GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Phaeobacter inhibens BS107

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF398 PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ

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



>FitnessBrowser__Phaeo:GFF398
          Length = 400

 Score =  533 bits (1374), Expect = e-156
 Identities = 267/399 (66%), Positives = 314/399 (78%), Gaps = 1/399 (0%)

Query: 3   DVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGE 62
           D FICDA RTPIGR+GGAL+ +R DDLAA+P+ AL   NP V W  +D+V  G ANQAGE
Sbjct: 2   DAFICDATRTPIGRYGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAGE 61

Query: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSR 122
            NRNVARMA LLAGLP ++PG T+NRLCASGMDA+G A R I +G+ ++AIAGGVESMSR
Sbjct: 62  SNRNVARMAALLAGLPTTVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMSR 121

Query: 123 APFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQD 182
           APFVM KA S ++R   + DTTIGWRF+N  M   YG DSMP+TADNVA+DY +SR DQD
Sbjct: 122 APFVMPKATSAFTRANAVYDTTIGWRFVNKKMHEMYGTDSMPQTADNVAEDYGISREDQD 181

Query: 183 AFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKG-ETIVERDEHLRPETTLEALTKLKPVN 241
           AFA RSQ + AAA  AG F +EI PV I  +KG + +V+ DEH RP T+ E L  LK VN
Sbjct: 182 AFAARSQARWAAAHEAGIFNDEITPVTIPQRKGDDLVVDTDEHPRPGTSAEKLAGLKGVN 241

Query: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301
           GPDK+VTAGNASGVNDGAAA+++A+  A  K+GL P AR++GM + GV PR+MGIGPVPA
Sbjct: 242 GPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEPRIMGIGPVPA 301

Query: 302 VRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMS 361
            RK+  R G+ +   DVIELNEAFASQGLA LRELGVADDAP VNPNGGAIALGHPLGMS
Sbjct: 302 TRKVLARTGLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGAIALGHPLGMS 361

Query: 362 GARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GARLVLTA +QL+++GGR  L TMCVGVGQG AL +ERV
Sbjct: 362 GARLVLTAAYQLQRTGGRYALCTMCVGVGQGTALILERV 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: 541
Number of extensions: 10
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 GFF398 PGA1_c04090 (beta-ketoadipyl-CoA thiolase PaaJ)
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.3637270.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-212  691.3  10.7   2.3e-212  691.1  10.7    1.0  1  lcl|FitnessBrowser__Phaeo:GFF398  PGA1_c04090 beta-ketoadipyl-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF398  PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.1  10.7  2.3e-212  2.3e-212       2     400 .]       2     400 .]       1     400 [] 1.00

  Alignments for each domain:
  == domain 1  score: 691.1 bits;  conditional E-value: 2.3e-212
                         TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaGlpv 78 
                                       +++i+da rtpiGrygG+ls++r+ddlaa+p++al arnp++d++++ddvilG anqaGe nrnvarmaallaGlp+
  lcl|FitnessBrowser__Phaeo:GFF398   2 DAFICDATRTPIGRYGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAGESNRNVARMAALLAGLPT 78 
                                       69*************************************************************************** PP

                         TIGR02430  79 svpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnpklka 155
                                       +vpgtt+nrlc+sg+da+g+a r+ikaG+ d+ iaGGvesmsrapfv+ ka saf+r + + dttiGwrfvn k+++
  lcl|FitnessBrowser__Phaeo:GFF398  79 TVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMSRAPFVMPKATSAFTRANAVYDTTIGWRFVNKKMHE 155
                                       ***************************************************************************** PP

                         TIGR02430 156 lyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehlraettle 232
                                       +yG+dsmp+ta+nvae++g+sredqdafa rsq+r+aaa+++G+f++ei+pv+i+q+kG++ vvd+deh+r+ t+ e
  lcl|FitnessBrowser__Phaeo:GFF398 156 MYGTDSMPQTADNVAEDYGISREDQDAFAARSQARWAAAHEAGIFNDEITPVTIPQRKGDDLVVDTDEHPRPGTSAE 232
                                       ***************************************************************************** PP

                         TIGR02430 233 alaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpavkkllara 309
                                       +la lk+v+ +d++vtaGnasGvndGaaa+l+a e a++++gl+p ari+++++aGvepr+mG+gpvpa++k+lar+
  lcl|FitnessBrowser__Phaeo:GFF398 233 KLAGLKGVNGPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEPRIMGIGPVPATRKVLART 309
                                       ***************************************************************************** PP

                         TIGR02430 310 glsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlc 386
                                       gl+++++dvielneafa+q+la+lrelg+add+ +vnpnGGaialGhplG+sGarlvlta +ql+++ggryal+t+c
  lcl|FitnessBrowser__Phaeo:GFF398 310 GLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGAIALGHPLGMSGARLVLTAAYQLQRTGGRYALCTMC 386
                                       ***************************************************************************** PP

                         TIGR02430 387 iGvGqGialvierv 400
                                       +GvGqG al++erv
  lcl|FitnessBrowser__Phaeo:GFF398 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.45
//
[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