Alignments for a candidate for catA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Paraburkholderia bryophila 376MFSha3.1

Align catechol 1,2-dioxygenase 1; EC 1.13.11.1 (characterized)
to candidate H281DRAFT_01643 H281DRAFT_01643 catechol 1,2-dioxygenase

Query= CharProtDB::CH_014952
         (311 letters)



>FitnessBrowser__Burk376:H281DRAFT_01643
          Length = 312

 Score =  520 bits (1338), Expect = e-152
 Identities = 253/311 (81%), Positives = 271/311 (87%)

Query: 1   MSIKVFGTKEVQDLLKAATNLEGKGGNARSKQIVHRLLSDLFKAIDDLDITPDEVWAGVN 60
           M++KVF T+EVQDLLKAA NL+   G+AR+KQI HRLLSDLFKAIDDLDITPDE WAGVN
Sbjct: 2   MNVKVFATQEVQDLLKAAANLDSDKGDARTKQIAHRLLSDLFKAIDDLDITPDETWAGVN 61

Query: 61  YLNKLGQDGEATLLAAGSGLEKYLDIRLDAADKAEGIEGGTPRTIEGPLYVAGATVHDGV 120
           YLNKLGQDGEA LLAAG GLEKYLDIR+DA D+   I+GGTPRTIEGPLYV GA V DGV
Sbjct: 62  YLNKLGQDGEAALLAAGLGLEKYLDIRMDAEDRQAEIDGGTPRTIEGPLYVEGAPVRDGV 121

Query: 121 SKIDINPDEDAGPLVIHGTVTGPDGKPVAGAVVECWHANSKGFYSHFDPTGAQSDFNLRG 180
           SKID++ D DAGPLVI GTV GPDGKPVAGAVVECWHANSKGFYSHFDPTGAQS FNLRG
Sbjct: 122 SKIDLDADADAGPLVIRGTVRGPDGKPVAGAVVECWHANSKGFYSHFDPTGAQSPFNLRG 181

Query: 181 AVKTGADGKYEFRTLMPVGYGCPPQGATQQLLNVLGRHGNRPAHVHFFVSSDSARKLTTQ 240
           AV+T  DG YEFRTLMPVGYGCPPQGATQQLLNVL RHGNRPAHVHFFV +D  RKLTTQ
Sbjct: 182 AVRTQDDGTYEFRTLMPVGYGCPPQGATQQLLNVLARHGNRPAHVHFFVKADGLRKLTTQ 241

Query: 241 FNIEGDPLIWDDFAYATREELIPPVTEKKGGTALGLKADTYKDIEFNLTLTSLVKGKDNQ 300
            NIEGDPLIWDDFAYATRE+LIPPV  K GG ALGLK D YK+IEFN TLT LV+GKDNQ
Sbjct: 242 INIEGDPLIWDDFAYATREDLIPPVVGKSGGAALGLKDDAYKEIEFNFTLTPLVEGKDNQ 301

Query: 301 VVHRLRAEVAA 311
           +V+RLR   AA
Sbjct: 302 LVNRLRTAAAA 312


Lambda     K      H
   0.316    0.136    0.404 

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: 479
Number of extensions: 16
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: 311
Length of database: 312
Length adjustment: 27
Effective length of query: 284
Effective length of database: 285
Effective search space:    80940
Effective search space used:    80940
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 H281DRAFT_01643 H281DRAFT_01643 (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.26657.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.8e-138  444.6   0.0   6.7e-138  444.4   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01643  H281DRAFT_01643 catechol 1,2-dio


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01643  H281DRAFT_01643 catechol 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.4   0.0  6.7e-138  6.7e-138       2     285 .]       9     291 ..       8     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 444.4 bits;  conditional E-value: 6.7e-138
                                    TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgl 67 
                                                  t+evq+llk++a+l++++g+ar+kqi +r+lsdlfkai+dldit+de wa+v+ylnklGq++e++l
  lcl|FitnessBrowser__Burk376:H281DRAFT_01643   9 TQEVQDLLKAAANLDSDKGDARTKQIAHRLLSDLFKAIDDLDITPDETWAGVNYLNKLGQDGEAAL 74 
                                                  79**************************************************************** PP

                                    TIGR02439  68 laaGlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkG 133
                                                  laaGlGle++ld+r+da d++a+++ggtPrtieGPlyv Gapv +G++++d +++ d a +lv++G
  lcl|FitnessBrowser__Burk376:H281DRAFT_01643  75 LAAGLGLEKYLDIRMDAEDRQAEIDGGTPRTIEGPLYVEGAPVRDGVSKIDLDADAD-AGPLVIRG 139
                                                  ******************************************************555.99****** PP

                                    TIGR02439 134 qvldaeGkpiagakvevwhanskGnysffdks..qsefnlrrtiitdaeGkyrarsvvPvGygvpp 197
                                                  +v+  +Gkp+aga+ve+whanskG+ys+fd++  qs+fnlr++++t+++G+y++r+++PvGyg+pp
  lcl|FitnessBrowser__Burk376:H281DRAFT_01643 140 TVRGPDGKPVAGAVVECWHANSKGFYSHFDPTgaQSPFNLRGAVRTQDDGTYEFRTLMPVGYGCPP 205
                                                  *******************************999******************************** PP

                                    TIGR02439 198 qgptqqllnllGrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkeved 263
                                                  qg+tqqlln+l rhG+rPahvhffv a+g rklttqin+egd++++ddfa+atre+l++ v  +++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01643 206 QGATQQLLNVLARHGNRPAHVHFFVKADGLRKLTTQINIEGDPLIWDDFAYATREDLIPPVVGKSG 271
                                                  ****************************************************************** PP

                                    TIGR02439 264 aaaakrrgvegrfaeiefdlel 285
                                                   aa     +++ ++eief+++l
  lcl|FitnessBrowser__Burk376:H281DRAFT_01643 272 GAALG--LKDDAYKEIEFNFTL 291
                                                  *9999..899**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (312 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: 00:00:00.01
# Mc/sec: 7.52
//
[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, or view the source code.

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