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_RS35130 RR42_RS35130 benzoyl-CoA-dihydrodiol lyase

Query= SwissProt::Q84HH6
         (555 letters)



>FitnessBrowser__Cup4G11:RR42_RS35130
          Length = 552

 Score =  749 bits (1933), Expect = 0.0
 Identities = 371/550 (67%), Positives = 439/550 (79%), Gaps = 5/550 (0%)

Query: 10  AELVDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDAL 69
           A  V+Y+T+PS+Y+H  L  DG IATL ++IDE+ G+RPGYKLKLNSYDLGVDIEL+DA+
Sbjct: 4   APRVEYQTDPSQYKHLKLTFDGPIATLAVDIDENAGLRPGYKLKLNSYDLGVDIELNDAV 63

Query: 70  QRVRFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQY 129
            R+RFEHPEVRTVVVTSGK K+FCSGANI+MLG+S+H+WKVNFCKFTNETRNG+EDSS++
Sbjct: 64  NRIRFEHPEVRTVVVTSGKDKVFCSGANIFMLGVSSHSWKVNFCKFTNETRNGLEDSSKH 123

Query: 130 SGLKFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDK 189
           SGLKFLAA NG  AGGGYELALACDEI+LVDDR+S+VSLPEVPLLGVLPGTGGLTRVTDK
Sbjct: 124 SGLKFLAAVNGACAGGGYELALACDEIILVDDRSSAVSLPEVPLLGVLPGTGGLTRVTDK 183

Query: 190 RRVRRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAK 249
           R VR D ADIFCT +EGVRGQRAKDWRLVDD+ K   FA+ +Q RA+ALA  SDRPA A 
Sbjct: 184 RHVRHDLADIFCTTTEGVRGQRAKDWRLVDDIAKPAVFAQKVQERAQALAALSDRPANAS 243

Query: 250 GVKLTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPL 309
           GV LT L RT++     Y +V   ID  GR  T TV+ P+A    + A I   G  W+PL
Sbjct: 244 GVALTPLARTLETDALRYTYVTVEIDRVGRKATFTVKGPSATQPTSVAAIAEAGAAWYPL 303

Query: 310 QMARELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRT 369
           Q+AREL+DAIL++RTN LD+G W ++TEGDA  VL +DAT+ AN+D+W VRETIG+LRRT
Sbjct: 304 QLARELEDAILSMRTNELDIGTWLIKTEGDAANVLAMDATLLANQDHWLVRETIGLLRRT 363

Query: 370 LARIDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML----DAAEAKNVVGLSAMNFGT 425
            +R+DVSSRSL+ALIEPGSCFAGT LE+ALA DRSY L    D A A  +  ++  NFG 
Sbjct: 364 FSRLDVSSRSLFALIEPGSCFAGTFLELALACDRSYHLALPDDEARAPRIT-VAETNFGL 422

Query: 426 FPMVNGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAI 485
           +PMV G SR+  RFY E+  + AV+AK G  L    A  +GLVTA PDD+DW +EVRIA+
Sbjct: 423 YPMVTGQSRLGRRFYDEQPALDAVRAKAGQPLDADAAFAVGLVTANPDDIDWTDEVRIAL 482

Query: 486 EERAALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSG 545
           EERAA+SPDALTG+EANLRF   E M TRIFGRL+AWQNWIF RPNAVGE GALK++G G
Sbjct: 483 EERAAMSPDALTGMEANLRFNGQENMFTRIFGRLTAWQNWIFQRPNAVGEKGALKVYGKG 542

Query: 546 KKAQFDWNRV 555
            KA FDWNRV
Sbjct: 543 DKAAFDWNRV 552


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: 830
Number of extensions: 28
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: 552
Length adjustment: 36
Effective length of query: 519
Effective length of database: 516
Effective search space:   267804
Effective search space used:   267804
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_RS35130 RR42_RS35130 (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.11170.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-297  973.3   0.1     2e-297  973.2   0.1    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS35130  RR42_RS35130 benzoyl-CoA-dihydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS35130  RR42_RS35130 benzoyl-CoA-dihydrodiol lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  973.2   0.1    2e-297    2e-297       1     548 []       7     552 .]       7     552 .] 1.00

  Alignments for each domain:
  == domain 1  score: 973.2 bits;  conditional E-value: 2e-297
                                 TIGR03222   1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpevrv 69 
                                               v+++t+ps+y+h kltfdGp+atl++d+de++glr+GyklklnsydlGvdiel+da++r+rfehpevr+
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130   7 VEYQTDPSQYKHLKLTFDGPIATLAVDIDENAGLRPGYKLKLNSYDLGVDIELNDAVNRIRFEHPEVRT 75 
                                               79******************************************************************* PP

                                 TIGR03222  70 vvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaGGGyela 138
                                               vv+ts+kdkvfc+Gani+mlg+s+h++kvnfckftnetrng+ed+s++sglkflaavnG++aGGGyela
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130  76 VVVTSGKDKVFCSGANIFMLGVSSHSWKVNFCKFTNETRNGLEDSSKHSGLKFLAAVNGACAGGGYELA 144
                                               ********************************************************************* PP

                                 TIGR03222 139 lacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGkrakewrlvd 207
                                               lacdei+lvddrssavslpevpll+vlpGtGGltrvtdkr+vr+dladifct++eGv+G+rak+wrlvd
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130 145 LACDEIILVDDRSSAVSLPEVPLLGVLPGTGGLTRVTDKRHVRHDLADIFCTTTEGVRGQRAKDWRLVD 213
                                               ********************************************************************* PP

                                 TIGR03222 208 evvksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidraartatitvkgp 276
                                               ++ k++ f+++v+era++laa sdrpa+a Gv+lt+l rt e+d++ry++v v+idr  r+at+tvkgp
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130 214 DIAKPAVFAQKVQERAQALAALSDRPANASGVALTPLARTLETDALRYTYVTVEIDRVGRKATFTVKGP 282
                                               ********************************************************************* PP

                                 TIGR03222 277 eaaapadlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdaelvlaadalleakedhw 345
                                               +a++p+++aai  +Ga++ypl+larel+dail++r+neldig+w+++teGda+ vla+da+l a++dhw
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130 283 SATQPTSVAAIAEAGAAWYPLQLARELEDAILSMRTNELDIGTWLIKTEGDAANVLAMDATLLANQDHW 351
                                               ********************************************************************* PP

                                 TIGR03222 346 lvreilgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymlegeleddedeeaaitlsel 414
                                               lvre++gll+rt+ rldvssrslfal+epgscfaGt++el++a+drsy l  +l+dde+ +++it++e+
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130 352 LVRETIGLLRRTFSRLDVSSRSLFALIEPGSCFAGTFLELALACDRSYHL--ALPDDEARAPRITVAET 418
                                               *************************************************9..9**************** PP

                                 TIGR03222 415 nfgayplsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleeras 483
                                               nfg yp+++g+srl +rf++e+ a++avr+k G+ lda +a   glvta +ddidw de+ri+leera+
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130 419 NFGLYPMVTGQSRLGRRFYDEQPALDAVRAKAGQPLDADAAFAVGLVTANPDDIDWTDEVRIALEERAA 487
                                               ********************************************************************* PP

                                 TIGR03222 484 lspdaltGleanlrfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548
                                               +spdaltG+eanlrf+g+e m trifgrltawqnwif+rpnavGekGalk+yG+G ka+fd++rv
  lcl|FitnessBrowser__Cup4G11:RR42_RS35130 488 MSPDALTGMEANLRFNGQENMFTRIFGRLTAWQNWIFQRPNAVGEKGALKVYGKGDKAAFDWNRV 552
                                               ****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (548 nodes)
Target sequences:                          1  (552 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: 7.81
//
[ok]

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

Downloads

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

Related tools

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