Alignments for a candidate for boxC in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for boxC in Sedimenticola selenatireducens DSM 17993

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate WP_037375998.1 A3GO_RS0118595 2,3-epoxybenzoyl-CoA dihydrolase

Query= SwissProt::Q84HH6
         (555 letters)



>NCBI__GCF_000428045.1:WP_037375998.1
          Length = 549

 Score =  616 bits (1588), Expect = 0.0
 Identities = 302/549 (55%), Positives = 392/549 (71%), Gaps = 5/549 (0%)

Query: 12  LVDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQR 71
           ++ ++T P+ Y+HW LA +G +A L +N+ EDGG+ PGY+LKLNSYDLGVDIEL+DA+QR
Sbjct: 1   MISFQTNPAAYQHWQLAFEGPVARLRMNVKEDGGLMPGYELKLNSYDLGVDIELYDAVQR 60

Query: 72  VRFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSG 131
           +RFEHPEV++V++ S K ++FC+GANI MLG STH  KVNFCKFTNETRN IED+S++SG
Sbjct: 61  LRFEHPEVKSVILESAKERVFCAGANIRMLGGSTHVHKVNFCKFTNETRNSIEDASEFSG 120

Query: 132 LKFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRR 191
            ++L A  GT AGGGYELALA D I+LVDD N+SVSLPEVPLL VLPGTGGLTR+ DKR+
Sbjct: 121 QRYLCAITGTAAGGGYELALAADHIMLVDDGNASVSLPEVPLLAVLPGTGGLTRLVDKRK 180

Query: 192 VRRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGV 251
           +RRD AD+FC+I EGV+GQRA DWRLVD+VV   +F E +  RA+A+A  SDRP    G+
Sbjct: 181 MRRDLADVFCSIEEGVKGQRAVDWRLVDEVVVSSKFQEAVDERAQAIAGGSDRPDNESGI 240

Query: 252 KLTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQM 311
           +L  LE   DE   HY  +D ++D   R  TL ++ P A      A  + QG  +WPL +
Sbjct: 241 ELEPLEIGGDETHLHYPHLDLSVDRATRVATLILKGPTASVPDDLAAAKVQGCHFWPLAL 300

Query: 312 ARELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRTLA 371
            RELD A+L+LRTN  + G    +T+GDA+ V   +  +  +RD+WF+RE +  L+RTL 
Sbjct: 301 IRELDSALLHLRTNEPETGTLIFKTQGDAEQVAAYERFLLQHRDDWFIREILLYLKRTLK 360

Query: 372 RIDVSSRSLYALIEPGSCFAGTLLEIALAADRSYMLDAA-----EAKNVVGLSAMNFGTF 426
           RID +SRS +A +EPGSCF+G L +I  A DRSYML+            + LS +NFG  
Sbjct: 361 RIDYTSRSTFAFVEPGSCFSGFLADILFAVDRSYMLEGQFEGDDRPAPTIRLSELNFGPL 420

Query: 427 PMVNGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAIE 486
           PM NGL+R++ RF  E   +   ++  G  LS   A + GLVT   DD+DW +++R  +E
Sbjct: 421 PMGNGLTRLETRFLGEPDTLEKARSLIGESLSAEAAADAGLVTFALDDIDWEDDIRFLLE 480

Query: 487 ERAALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSGK 546
           ERA+ SPDALTG+EANLRF   ETM T+IFGRLSAWQNWIF RPNAVGE GALK FG+G+
Sbjct: 481 ERASYSPDALTGMEANLRFAGPETMETKIFGRLSAWQNWIFQRPNAVGEQGALKCFGTGE 540

Query: 547 KAQFDWNRV 555
           +  +D  RV
Sbjct: 541 RPHYDQKRV 549


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: 743
Number of extensions: 25
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: 549
Length adjustment: 36
Effective length of query: 519
Effective length of database: 513
Effective search space:   266247
Effective search space used:   266247
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 WP_037375998.1 A3GO_RS0118595 (2,3-epoxybenzoyl-CoA dihydrolase)
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.12506.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.5e-283  924.8   0.0   1.1e-282  924.6   0.0    1.0  1  lcl|NCBI__GCF_000428045.1:WP_037375998.1  A3GO_RS0118595 2,3-epoxybenzoyl-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_037375998.1  A3GO_RS0118595 2,3-epoxybenzoyl-CoA dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  924.6   0.0  1.1e-282  1.1e-282       1     548 []       2     549 .]       2     549 .] 1.00

  Alignments for each domain:
  == domain 1  score: 924.6 bits;  conditional E-value: 1.1e-282
                                 TIGR03222   1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpevrv 69 
                                               + f+t+p  y+hw+l+f+Gpva l ++v+edggl++Gy+lklnsydlGvdiel+da+qrlrfehpev++
  lcl|NCBI__GCF_000428045.1:WP_037375998.1   2 ISFQTNPAAYQHWQLAFEGPVARLRMNVKEDGGLMPGYELKLNSYDLGVDIELYDAVQRLRFEHPEVKS 70 
                                               68******************************************************************* PP

                                 TIGR03222  70 vvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaGGGyela 138
                                               v+l+sak++vfcaGani+mlg+sth+hkvnfckftnetrn+iedase sg+++l+a++GtaaGGGyela
  lcl|NCBI__GCF_000428045.1:WP_037375998.1  71 VILESAKERVFCAGANIRMLGGSTHVHKVNFCKFTNETRNSIEDASEFSGQRYLCAITGTAAGGGYELA 139
                                               ********************************************************************* PP

                                 TIGR03222 139 lacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGkrakewrlvd 207
                                               la+d+i+lvdd++++vslpevpllavlpGtGGltr++dkr++rrdlad+fc+ieeGvkG+ra++wrlvd
  lcl|NCBI__GCF_000428045.1:WP_037375998.1 140 LAADHIMLVDDGNASVSLPEVPLLAVLPGTGGLTRLVDKRKMRRDLADVFCSIEEGVKGQRAVDWRLVD 208
                                               ********************************************************************* PP

                                 TIGR03222 208 evvksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidraartatitvkgp 276
                                               evv sskf++av era+++a  sdrp ++ G+el +le   +e+ ++y ++d+++dra+r+at+ +kgp
  lcl|NCBI__GCF_000428045.1:WP_037375998.1 209 EVVVSSKFQEAVDERAQAIAGGSDRPDNESGIELEPLEIGGDETHLHYPHLDLSVDRATRVATLILKGP 277
                                               ********************************************************************* PP

                                 TIGR03222 277 eaaapadlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdaelvlaadalleakedhw 345
                                                a++p dlaa k qG +f+pl+l reld a+lhlr+ne + g+ +++t+Gdae+v+a++  l +++d+w
  lcl|NCBI__GCF_000428045.1:WP_037375998.1 278 TASVPDDLAAAKVQGCHFWPLALIRELDSALLHLRTNEPETGTLIFKTQGDAEQVAAYERFLLQHRDDW 346
                                               ********************************************************************* PP

                                 TIGR03222 346 lvreilgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymlegeleddedeeaaitlsel 414
                                               ++reil +lkrtlkr+d +srs fa+vepgscf+G+la+++fa+drsymleg++e+d++++++i+lsel
  lcl|NCBI__GCF_000428045.1:WP_037375998.1 347 FIREILLYLKRTLKRIDYTSRSTFAFVEPGSCFSGFLADILFAVDRSYMLEGQFEGDDRPAPTIRLSEL 415
                                               ********************************************************************* PP

                                 TIGR03222 415 nfgayplsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleeras 483
                                               nfg +p++ngl+rl++rfl+e++++e++r+ iGe+l+a++a+  glvt+alddidwed+ir lleeras
  lcl|NCBI__GCF_000428045.1:WP_037375998.1 416 NFGPLPMGNGLTRLETRFLGEPDTLEKARSLIGESLSAEAAADAGLVTFALDDIDWEDDIRFLLEERAS 484
                                               ********************************************************************* PP

                                 TIGR03222 484 lspdaltGleanlrfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548
                                               +spdaltG+eanlrfagpetmet+ifgrl+awqnwif+rpnavGe+Galk +G+G+++++d++rv
  lcl|NCBI__GCF_000428045.1:WP_037375998.1 485 YSPDALTGMEANLRFAGPETMETKIFGRLSAWQNWIFQRPNAVGEQGALKCFGTGERPHYDQKRV 549
                                               ***************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (548 nodes)
Target sequences:                          1  (549 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: 12.48
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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