHGVSGRFAEIEFDFTLQSSAQPEEQHR 300

Query: 301 HERVRALED 309
           HERVRALED
Sbjct: 301 HERVRALED 309


Lambda     K      H
   0.317    0.136    0.401 

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: 501
Number of extensions: 11
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate AO353_23525 AO353_23525 (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.12817.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     5e-143  461.2   0.1   5.7e-143  461.0   0.1    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_23525  AO353_23525 catechol 1,2-dioxyge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_23525  AO353_23525 catechol 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.0   0.1  5.7e-143  5.7e-143       2     285 .]       8     289 ..       7     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 461.0 bits;  conditional E-value: 5.7e-143
                                     TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelg 66 
                                                   t+  q++l++++gl ++ gn+r+k ++ r+l+d ++ iedl++t++efw+av+yln+lG+++e+g
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_23525   8 TASAQKFLEEASGLLNDAGNPRAKALIYRILRDSVNIIEDLEVTPEEFWKAVNYLNELGARQEAG 72 
                                                   66789************************************************************ PP

                                     TIGR02439  67 llaaGlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvl 131
                                                   ll+aGlGleh+ldl++da da+ag +ggtPrtieGPlyvaGap+s+G+arlddg   d + +l++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_23525  73 LLVAGLGLEHYLDLLMDAEDAQAGKTGGTPRTIEGPLYVAGAPLSNGEARLDDGV--DPGVVLFM 135
                                                   *******************************************************..668***** PP

                                     TIGR02439 132 kGqvldaeGkpiagakvevwhanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvp 196
                                                   +Gqv +++Gkp+aga+v+vwhan+ G+ys+fd sqsefnlrr+i+tdaeG+yr+rs+vP+Gyg+p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_23525 136 QGQVKNTDGKPLAGAVVDVWHANTGGTYSYFDGSQSEFNLRRRIVTDAEGRYRFRSIVPSGYGCP 200
                                                   ***************************************************************** PP

                                     TIGR02439 197 pqgptqqllnllGrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkev 261
                                                   p+gptqqll++lGrhG+rPah+hff+sa+ +r+lttqinl+gdkyl+ddfa+atr++l+a++++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_23525 201 PDGPTQQLLDQLGRHGQRPAHIHFFISADDHRHLTTQINLDGDKYLHDDFAYATRDELIAKITFS 265
                                                   ***************************************************************** PP

                                     TIGR02439 262 edaaaakrrgvegrfaeiefdlel 285
                                                   +d+++a+++gv grfaeiefd++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_23525 266 DDQQRAREHGVSGRFAEIEFDFTL 289
                                                   **********************87 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.87
//
[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