Alignments for a candidate for boxC in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for boxC in Cupriavidus basilensis 4G11

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate RR42_RS07510 RR42_RS07510 benzoyl-CoA-dihydrodiol lyase

Query= SwissProt::Q84HH6
         (555 letters)



>FitnessBrowser__Cup4G11:RR42_RS07510
          Length = 566

 Score =  789 bits (2037), Expect = 0.0
 Identities = 390/546 (71%), Positives = 449/546 (82%), Gaps = 3/546 (0%)

Query: 13  VDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQRV 72
           V +  +P++YRHW L   G +ATL+++IDEDGG+RPGY LKLNSYDLGVDIELHDA+QR+
Sbjct: 21  VTFERDPAQYRHWKLTFAGPVATLSMDIDEDGGLRPGYALKLNSYDLGVDIELHDAVQRI 80

Query: 73  RFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSGL 132
           RFEHPEVRTV++TS K +IFCSGANI+MLG S+HAWKVNFCKFTNETRNGIED+S++SGL
Sbjct: 81  RFEHPEVRTVILTSAKDRIFCSGANIFMLGKSSHAWKVNFCKFTNETRNGIEDASRHSGL 140

Query: 133 KFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRRV 192
           KF+AACNGTTAGGGYELALACDEIVLVDDR+S+VSLPEVPLLGVLPGTGGLTR+TDKRRV
Sbjct: 141 KFIAACNGTTAGGGYELALACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRLTDKRRV 200

Query: 193 RRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGVK 252
           RRDHADIFCT +EGVRGQRA DW+LVD VVK  +FAEH+Q RA ALA  SDRPAG  GVK
Sbjct: 201 RRDHADIFCTTTEGVRGQRAHDWKLVDAVVKPARFAEHVQQRALALAAQSDRPAGHDGVK 260

Query: 253 LTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQMA 312
           LT L R+ +  GY Y+ V   ID   R  TLTV  PA    +  A I A G  WWPL+MA
Sbjct: 261 LTPLSRSQEAHGYRYDTVQVHIDPRARKATLTVFGPAKHQPQALAAILAAGADWWPLKMA 320

Query: 313 RELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRTLAR 372
           RELDDAIL LR NHLD+G+W L+TEGD   VL  DA +DA+  +WFVRETIGMLRRTLAR
Sbjct: 321 RELDDAILTLRANHLDIGIWILKTEGDPHQVLATDALLDAHASHWFVRETIGMLRRTLAR 380

Query: 373 IDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML---DAAEAKNVVGLSAMNFGTFPMV 429
           ++VSSR+L+ALIEP SCFAGTLLE+ALAADRSYML   DA +    V  S  NFG +P V
Sbjct: 381 LEVSSRTLFALIEPDSCFAGTLLELALAADRSYMLHLPDAPDDAPRVFASTANFGRYPAV 440

Query: 430 NGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAIEERA 489
           NGL+R+ ARF Q+E  + AV+   G+ L    A  LGLVTA PDD+DW +E+RIAIEERA
Sbjct: 441 NGLTRLAARFCQDEVAIQAVQDHIGAPLDAINAASLGLVTATPDDIDWEDEIRIAIEERA 500

Query: 490 ALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSGKKAQ 549
           +LSPDALTGLEANLRFGPVETM TRIFGRL+AWQNWIFNRPNAVGE GALK+FGSG KA+
Sbjct: 501 SLSPDALTGLEANLRFGPVETMETRIFGRLTAWQNWIFNRPNAVGEQGALKVFGSGNKAR 560

Query: 550 FDWNRV 555
           FDW+RV
Sbjct: 561 FDWDRV 566


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: 909
Number of extensions: 31
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: 566
Length adjustment: 36
Effective length of query: 519
Effective length of database: 530
Effective search space:   275070
Effective search space used:   275070
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 RR42_RS07510 RR42_RS07510 (benzoyl-CoA-dihydrodiol lyase)
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.32530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-306 1003.6   0.0   1.4e-306 1003.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS07510  RR42_RS07510 benzoyl-CoA-dihydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS07510  RR42_RS07510 benzoyl-CoA-dihydrodiol lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1003.4   0.0  1.4e-306  1.4e-306       1     548 []      21     566 .]      21     566 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1003.4 bits;  conditional E-value: 1.4e-306
                                 TIGR03222   1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpevrv 69 
                                               v+f+++p +yrhwkltf Gpvatl++d+dedgglr+Gy lklnsydlGvdiel+da+qr+rfehpevr+
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510  21 VTFERDPAQYRHWKLTFAGPVATLSMDIDEDGGLRPGYALKLNSYDLGVDIELHDAVQRIRFEHPEVRT 89 
                                               78******************************************************************* PP

                                 TIGR03222  70 vvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaGGGyela 138
                                               v+ltsakd++fc+Gani+mlg+s+ha+kvnfckftnetrngiedas++sglkf+aa+nGt+aGGGyela
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510  90 VILTSAKDRIFCSGANIFMLGKSSHAWKVNFCKFTNETRNGIEDASRHSGLKFIAACNGTTAGGGYELA 158
                                               ********************************************************************* PP

                                 TIGR03222 139 lacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGkrakewrlvd 207
                                               lacdeivlvddrssavslpevpll+vlpGtGGltr+tdkrrvrrd+adifct++eGv+G+ra +w+lvd
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510 159 LACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRLTDKRRVRRDHADIFCTTTEGVRGQRAHDWKLVD 227
                                               ********************************************************************* PP

                                 TIGR03222 208 evvksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidraartatitvkgp 276
                                                vvk+++f+++v++ra +laa+sdrpa + Gv+lt+l+r++e++g+ry+tv+v+id  ar+at+tv gp
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510 228 AVVKPARFAEHVQQRALALAAQSDRPAGHDGVKLTPLSRSQEAHGYRYDTVQVHIDPRARKATLTVFGP 296
                                               ********************************************************************* PP

                                 TIGR03222 277 eaaapadlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdaelvlaadalleakedhw 345
                                               ++++p+ laai a+Ga+++plk+arelddail+lr+n+ldig+w+l+teGd ++vla+dall a+++hw
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510 297 AKHQPQALAAILAAGADWWPLKMARELDDAILTLRANHLDIGIWILKTEGDPHQVLATDALLDAHASHW 365
                                               ********************************************************************* PP

                                 TIGR03222 346 lvreilgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymlegeleddedeeaaitlsel 414
                                               +vre++g+l+rtl+rl+vssr+lfal+ep+scfaGtl+el++aadrsyml  +l+d++d++++++ s +
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510 366 FVRETIGMLRRTLARLEVSSRTLFALIEPDSCFAGTLLELALAADRSYML--HLPDAPDDAPRVFASTA 432
                                               *************************************************9..9**************** PP

                                 TIGR03222 415 nfgayplsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleeras 483
                                               nfg+yp +ngl+rlaarf ++e a++av+d+iG  lda +a++lglvta++ddidwedeiri++eeras
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510 433 NFGRYPAVNGLTRLAARFCQDEVAIQAVQDHIGAPLDAINAASLGLVTATPDDIDWEDEIRIAIEERAS 501
                                               ********************************************************************* PP

                                 TIGR03222 484 lspdaltGleanlrfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548
                                               lspdaltGleanlrf+++etmetrifgrltawqnwifnrpnavGe+Galk++GsG+ka+fd++rv
  lcl|FitnessBrowser__Cup4G11:RR42_RS07510 502 LSPDALTGLEANLRFGPVETMETRIFGRLTAWQNWIFNRPNAVGEQGALKVFGSGNKARFDWDRV 566
                                               ****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (548 nodes)
Target sequences:                          1  (566 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: 00:00:00.02
# Mc/sec: 12.85
//
[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