GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Caulobacter crescentus NA1000

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate CCNA_02490 CCNA_02490 3-ketoacyl-CoA thiolase

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__Caulo:CCNA_02490
          Length = 399

 Score =  567 bits (1462), Expect = e-166
 Identities = 289/396 (72%), Positives = 331/396 (83%), Gaps = 1/396 (0%)

Query: 6   YICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGEDN 65
           YICD +RTPIGR+GGSL+ VRADDLAA+P+KALV RNP +D + +DE+ LG ANQAGEDN
Sbjct: 5   YICDGIRTPIGRYGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQAGEDN 64

Query: 66  RNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRAP 125
           RNVARMALLLAG P SVPGVT+NRLCASG++AVG A RAIASG  +LVIAGGVESMSRAP
Sbjct: 65  RNVARMALLLAGYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVESMSRAP 124

Query: 126 YVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDAF 185
           +VMGKADSAF R  +I DTTIGWRF+NP M+  YGVD+MPETA+NVA DY V+R DQDAF
Sbjct: 125 FVMGKADSAFSRSAEIFDTTIGWRFVNPAMRKLYGVDSMPETAENVATDYGVNREDQDAF 184

Query: 186 ALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGPD 245
           ALRSQ     AQA G+ A EI PV I GK G T+VD DEH R +TT+EALAKLKP+    
Sbjct: 185 ALRSQARTAAAQANGFLAGEITPVEIPGKAGPTIVDRDEHPR-ETTMEALAKLKPIVREG 243

Query: 246 KTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVRK 305
            TVTAGNASGVNDG+VAL++AS +AVK+HGL  RA++ G ASAGV PRVMGIGPVPAVRK
Sbjct: 244 GTVTAGNASGVNDGAVALVIASEDAVKRHGLTPRARITGYASAGVEPRVMGIGPVPAVRK 303

Query: 306 LLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGAR 365
           L+ +  L++ DFDV+ELNEAFAAQGLAV R+LG+ DD A VN NGGAIALGHPLGASGAR
Sbjct: 304 LMAKTGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNANGGAIALGHPLGASGAR 363

Query: 366 LVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           LVLTA+ QLE SGGQRGL T+C+GVGQG ALA ERV
Sbjct: 364 LVLTALRQLEASGGQRGLATLCIGVGQGAALAFERV 399


Lambda     K      H
   0.317    0.134    0.379 

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: 559
Number of extensions: 23
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: 401
Length of database: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate CCNA_02490 CCNA_02490 (3-ketoacyl-CoA thiolase)
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.8154.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.3e-227  738.9  11.6   8.2e-227  738.7  11.6    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02490  CCNA_02490 3-ketoacyl-CoA thiola


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02490  CCNA_02490 3-ketoacyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  738.7  11.6  8.2e-227  8.2e-227       2     400 .]       3     399 .]       2     399 .] 1.00

  Alignments for each domain:
  == domain 1  score: 738.7 bits;  conditional E-value: 8.2e-227
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           ++yi+d+irtpiGrygGsls+vraddlaa+plkal+arnpsld+aaid+++lG+anqaGednrnvarma+lla
  lcl|FitnessBrowser__Caulo:CCNA_02490   3 AAYICDGIRTPIGRYGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQAGEDNRNVARMALLLA 75 
                                           69*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           G+pvsvpg+tvnrlc+sgl+a+g+aarai++G++dlviaGGvesmsrapfv+Gkadsafsrsa+++dttiGwr
  lcl|FitnessBrowser__Caulo:CCNA_02490  76 GYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVESMSRAPFVMGKADSAFSRSAEIFDTTIGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnp++++lyGvdsmpetaenva+++gv+redqdafalrsq+rtaaaqa+Gf+a ei+pvei++k G +t+vd
  lcl|FitnessBrowser__Caulo:CCNA_02490 149 FVNPAMRKLYGVDSMPETAENVATDYGVNREDQDAFALRSQARTAAAQANGFLAGEITPVEIPGKAG-PTIVD 220
                                           *******************************************************************.9**** PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           +deh+r ett+ealaklk++vre+gtvtaGnasGvndGa+al++ase+avkrhgltprari+++asaGveprv
  lcl|FitnessBrowser__Caulo:CCNA_02490 221 RDEHPR-ETTMEALAKLKPIVREGGTVTAGNASGVNDGAVALVIASEDAVKRHGLTPRARITGYASAGVEPRV 292
                                           ******.****************************************************************** PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gpvpav+kl+a++gl++ d+dv+elneafaaq+lavlr+lgl+dd+a+vn+nGGaialGhplGasGarlv
  lcl|FitnessBrowser__Caulo:CCNA_02490 293 MGIGPVPAVRKLMAKTGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNANGGAIALGHPLGASGARLV 365
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                           ltal+qle+sgg+++latlciGvGqG al++erv
  lcl|FitnessBrowser__Caulo:CCNA_02490 366 LTALRQLEASGGQRGLATLCIGVGQGAALAFERV 399
                                           *********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (399 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.51
//
[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