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

GapMind for catabolism of small carbon sources

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

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate H281DRAFT_00373 H281DRAFT_00373 2,3-dihydro-2,3-dihydroxybenzoyl-CoA ring cleavage enzyme

Query= SwissProt::Q84HH6
         (555 letters)



>FitnessBrowser__Burk376:H281DRAFT_00373
          Length = 556

 Score =  756 bits (1952), Expect = 0.0
 Identities = 377/546 (69%), Positives = 438/546 (80%), Gaps = 3/546 (0%)

Query: 13  VDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQRV 72
           VDYRT+PS+Y+HW L+ +G +ATL ++I EDGGIR GYKLKLNSYDLGVDIELHDA+QR+
Sbjct: 11  VDYRTDPSQYKHWKLSFNGPVATLGIDIAEDGGIRDGYKLKLNSYDLGVDIELHDAIQRI 70

Query: 73  RFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSGL 132
           RFEHPEV+TVV+TS K ++FCSGANI+MLGLS+HAWKVNFCKFTNETRNG+EDSS++SGL
Sbjct: 71  RFEHPEVKTVVLTSLKDRVFCSGANIFMLGLSSHAWKVNFCKFTNETRNGLEDSSRHSGL 130

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

Query: 193 RRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGVK 252
           R D ADIFCT+ EG+RG+RAK WRLVD+VVK  QF + IQARA  LA  SDRP+ A+GV 
Sbjct: 191 RHDRADIFCTVVEGIRGERAKAWRLVDEVVKPNQFDQAIQARALELAAQSDRPSDAQGVM 250

Query: 253 LTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQMA 312
           LT ++RT  + G  Y  +D TID   R  T T +AP          I A G  WWPLQ A
Sbjct: 251 LTRIQRTDRDDGLTYRTLDVTIDRAKRIATFTAKAPQTEQPTNIDVIVAAGANWWPLQFA 310

Query: 313 RELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRTLAR 372
           RELDDAIL++RTN L+VG W  RTEGDA+ VL  DA +  ++D+WFVRETIGMLRRTLAR
Sbjct: 311 RELDDAILSMRTNELEVGTWIFRTEGDARNVLAADAVLMQHKDHWFVRETIGMLRRTLAR 370

Query: 373 IDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML---DAAEAKNVVGLSAMNFGTFPMV 429
           IDVSSRSL+ALIEPGSCFAGT  E+A AADRSYM       E +  + LS  NFG +PMV
Sbjct: 371 IDVSSRSLFALIEPGSCFAGTFAELAFAADRSYMAALPGNEEEEPAITLSEANFGLYPMV 430

Query: 430 NGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAIEERA 489
              SR+  RFY+E AP+ AV++  G  + P EA  LGLVTA PDD+DWA+E+RIA+EERA
Sbjct: 431 THQSRLARRFYEEAAPLDAVRSLIGQAVKPVEAERLGLVTAAPDDIDWADEIRIALEERA 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: 30
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 H281DRAFT_00373 H281DRAFT_00373 (2,3-dihydro-2,3-dihydroxybenzoyl-CoA ring cleavage enzyme)
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.19813.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 1030.8   0.2          0 1030.6   0.2    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00373  H281DRAFT_00373 2,3-dihydro-2,3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00373  H281DRAFT_00373 2,3-dihydro-2,3-dihydroxybenzoyl-CoA ring cleavage enzym
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1030.6   0.2         0         0       1     548 []      11     556 .]      11     556 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1030.6 bits;  conditional E-value: 0
                                    TIGR03222   1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpe 66 
                                                  vd+rt+ps+y+hwkl+f+Gpvatl++d++edgg+rdGyklklnsydlGvdiel+da+qr+rfehpe
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373  11 VDYRTDPSQYKHWKLSFNGPVATLGIDIAEDGGIRDGYKLKLNSYDLGVDIELHDAIQRIRFEHPE 76 
                                                  89**************************************************************** PP

                                    TIGR03222  67 vrvvvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaG 132
                                                  v++vvlts kd+vfc+Gani+mlgls+ha+kvnfckftnetrng+ed+s++sglkflaavnG++aG
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373  77 VKTVVLTSLKDRVFCSGANIFMLGLSSHAWKVNFCKFTNETRNGLEDSSRHSGLKFLAAVNGACAG 142
                                                  ****************************************************************** PP

                                    TIGR03222 133 GGyelalacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGk 198
                                                  GGyelalacdei+lvddrss+vslpevpll+vlpGtGGltrvtdkr+vr+d+adifct++eG++G+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373 143 GGYELALACDEIYLVDDRSSSVSLPEVPLLGVLPGTGGLTRVTDKRKVRHDRADIFCTVVEGIRGE 208
                                                  ****************************************************************** PP

                                    TIGR03222 199 rakewrlvdevvksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidr 264
                                                  rak wrlvdevvk+++fd+a+++ra elaa+sdrp+da+Gv lt+++rt ++dg++y+t+dv+idr
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373 209 RAKAWRLVDEVVKPNQFDQAIQARALELAAQSDRPSDAQGVMLTRIQRTDRDDGLTYRTLDVTIDR 274
                                                  ****************************************************************** PP

                                    TIGR03222 265 aartatitvkgpeaaapadlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdael 330
                                                  a+r+at+t+k+p++++p++++ i+a+Ga+++pl++arelddail++r+nel++g+w++rteGda+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373 275 AKRIATFTAKAPQTEQPTNIDVIVAAGANWWPLQFARELDDAILSMRTNELEVGTWIFRTEGDARN 340
                                                  ****************************************************************** PP

                                    TIGR03222 331 vlaadalleakedhwlvreilgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymle 396
                                                  vlaada+l++++dhw+vre++g+l+rtl+r+dvssrslfal+epgscfaGt+ael+faadrsym+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373 341 VLAADAVLMQHKDHWFVRETIGMLRRTLARIDVSSRSLFALIEPGSCFAGTFAELAFAADRSYMA- 405
                                                  ****************************************************************7. PP

                                    TIGR03222 397 geleddedeeaaitlselnfgayplsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvt 462
                                                   +l+++e+ee+aitlse+nfg yp+++++srla+rf++e a+++avr+ iG+a++++eae+lglvt
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373 406 -ALPGNEEEEPAITLSEANFGLYPMVTHQSRLARRFYEEAAPLDAVRSLIGQAVKPVEAERLGLVT 470
                                                  .9**************************************************************** PP

                                    TIGR03222 463 aalddidwedeirilleeraslspdaltGleanlrfagpetmetrifgrltawqnwifnrpnavGe 528
                                                  aa+ddidw+deiri+leera++spdaltGleanlrf+gpetmetrifgrltawqnwifnrpnavGe
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373 471 AAPDDIDWADEIRIALEERAAMSPDALTGLEANLRFNGPETMETRIFGRLTAWQNWIFNRPNAVGE 536
                                                  ****************************************************************** PP

                                    TIGR03222 529 kGalklyGsGkkaqfdlerv 548
                                                  kGalk+yG+G+kaqfd++rv
  lcl|FitnessBrowser__Burk376:H281DRAFT_00373 537 KGALKVYGKGSKAQFDVSRV 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.81
//
[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