GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas fluorescens GW456-L13

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate PfGW456L13_4590 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590
          Length = 400

 Score =  713 bits (1841), Expect = 0.0
 Identities = 362/400 (90%), Positives = 384/400 (96%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           MRDV+ICDAIRTPIGRFGG L+ VRADDLAAVP+KAL+E NP+V W+ VDEVF GCANQA
Sbjct: 1   MRDVYICDAIRTPIGRFGGGLSTVRADDLAAVPIKALMERNPSVDWNAVDEVFLGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAGLPE+IPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPETIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKA++ +SRNMKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY+VSRAD
Sbjct: 121 SRAPFVMGKADAAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYKVSRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDAFALRSQQ+ AAAQAAGFFAEEIV VRIAHKKGET+V +DEH R +TTLEALTKLKPV
Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVEVRIAHKKGETVVSQDEHPRADTTLEALTKLKPV 240

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
           NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLT RA+VLGMAS GVAPRVMGIGPVP
Sbjct: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARAKVLGMASAGVAPRVMGIGPVP 300

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AVRKL ERLGVAVSDFDVIELNEAFASQGLAVLRELG+ADDA QVNPNGGAIALGHPLGM
Sbjct: 301 AVRKLIERLGVAVSDFDVIELNEAFASQGLAVLRELGIADDAAQVNPNGGAIALGHPLGM 360

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLVLTALHQLEK+GG+KGLATMCVGVGQGLALAIERV
Sbjct: 361 SGARLVLTALHQLEKTGGKKGLATMCVGVGQGLALAIERV 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: 648
Number of extensions: 15
Number of successful extensions: 1
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 PfGW456L13_4590 (Beta-ketoadipyl CoA thiolase (EC 2.3.1.-))
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.9022.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   9.6e-227  738.5  12.9   1.1e-226  738.3  12.9    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590  Beta-ketoadipyl CoA thiolase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590  Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  738.3  12.9  1.1e-226  1.1e-226       1     400 []       2     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 738.3 bits;  conditional E-value: 1.1e-226
                                               TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGc 55 
                                                             ++vyi+dairtpiGr+gG+ls+vraddlaavp+kal++rnps+d++a+d+v+lGc
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590   2 RDVYICDAIRTPIGRFGGGLSTVRADDLAAVPIKALMERNPSVDWNAVDEVFLGC 56 
                                                             689**************************************************** PP

                                               TIGR02430  56 anqaGednrnvarmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadl 110
                                                             anqaGednrnvarma+llaGlp+++pg+t+nrlc+sg+da+g+a+rai++Ge +l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590  57 ANQAGEDNRNVARMALLLAGLPETIPGVTLNRLCASGMDAIGTAFRAIASGEMEL 111
                                                             ******************************************************* PP

                                               TIGR02430 111 viaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnpklkalyGvdsmpet 165
                                                              iaGGvesmsrapfv+Gkad+afsr+ kledttiGwrf+np +ka+yGvd+mp+t
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590 112 AIAGGVESMSRAPFVMGKADAAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQT 166
                                                             ******************************************************* PP

                                               TIGR02430 166 aenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                                             a+nva++++vsr+dqdafalrsqqrtaaaqa+Gffaeeiv+v+i++kkG etvv+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590 167 ADNVADDYKVSRADQDAFALRSQQRTAAAQAAGFFAEEIVEVRIAHKKG-ETVVS 220
                                                             *************************************************.899** PP

                                               TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgl 275
                                                             +deh+ra+ttleal+klk+v+ +d+tvtaGnasGvndGaaal+las+eavk+hgl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590 221 QDEHPRADTTLEALTKLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGL 275
                                                             ******************************************************* PP

                                               TIGR02430 276 tprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqal 330
                                                             t+ra++l++asaGv+prvmG+gpvpav+kl++r+g++++d+dvielneafa+q+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590 276 TARAKVLGMASAGVAPRVMGIGPVPAVRKLIERLGVAVSDFDVIELNEAFASQGL 330
                                                             ******************************************************* PP

                                               TIGR02430 331 avlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatl 385
                                                             avlrelg+add+a+vnpnGGaialGhplG+sGarlvltal+qlek+gg+ +lat+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590 331 AVLRELGIADDAAQVNPNGGAIALGHPLGMSGARLVLTALHQLEKTGGKKGLATM 385
                                                             ******************************************************* PP

                                               TIGR02430 386 ciGvGqGialvierv 400
                                                             c+GvGqG+al+ierv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590 386 CVGVGQGLALAIERV 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: 00:00:00.02
# Mc/sec: 7.88
//
[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:

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