GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Dinoroseobacter shibae DFL-12

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate 3610436 Dshi_3817 beta-ketoadipyl CoA thiolase (RefSeq)

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__Dino:3610436
          Length = 400

 Score =  543 bits (1400), Expect = e-159
 Identities = 272/399 (68%), Positives = 321/399 (80%), Gaps = 1/399 (0%)

Query: 3   DVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGE 62
           D  ICD +RTPIGR+GGAL+ VRADDLAA+P+ AL+  NP V W +VDEV +G ANQAGE
Sbjct: 2   DAVICDGVRTPIGRYGGALSSVRADDLAALPIAALMARNPGVDWARVDEVIYGAANQAGE 61

Query: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSR 122
           DNRNVARMA LLAGLPE +PG+T+NRLCASGMDA+G A R I +GE +LAIAGG+ESMSR
Sbjct: 62  DNRNVARMAALLAGLPEEVPGLTVNRLCASGMDAVGAAARGIKAGEYDLAIAGGIESMSR 121

Query: 123 APFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQD 182
           APFVM KAES ++R   + DTTIGWRF+NP + + +G+D+MP+TAD VA  Y++SRADQD
Sbjct: 122 APFVMPKAESAFTRAATVHDTTIGWRFVNPKIAAMHGIDTMPQTADTVAAAYEISRADQD 181

Query: 183 AFALRSQQKAAAAQAAGFFAEEIVPVRIAHK-KGETIVERDEHLRPETTLEALTKLKPVN 241
           AFA RSQ + AAA AAG FA+EIVPV +  +     +V+RDEH RP T    L  LK +N
Sbjct: 182 AFAARSQARWAAADAAGLFADEIVPVPVPQRGSAPILVDRDEHPRPGTDAARLAGLKGIN 241

Query: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301
           GP  +VTAGNASGVNDGAAAL++ASA A + HGLTP ARV+GMAS GVAPRVMGIGPVPA
Sbjct: 242 GPGLSVTAGNASGVNDGAAALLIASAAAARAHGLTPMARVVGMASAGVAPRVMGIGPVPA 301

Query: 302 VRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMS 361
            RKL +R G+ +   DVIELNEAFASQ LA LR+LG+ADD  +VNPNGGAIA+GHPLGMS
Sbjct: 302 SRKLLDRAGLTLDQMDVIELNEAFASQSLATLRQLGLADDDVRVNPNGGAIAMGHPLGMS 361

Query: 362 GARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GARLVLTA HQL ++GGR  L TMCVGVGQG AL +ERV
Sbjct: 362 GARLVLTAAHQLRRTGGRYALCTMCVGVGQGTALILERV 400


Lambda     K      H
   0.318    0.134    0.383 

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: 524
Number of extensions: 15
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 3610436 Dshi_3817 (beta-ketoadipyl CoA thiolase (RefSeq))
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.18669.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-207  674.9  15.8   2.3e-207  674.7  15.8    1.0  1  lcl|FitnessBrowser__Dino:3610436  Dshi_3817 beta-ketoadipyl CoA th


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610436  Dshi_3817 beta-ketoadipyl CoA thiolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.7  15.8  2.3e-207  2.3e-207       2     400 .]       2     400 .]       1     400 [] 1.00

  Alignments for each domain:
  == domain 1  score: 674.7 bits;  conditional E-value: 2.3e-207
                         TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaGlpv 78 
                                       ++ i+d++rtpiGrygG+lssvraddlaa+p++al+arnp +d+a +d+vi+G+anqaGednrnvarmaallaGlp+
  lcl|FitnessBrowser__Dino:3610436   2 DAVICDGVRTPIGRYGGALSSVRADDLAALPIAALMARNPGVDWARVDEVIYGAANQAGEDNRNVARMAALLAGLPE 78 
                                       578************************************************************************** PP

                         TIGR02430  79 svpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnpklka 155
                                       +vpg tvnrlc+sg+da+g aar+ikaGe dl iaGG+esmsrapfv+ ka+saf+r a ++dttiGwrfvnpk++a
  lcl|FitnessBrowser__Dino:3610436  79 EVPGLTVNRLCASGMDAVGAAARGIKAGEYDLAIAGGIESMSRAPFVMPKAESAFTRAATVHDTTIGWRFVNPKIAA 155
                                       ***************************************************************************** PP

                         TIGR02430 156 lyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehlraettle 232
                                       ++G+d+mp+ta+ va  +++sr+dqdafa rsq+r+aaa+a+G+fa+eivpv ++q+   +  vd+deh+r+ t   
  lcl|FitnessBrowser__Dino:3610436 156 MHGIDTMPQTADTVAAAYEISRADQDAFAARSQARWAAADAAGLFADEIVPVPVPQRGSAPILVDRDEHPRPGTDAA 232
                                       ***************************************************************************** PP

                         TIGR02430 233 alaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpavkkllara 309
                                       +la lk+++ ++ +vtaGnasGvndGaaall+as+ a+++hgltp ar++++asaGv+prvmG+gpvpa +kll+ra
  lcl|FitnessBrowser__Dino:3610436 233 RLAGLKGINGPGLSVTAGNASGVNDGAAALLIASAAAARAHGLTPMARVVGMASAGVAPRVMGIGPVPASRKLLDRA 309
                                       ***************************************************************************** PP

                         TIGR02430 310 glsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlc 386
                                       gl+l+++dvielneafa+q+la+lr+lgladdd rvnpnGGaia+GhplG+sGarlvlta +ql+++ggryal+t+c
  lcl|FitnessBrowser__Dino:3610436 310 GLTLDQMDVIELNEAFASQSLATLRQLGLADDDVRVNPNGGAIAMGHPLGMSGARLVLTAAHQLRRTGGRYALCTMC 386
                                       ***************************************************************************** PP

                         TIGR02430 387 iGvGqGialvierv 400
                                       +GvGqG al++erv
  lcl|FitnessBrowser__Dino:3610436 387 VGVGQGTALILERV 400
                                       *************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (400 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: 7.04
//
[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:

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:

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:

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:

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