Alignments for a candidate for catA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Pseudomonas fluorescens GW456-L13

Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate PfGW456L13_3822 Catechol 1,2-dioxygenase (EC 1.13.11.1)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3822
         (309 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822
          Length = 309

 Score =  625 bits (1613), Expect = 0.0
 Identities = 309/309 (100%), Positives = 309/309 (100%)

Query: 1   MNVKISHTAEVQKFLEEASGLLNDAGNPRTKALVYRILRDSVNIIEDLAVTPEEFWKAVN 60
           MNVKISHTAEVQKFLEEASGLLNDAGNPRTKALVYRILRDSVNIIEDLAVTPEEFWKAVN
Sbjct: 1   MNVKISHTAEVQKFLEEASGLLNDAGNPRTKALVYRILRDSVNIIEDLAVTPEEFWKAVN 60

Query: 61  YLNVLGARQEAGLVVAGLGLEHYLDLLMDAEDEQAGKSGGTPRTIEGPLYVAGAPLSQGE 120
           YLNVLGARQEAGLVVAGLGLEHYLDLLMDAEDEQAGKSGGTPRTIEGPLYVAGAPLSQGE
Sbjct: 61  YLNVLGARQEAGLVVAGLGLEHYLDLLMDAEDEQAGKSGGTPRTIEGPLYVAGAPLSQGE 120

Query: 121 ARLDDGVDPGVTLFMQGRVFNTAGEPLAGAVVDVWHANTGGTYSYFDTTQSEFNLRRRIV 180
           ARLDDGVDPGVTLFMQGRVFNTAGEPLAGAVVDVWHANTGGTYSYFDTTQSEFNLRRRIV
Sbjct: 121 ARLDDGVDPGVTLFMQGRVFNTAGEPLAGAVVDVWHANTGGTYSYFDTTQSEFNLRRRIV 180

Query: 181 TDAEGRYRFRSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHVHFFISAPDHRHLTTQINL 240
           TDAEGRYRFRSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHVHFFISAPDHRHLTTQINL
Sbjct: 181 TDAEGRYRFRSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHVHFFISAPDHRHLTTQINL 240

Query: 241 DGDQYLHDDFAYATRDELIAKITFSDDQQRAAAHGVSGRFAEIDFDFTLQSSAQPEEQQR 300
           DGDQYLHDDFAYATRDELIAKITFSDDQQRAAAHGVSGRFAEIDFDFTLQSSAQPEEQQR
Sbjct: 241 DGDQYLHDDFAYATRDELIAKITFSDDQQRAAAHGVSGRFAEIDFDFTLQSSAQPEEQQR 300

Query: 301 HERVRALED 309
           HERVRALED
Sbjct: 301 HERVRALED 309


Lambda     K      H
   0.318    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: 519
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate PfGW456L13_3822 (Catechol 1,2-dioxygenase (EC 1.13.11.1))
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.2751.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     1e-141  456.9   0.1   1.1e-141  456.7   0.1    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822  Catechol 1,2-dioxygenase (EC 1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822  Catechol 1,2-dioxygenase (EC 1.13.11.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.7   0.1  1.1e-141  1.1e-141       2     285 .]       8     289 ..       7     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.7 bits;  conditional E-value: 1.1e-141
                                               TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveyl 56 
                                                             t+evq++l++++gl ++ gn+r+k +v r+l+d ++ iedl +t++efw+av+yl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822   8 TAEVQKFLEEASGLLNDAGNPRTKALVYRILRDSVNIIEDLAVTPEEFWKAVNYL 62 
                                                             78***************************************************** PP

                                               TIGR02439  57 nklGqanelgllaaGlGlehfldlrldaadakagleggtPrtieGPlyvaGapvs 111
                                                             n lG+++e+gl++aGlGleh+ldl++da d++ag +ggtPrtieGPlyvaGap+s
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822  63 NVLGARQEAGLVVAGLGLEHYLDLLMDAEDEQAGKSGGTPRTIEGPLYVAGAPLS 117
                                                             ******************************************************* PP

                                               TIGR02439 112 eGfarlddgseddkaetlvlkGqvldaeGkpiagakvevwhanskGnysffdksq 166
                                                             +G+arlddg   d + tl+++G+v++++G+p+aga+v+vwhan+ G+ys+fd +q
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822 118 QGEARLDDGV--DPGVTLFMQGRVFNTAGEPLAGAVVDVWHANTGGTYSYFDTTQ 170
                                                             **********..668**************************************** PP

                                               TIGR02439 167 sefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPahvhff 221
                                                             sefnlrr+i+tdaeG+yr+rs+vP+Gyg+pp+gptqqll++lGrhG+rPahvhff
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822 171 SEFNLRRRIVTDAEGRYRFRSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHVHFF 225
                                                             ******************************************************* PP

                                               TIGR02439 222 vsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrf 276
                                                             +sap +r+lttqinl+gd+yl+ddfa+atr++l+a++++ +d+++a+++gv grf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822 226 ISAPDHRHLTTQINLDGDQYLHDDFAYATRDELIAKITFSDDQQRAAAHGVSGRF 280
                                                             ******************************************************* PP

                                               TIGR02439 277 aeiefdlel 285
                                                             aei+fd++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3822 281 AEIDFDFTL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 10.55
//
[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