GapMind for catabolism of small carbon sources

 

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

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate H281DRAFT_01594 H281DRAFT_01594 3-oxoadipate enol-lactonase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__Burk376:H281DRAFT_01594
          Length = 263

 Score =  487 bits (1254), Expect = e-143
 Identities = 238/263 (90%), Positives = 251/263 (95%)

Query: 1   MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60
           MPYAAVNGTELHYRIDG+RHGNAPWIVLSNSLG+DLSMW PQVAALSKHFRVLRYDTRGH
Sbjct: 1   MPYAAVNGTELHYRIDGDRHGNAPWIVLSNSLGSDLSMWTPQVAALSKHFRVLRYDTRGH 60

Query: 61  GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120
           GHSEAPKGPYTIEQL+GDVLGLMDTLKIARANFCG+SMGGLTGVALAARHA+R ERV L 
Sbjct: 61  GHSEAPKGPYTIEQLSGDVLGLMDTLKIARANFCGVSMGGLTGVALAARHANRFERVVLA 120

Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180
           NTAARIGSPEVWVPRA +ARTEGM AL+DAVLPRWFTADY+EREPVVLAMIRDVFVHTDK
Sbjct: 121 NTAARIGSPEVWVPRAARARTEGMLALSDAVLPRWFTADYIEREPVVLAMIRDVFVHTDK 180

Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVELDAS 240
           EGYASNC+AIDA DLRPE  GIK+P LVISGTHD+AATPAQGRELAQAI GARYVELDAS
Sbjct: 181 EGYASNCDAIDATDLRPETHGIKLPVLVISGTHDVAATPAQGRELAQAIPGARYVELDAS 240

Query: 241 HISNIERADAFTKTVVDFLTEQK 263
           HISNIE+ADAFTKTV+DFLTE K
Sbjct: 241 HISNIEKADAFTKTVIDFLTEPK 263


Lambda     K      H
   0.320    0.134    0.402 

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: 372
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: 263
Length of database: 263
Length adjustment: 25
Effective length of query: 238
Effective length of database: 238
Effective search space:    56644
Effective search space used:    56644
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate H281DRAFT_01594 H281DRAFT_01594 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

# 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/TIGR02427.hmm
# target sequence database:        /tmp/gapView.22642.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02427  [M=251]
Accession:   TIGR02427
Description: protocat_pcaD: 3-oxoadipate enol-lactonase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.7e-103  331.4   0.1   1.9e-103  331.2   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01594  H281DRAFT_01594 3-oxoadipate eno


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01594  H281DRAFT_01594 3-oxoadipate enol-lactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.2   0.1  1.9e-103  1.9e-103       2     251 .]      11     260 ..      10     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 331.2 bits;  conditional E-value: 1.9e-103
                                    TIGR02427   2 lhyrlegae.adkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedla 66 
                                                  lhyr++g++  ++p++vl+nSLG+dl++w ++++al+k+frvlryD+rGHG+S++p+gpy+ie+l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01594  11 LHYRIDGDRhGNAPWIVLSNSLGSDLSMWTPQVAALSKHFRVLRYDTRGHGHSEAPKGPYTIEQLS 76 
                                                  9*****8762589***************************************************** PP

                                    TIGR02427  67 ddvlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavrae 132
                                                  +dvl+l+D+l+i++a++cG+S+GGl++ aLaar+++r+e++vl+ntaa+ig++e+W +R+a+ r+e
  lcl|FitnessBrowser__Burk376:H281DRAFT_01594  77 GDVLGLMDTLKIARANFCGVSMGGLTGVALAARHANRFERVVLANTAARIGSPEVWVPRAARARTE 142
                                                  ****************************************************************** PP

                                    TIGR02427 133 GlaaladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlv 198
                                                  G+ al+davl rwFt+++ e+ep  l+++r+++v++++egYa++c+Ai ++dlr +++ i++P+lv
  lcl|FitnessBrowser__Burk376:H281DRAFT_01594 143 GMLALSDAVLPRWFTADYIEREPVVLAMIRDVFVHTDKEGYASNCDAIDATDLRPETHGIKLPVLV 208
                                                  ****************************************************************** PP

                                    TIGR02427 199 iaGdeDgstPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdflk 251
                                                  i+G++D+++ p++ re+a+++pgar++e++ a+H++n+e+++af+++++dfl+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01594 209 ISGTHDVAATPAQGRELAQAIPGARYVELD-ASHISNIEKADAFTKTVIDFLT 260
                                                  ******************************.********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (263 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: 8.10
//
[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:

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:

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:

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:

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