Alignments for a candidate for boxC in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for boxC in Burkholderia phytofirmans PsJN

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate BPHYT_RS13345 BPHYT_RS13345 crotonase

Query= SwissProt::Q84HH6
         (555 letters)



>FitnessBrowser__BFirm:BPHYT_RS13345
          Length = 556

 Score =  761 bits (1964), Expect = 0.0
 Identities = 379/546 (69%), Positives = 443/546 (81%), Gaps = 3/546 (0%)

Query: 13  VDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQRV 72
           VDYRTEPS+Y+HW L+ +G +ATL ++I EDGGIR GYKLKLNSYDLGVDIELHDA+QR+
Sbjct: 11  VDYRTEPSQYKHWKLSFNGPVATLGIDIAEDGGIRDGYKLKLNSYDLGVDIELHDAVQRI 70

Query: 73  RFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSGL 132
           RFEHPEV+TVV+TS K ++FCSGANI+MLGLSTHAWKVNFCKFTNETRNG+EDSS++SGL
Sbjct: 71  RFEHPEVKTVVLTSLKDRVFCSGANIFMLGLSTHAWKVNFCKFTNETRNGLEDSSRHSGL 130

Query: 133 KFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRRV 192
           KFLAA NG  AGGGYELALACDEI LVDDR+SSVSLPEVPLLGVLPGTGGLTRVTDKR+V
Sbjct: 131 KFLAAVNGACAGGGYELALACDEIYLVDDRSSSVSLPEVPLLGVLPGTGGLTRVTDKRKV 190

Query: 193 RRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGVK 252
           R D ADIFCT+ EGVRG+RAK WRLVD+VVK  QF + IQARA  LA+ SDRPA A+GV 
Sbjct: 191 RHDRADIFCTVVEGVRGERAKAWRLVDEVVKPNQFDQAIQARALELAEQSDRPADAQGVV 250

Query: 253 LTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQMA 312
           LT +ERT  E+G  Y+ +D TID   R  T T +AP +       EI A G+ WWPLQ A
Sbjct: 251 LTRIERTDREEGLTYKTLDVTIDRAKRIATFTAKAPQSEPPTNIDEIVAAGVNWWPLQFA 310

Query: 313 RELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRTLAR 372
           RELDDAIL +RTN L VG W  +TEGDA+ +L  DA++  ++D+WFVRETIG+LRRTLAR
Sbjct: 311 RELDDAILCMRTNELAVGTWVFKTEGDARNLLAADASLMQHKDHWFVRETIGLLRRTLAR 370

Query: 373 IDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML---DAAEAKNVVGLSAMNFGTFPMV 429
           IDVSSRSL+ALIEPGSCFAGT  E+A AADR+YM       E +  + LS +NFG +PMV
Sbjct: 371 IDVSSRSLFALIEPGSCFAGTFAELAFAADRTYMAALPSNEEEEPAITLSEVNFGLYPMV 430

Query: 430 NGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAIEERA 489
              SR+  RFY+E  P+ AV++  G  + P EA  LGLVTA PDD+DWA+E+RIA+EERA
Sbjct: 431 THQSRLGRRFYEEAEPLDAVRSLIGQPIKPVEAERLGLVTASPDDIDWADEIRIALEERA 490

Query: 490 ALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSGKKAQ 549
           A+SPDALTGLEANLRF   ETM TRIFGRL+AWQNWIFNRPNAVGE GALK++G G KAQ
Sbjct: 491 AMSPDALTGLEANLRFNGPETMETRIFGRLTAWQNWIFNRPNAVGEKGALKVYGKGSKAQ 550

Query: 550 FDWNRV 555
           FD +RV
Sbjct: 551 FDVSRV 556


Lambda     K      H
   0.318    0.134    0.397 

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: 851
Number of extensions: 28
Number of successful extensions: 2
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: 555
Length of database: 556
Length adjustment: 36
Effective length of query: 519
Effective length of database: 520
Effective search space:   269880
Effective search space used:   269880
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate BPHYT_RS13345 BPHYT_RS13345 (crotonase)
to HMM TIGR03222 (boxC: benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44))

# 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/TIGR03222.hmm
# target sequence database:        /tmp/gapView.28113.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03222  [M=548]
Accession:   TIGR03222
Description: benzo_boxC: benzoyl-CoA-dihydrodiol lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
          0 1017.6   0.0          0 1017.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13345  BPHYT_RS13345 crotonase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13345  BPHYT_RS13345 crotonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1017.4   0.0         0         0       1     548 []      11     556 .]      11     556 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1017.4 bits;  conditional E-value: 0
                                TIGR03222   1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpevrvv 70 
                                              vd+rteps+y+hwkl+f+Gpvatl++d++edgg+rdGyklklnsydlGvdiel+da+qr+rfehpev++v
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345  11 VDYRTEPSQYKHWKLSFNGPVATLGIDIAEDGGIRDGYKLKLNSYDLGVDIELHDAVQRIRFEHPEVKTV 80 
                                              89******************************************************************** PP

                                TIGR03222  71 vltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaGGGyelala 140
                                              vlts kd+vfc+Gani+mlglstha+kvnfckftnetrng+ed+s++sglkflaavnG++aGGGyelala
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345  81 VLTSLKDRVFCSGANIFMLGLSTHAWKVNFCKFTNETRNGLEDSSRHSGLKFLAAVNGACAGGGYELALA 150
                                              ********************************************************************** PP

                                TIGR03222 141 cdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGkrakewrlvdevv 210
                                              cdei+lvddrss+vslpevpll+vlpGtGGltrvtdkr+vr+d+adifct++eGv+G+rak wrlvdevv
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345 151 CDEIYLVDDRSSSVSLPEVPLLGVLPGTGGLTRVTDKRKVRHDRADIFCTVVEGVRGERAKAWRLVDEVV 220
                                              ********************************************************************** PP

                                TIGR03222 211 ksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidraartatitvkgpeaaa 280
                                              k+++fd+a+++ra ela +sdrpada+Gv+lt++ert +e+g++y+t+dv+idra+r+at+t+k+p+++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345 221 KPNQFDQAIQARALELAEQSDRPADAQGVVLTRIERTDREEGLTYKTLDVTIDRAKRIATFTAKAPQSEP 290
                                              ********************************************************************** PP

                                TIGR03222 281 padlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdaelvlaadalleakedhwlvrei 350
                                              p+++++i+a+G++++pl++arelddail +r+nel +g+wv++teGda+ +laada l++++dhw+vre+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345 291 PTNIDEIVAAGVNWWPLQFARELDDAILCMRTNELAVGTWVFKTEGDARNLLAADASLMQHKDHWFVRET 360
                                              ********************************************************************** PP

                                TIGR03222 351 lgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymlegeleddedeeaaitlselnfgayp 420
                                              +gll+rtl+r+dvssrslfal+epgscfaGt+ael+faadr+ym+  +l+++e+ee+aitlse+nfg yp
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345 361 IGLLRRTLARIDVSSRSLFALIEPGSCFAGTFAELAFAADRTYMA--ALPSNEEEEPAITLSEVNFGLYP 428
                                              ********************************************7..9********************** PP

                                TIGR03222 421 lsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleeraslspdalt 490
                                              +++++srl +rf++e ++++avr+ iG+ ++++eae+lglvta +ddidw+deiri+leera++spdalt
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345 429 MVTHQSRLGRRFYEEAEPLDAVRSLIGQPIKPVEAERLGLVTASPDDIDWADEIRIALEERAAMSPDALT 498
                                              ********************************************************************** PP

                                TIGR03222 491 GleanlrfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548
                                              Gleanlrf+gpetmetrifgrltawqnwifnrpnavGekGalk+yG+G+kaqfd++rv
  lcl|FitnessBrowser__BFirm:BPHYT_RS13345 499 GLEANLRFNGPETMETRIFGRLTAWQNWIFNRPNAVGEKGALKVYGKGSKAQFDVSRV 556
                                              ********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (548 nodes)
Target sequences:                          1  (556 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.49
//
[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