Alignments for a candidate for boxC in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for boxC in Magnetospirillum magneticum AMB-1

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate WP_011382621.1 AMB_RS00885 2,3-epoxybenzoyl-CoA dihydrolase

Query= SwissProt::Q84HH6
         (555 letters)



>NCBI__GCF_000009985.1:WP_011382621.1
          Length = 550

 Score =  613 bits (1582), Expect = e-180
 Identities = 303/550 (55%), Positives = 388/550 (70%), Gaps = 6/550 (1%)

Query: 12  LVDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQR 71
           +++++T P  YRHW LA DG +ATLT+++D    + PGY+LK+NSYDLGVDIEL+DA+QR
Sbjct: 1   MINFQTSPESYRHWKLAFDGPVATLTMDVDPASTLAPGYELKMNSYDLGVDIELYDAVQR 60

Query: 72  VRFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSG 131
           +RFEHPEVR VV+ S  PKIFC+GANI MLG+S+H  KVNFCKFTNETRN IED+S+ S 
Sbjct: 61  LRFEHPEVRAVVMASANPKIFCAGANIKMLGVSSHGHKVNFCKFTNETRNSIEDASENSR 120

Query: 132 LKFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRR 191
             +L A  GT AGGGYELALA D I++VDD N++VSLPEVPLL VLPGTGGLTRV DKR+
Sbjct: 121 QTYLCAVTGTAAGGGYELALATDYIMMVDDGNTAVSLPEVPLLAVLPGTGGLTRVVDKRK 180

Query: 192 VRRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGV 251
           VRRD ADIFC+I EGV+G+RA +WRLVD+V+    F   +  +A  LA  SDRP   KGV
Sbjct: 181 VRRDLADIFCSIEEGVKGKRAVEWRLVDEVIPSSAFKAAVAKKAAELAARSDRPTAEKGV 240

Query: 252 KLTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQM 311
            L+ + R +      Y  +D   D   R   +T++ P A      A I+AQG+ ++PL +
Sbjct: 241 VLSQVSRVIGTDSVTYPHIDIAFDRATRAANITIKGPKAACPADLAGIKAQGVDFYPLAL 300

Query: 312 ARELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDA-NRDNWFVRETIGMLRRTL 370
           ARELDDAIL+LR N   +  W  RT+GDA +V+  DA +      +W VRE +   +RT+
Sbjct: 301 ARELDDAILHLRANETTIATWVFRTQGDADLVMGYDAALQTFGASDWLVREILLYWKRTM 360

Query: 371 ARIDVSSRSLYALIEPGSCFAGTLLEIALAADRSYMLDAAEAKN-----VVGLSAMNFGT 425
            R+DV+SR+L+AL+EPGSCFAG + EI  A DRS+MLD     N      + LSA+NF  
Sbjct: 361 KRLDVTSRTLFALVEPGSCFAGFVAEILFAVDRSFMLDGTFEDNPAPAAAIRLSALNFDG 420

Query: 426 FPMVNGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAI 485
            PM NG+SR+  RF  E   V   +   G  L  A   +LGLVT  PDD+DW +E+R+ I
Sbjct: 421 LPMGNGISRLATRFLGEPDSVGKARDTIGKDLDAAACAKLGLVTGTPDDIDWEDEIRLMI 480

Query: 486 EERAALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSG 545
           EERA+ SPD+LTG+EANLRF   ETM T+IFGRL+AWQNWIF RPNAVG+ GALKL+G+G
Sbjct: 481 EERASFSPDSLTGMEANLRFAGPETMETKIFGRLTAWQNWIFQRPNAVGDQGALKLYGTG 540

Query: 546 KKAQFDWNRV 555
           K+A ++  RV
Sbjct: 541 KRAAYNQERV 550


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: 778
Number of extensions: 32
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: 550
Length adjustment: 36
Effective length of query: 519
Effective length of database: 514
Effective search space:   266766
Effective search space used:   266766
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_011382621.1 AMB_RS00885 (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.24526.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 1021.9   0.1          0 1021.7   0.1    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011382621.1  AMB_RS00885 2,3-epoxybenzoyl-CoA


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011382621.1  AMB_RS00885 2,3-epoxybenzoyl-CoA dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.7   0.1         0         0       1     548 []       2     550 .]       2     550 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1021.7 bits;  conditional E-value: 0
                                 TIGR03222   1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpevrv 69 
                                               ++f+t+p++yrhwkl+fdGpvatlt+dvd++++l++Gy+lk+nsydlGvdiel+da+qrlrfehpevr+
  lcl|NCBI__GCF_000009985.1:WP_011382621.1   2 INFQTSPESYRHWKLAFDGPVATLTMDVDPASTLAPGYELKMNSYDLGVDIELYDAVQRLRFEHPEVRA 70 
                                               79******************************************************************* PP

                                 TIGR03222  70 vvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaGGGyela 138
                                               vv++sa++k+fcaGanikmlg+s+h+hkvnfckftnetrn+iedase+s++++l+av+GtaaGGGyela
  lcl|NCBI__GCF_000009985.1:WP_011382621.1  71 VVMASANPKIFCAGANIKMLGVSSHGHKVNFCKFTNETRNSIEDASENSRQTYLCAVTGTAAGGGYELA 139
                                               ********************************************************************* PP

                                 TIGR03222 139 lacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGkrakewrlvd 207
                                               la+d+i++vdd+++avslpevpllavlpGtGGltrv+dkr+vrrdladifc+ieeGvkGkra+ewrlvd
  lcl|NCBI__GCF_000009985.1:WP_011382621.1 140 LATDYIMMVDDGNTAVSLPEVPLLAVLPGTGGLTRVVDKRKVRRDLADIFCSIEEGVKGKRAVEWRLVD 208
                                               ********************************************************************* PP

                                 TIGR03222 208 evvksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidraartatitvkgp 276
                                               ev++ss+f+aava++aaelaa+sdrp+++kGv+l++++r+i +d+v+y ++d+a+dra+r+a+it+kgp
  lcl|NCBI__GCF_000009985.1:WP_011382621.1 209 EVIPSSAFKAAVAKKAAELAARSDRPTAEKGVVLSQVSRVIGTDSVTYPHIDIAFDRATRAANITIKGP 277
                                               ********************************************************************* PP

                                 TIGR03222 277 eaaapadlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdaelvlaadalleakedh. 344
                                               +aa+padla+ikaqG++fypl+larelddailhlr+ne++i++wv+rt+Gda+lv+++da+l+++ ++ 
  lcl|NCBI__GCF_000009985.1:WP_011382621.1 278 KAACPADLAGIKAQGVDFYPLALARELDDAILHLRANETTIATWVFRTQGDADLVMGYDAALQTFGASd 346
                                               ****************************************************************98766 PP

                                 TIGR03222 345 wlvreilgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymlegeleddedeeaaitlse 413
                                               wlvreil ++krt+krldv+sr+lfalvepgscfaG++ae++fa+drs+ml+g++ed+++++aai+ls+
  lcl|NCBI__GCF_000009985.1:WP_011382621.1 347 WLVREILLYWKRTMKRLDVTSRTLFALVEPGSCFAGFVAEILFAVDRSFMLDGTFEDNPAPAAAIRLSA 415
                                               ********************************************************************* PP

                                 TIGR03222 414 lnfgayplsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleera 482
                                               lnf+ +p++ng+srla+rfl+e+++v ++rd+iG++ldaa+++klglvt ++ddidwedeir+++eera
  lcl|NCBI__GCF_000009985.1:WP_011382621.1 416 LNFDGLPMGNGISRLATRFLGEPDSVGKARDTIGKDLDAAACAKLGLVTGTPDDIDWEDEIRLMIEERA 484
                                               ********************************************************************* PP

                                 TIGR03222 483 slspdaltGleanlrfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548
                                               s+spd+ltG+eanlrfagpetmet+ifgrltawqnwif+rpnavG++GalklyG+Gk+a++++erv
  lcl|NCBI__GCF_000009985.1:WP_011382621.1 485 SFSPDSLTGMEANLRFAGPETMETKIFGRLTAWQNWIFQRPNAVGDQGALKLYGTGKRAAYNQERV 550
                                               *****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (548 nodes)
Target sequences:                          1  (550 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: 8.88
//
[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