Alignments for a candidate for boxC in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for boxC in Acidovorax sp. GW101-3H11

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate Ac3H11_3085 Benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44)

Query= SwissProt::Q84HH6
         (555 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3085
          Length = 556

 Score =  736 bits (1901), Expect = 0.0
 Identities = 366/546 (67%), Positives = 429/546 (78%), Gaps = 3/546 (0%)

Query: 13  VDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQRV 72
           VDYRT+P++YRHW LA DG +A L+L+I EDGGIRPGYKLKLNSYDLGVDIELHDAL R+
Sbjct: 11  VDYRTDPTQYRHWKLAVDGAVARLSLDIAEDGGIRPGYKLKLNSYDLGVDIELHDALNRI 70

Query: 73  RFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSGL 132
           RFEHP+VR+V+VTS + +IFCSGANI+MLG+S+HAWKVNFCKFTNETRNGIEDSS++SGL
Sbjct: 71  RFEHPQVRSVIVTSARDRIFCSGANIFMLGVSSHAWKVNFCKFTNETRNGIEDSSKHSGL 130

Query: 133 KFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRRV 192
           KF+AA NG  AGGGYELALACDEIVLVDDR+S+VSLPEVPLLGVLPGTGGLTRVTDKR V
Sbjct: 131 KFVAAVNGACAGGGYELALACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRVTDKRHV 190

Query: 193 RRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGVK 252
           R D ADIFCT  EGVRGQRA DWRLVD + K  QFA  +   A  L + S RP+ A+GV 
Sbjct: 191 RHDLADIFCTSVEGVRGQRAVDWRLVDRIAKPAQFAAAVDDTAARLTEGSPRPSHAQGVA 250

Query: 253 LTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQMA 312
           L  +ER        Y  V  +ID   RT TLT++AP        A+IEA G  WWPL +A
Sbjct: 251 LPRVEREETADSLRYTHVSVSIDRTRRTATLTLKAPTGPQPTDIADIEAAGAAWWPLALA 310

Query: 313 RELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRTLAR 372
           R+LDDAILNLRTN LD+G W L+TEGDAQ VL  DAT+ A++ +W VRETIG LRRT AR
Sbjct: 311 RQLDDAILNLRTNELDIGTWLLKTEGDAQAVLASDATLIAHQGHWLVRETIGALRRTFAR 370

Query: 373 IDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML---DAAEAKNVVGLSAMNFGTFPMV 429
           +DVSSRSL+AL+EPGS FAG+L E++ AADR+YML   D  E    + L+  NFG  PMV
Sbjct: 371 LDVSSRSLFALVEPGSAFAGSLAELSFAADRTYMLALPDDTERAPKITLNEFNFGLLPMV 430

Query: 430 NGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAIEERA 489
           N  SR+  RFY+E AP+ A +A  G       A+ LGLVTA PDD+DW +E+RIAIEERA
Sbjct: 431 NDQSRLQRRFYEEAAPLEAARAAAGKPQDADAALALGLVTAAPDDIDWDDEIRIAIEERA 490

Query: 490 ALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSGKKAQ 549
           A+SPD+LTGLEANLRF   E MNTRIFGRL+AWQNWIFNRPNAVG+ GALK++G+G+KA 
Sbjct: 491 AMSPDSLTGLEANLRFASKENMNTRIFGRLTAWQNWIFNRPNAVGDKGALKVYGTGQKAG 550

Query: 550 FDWNRV 555
           FD NRV
Sbjct: 551 FDLNRV 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: 800
Number of extensions: 29
Number of successful extensions: 3
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 Ac3H11_3085 (Benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44))
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.19776.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.5e-292  957.2   0.3   1.7e-292  957.0   0.3    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085  Benzoyl-CoA-dihydrodiol lyase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085  Benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  957.0   0.3  1.7e-292  1.7e-292       1     548 []      11     556 .]      11     556 .] 1.00

  Alignments for each domain:
  == domain 1  score: 957.0 bits;  conditional E-value: 1.7e-292
                                        TIGR03222   1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrf 62 
                                                      vd+rt+p +yrhwkl++dG+va l+ld++edgg+r+GyklklnsydlGvdiel+dal+r+rf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085  11 VDYRTDPTQYRHWKLAVDGAVARLSLDIAEDGGIRPGYKLKLNSYDLGVDIELHDALNRIRF 72 
                                                      89************************************************************ PP

                                        TIGR03222  63 ehpevrvvvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkfla 124
                                                      ehp+vr+v++tsa+d++fc+Gani+mlg+s+ha+kvnfckftnetrngied+s++sglkf+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085  73 EHPQVRSVIVTSARDRIFCSGANIFMLGVSSHAWKVNFCKFTNETRNGIEDSSKHSGLKFVA 134
                                                      ************************************************************** PP

                                        TIGR03222 125 avnGtaaGGGyelalacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdlad 186
                                                      avnG++aGGGyelalacdeivlvddrssavslpevpll+vlpGtGGltrvtdkr+vr+dlad
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 135 AVNGACAGGGYELALACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRVTDKRHVRHDLAD 196
                                                      ************************************************************** PP

                                        TIGR03222 187 ifctieeGvkGkrakewrlvdevvksskfdaavaeraaelaaksdrpadakGveltklerti 248
                                                      ifct +eGv+G+ra++wrlvd + k+++f+aav + aa l+  s+rp++a+Gv+l ++er +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 197 IFCTSVEGVRGQRAVDWRLVDRIAKPAQFAAAVDDTAARLTEGSPRPSHAQGVALPRVEREE 258
                                                      ************************************************************** PP

                                        TIGR03222 249 eedgvryetvdvaidraartatitvkgpeaaapadlaaikaqGaefyplklarelddailhl 310
                                                      ++d++ry++v+v+idr+ rtat+t+k+p   +p+d+a+i+a+Ga+++pl+lar+lddail+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 259 TADSLRYTHVSVSIDRTRRTATLTLKAPTGPQPTDIADIEAAGAAWWPLALARQLDDAILNL 320
                                                      ************************************************************** PP

                                        TIGR03222 311 rlneldiglwvlrteGdaelvlaadalleakedhwlvreilgllkrtlkrldvssrslfalv 372
                                                      r+neldig+w+l+teGda++vla da+l+a++ hwlvre++g l+rt++rldvssrslfalv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 321 RTNELDIGTWLLKTEGDAQAVLASDATLIAHQGHWLVRETIGALRRTFARLDVSSRSLFALV 382
                                                      ************************************************************** PP

                                        TIGR03222 373 epgscfaGtlaelvfaadrsymlegeleddedeeaaitlselnfgayplsnglsrlaarfla 434
                                                      epgs faG lael faadr+yml  +l+dd++ +++itl e nfg +p++n++srl++rf++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 383 EPGSAFAGSLAELSFAADRTYML--ALPDDTERAPKITLNEFNFGLLPMVNDQSRLQRRFYE 442
                                                      **********************9..9************************************ PP

                                        TIGR03222 435 eeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleeraslspdaltGleanl 496
                                                      e a++ea+r+  G+  da +a  lglvtaa+ddidw+deiri++eera++spd+ltGleanl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 443 EAAPLEAARAAAGKPQDADAALALGLVTAAPDDIDWDDEIRIAIEERAAMSPDSLTGLEANL 504
                                                      ************************************************************** PP

                                        TIGR03222 497 rfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548
                                                      rfa+ e m+trifgrltawqnwifnrpnavG+kGalk+yG+G+ka fdl+rv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 505 RFASKENMNTRIFGRLTAWQNWIFNRPNAVGDKGALKVYGTGQKAGFDLNRV 556
                                                      ***************************************************8 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.07
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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