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

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.21161.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.27
//
[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:

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