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

GapMind for catabolism of small carbon sources

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

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PfGW456L13_2430 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430
          Length = 403

 Score =  694 bits (1790), Expect = 0.0
 Identities = 348/401 (86%), Positives = 375/401 (93%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+ALIIDAVRTPIGRYAG L+SVRADDLGA+PL+ L+ RHPQ+DW+ VDDVIYGCANQA
Sbjct: 1   MNDALIIDAVRTPIGRYAGVLSSVRADDLGAVPLRELLRRHPQVDWNTVDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLPVSVPGTTLNRLCGSGLDA+G+AARA+R GE GLML GGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPVSVPGTTLNRLCGSGLDAIGTAARAIRSGETGLMLVGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAP VMGK+EQAF R+AE+FDTTIGWRFVN LM++ +GIDSMPETAENVA QFNISRAD
Sbjct: 121 SRAPLVMGKAEQAFSRTAEVFDTTIGWRFVNPLMKKTYGIDSMPETAENVAEQFNISRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFALRSQ +AAAA A+GRLAKEIVAVEI QRKGPAK+VEHDEHPRGDTTLEQLAKLGT
Sbjct: 181 QDAFALRSQQRAAAAQASGRLAKEIVAVEIPQRKGPAKVVEHDEHPRGDTTLEQLAKLGT 240

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR+GGS+TAGNASGVNDGACALLLAS E A+R GL AR RVV MATAGVEPRIMGIGPV
Sbjct: 241 PFREGGSITAGNASGVNDGACALLLASPEVAKRQGLTARGRVVAMATAGVEPRIMGIGPV 300

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PATRKVLE+  L+LADMDVIELNEAFAAQGLAVLRELGL+D D RVNPNGGAIALGHPLG
Sbjct: 301 PATRKVLEVANLSLADMDVIELNEAFAAQGLAVLRELGLSDTDPRVNPNGGAIALGHPLG 360

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTALHELEER GRYALCTMCIGVGQGIALIIER+
Sbjct: 361 MSGARLVTTALHELEERNGRYALCTMCIGVGQGIALIIERL 401


Lambda     K      H
   0.319    0.134    0.384 

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: 639
Number of extensions: 16
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: 401
Length of database: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate PfGW456L13_2430 (Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ 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.16416.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.3e-224  731.5   7.9   1.5e-224  731.3   7.9    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430  Acetyl-CoA acetyltransferase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430  Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  731.3   7.9  1.5e-224  1.5e-224       2     400 .]       3     401 ..       2     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 731.3 bits;  conditional E-value: 1.5e-224
                                               TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGca 56 
                                                             ++ i+da+rtpiGry+G+lssvraddl+avpl++ll+r+p++d++++ddvi+Gca
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430   3 DALIIDAVRTPIGRYAGVLSSVRADDLGAVPLRELLRRHPQVDWNTVDDVIYGCA 57 
                                                             689**************************************************** PP

                                               TIGR02430  57 nqaGednrnvarmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlv 111
                                                             nqaGednrnvarm+allaGlpvsvpgtt+nrlcgsglda+g+aarai++Ge+ l+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430  58 NQAGEDNRNVARMSALLAGLPVSVPGTTLNRLCGSGLDAIGTAARAIRSGETGLM 112
                                                             ******************************************************* PP

                                               TIGR02430 112 iaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnpklkalyGvdsmpeta 166
                                                             + GGvesmsrap v+Gka+ afsr+a+++dttiGwrfvnp +k+ yG+dsmpeta
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 113 LVGGVESMSRAPLVMGKAEQAFSRTAEVFDTTIGWRFVNPLMKKTYGIDSMPETA 167
                                                             ******************************************************* PP

                                               TIGR02430 167 envaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdk 221
                                                             envae+f++sr+dqdafalrsqqr+aaaqa+G +a+eiv vei+q+kG ++vv++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 168 ENVAEQFNISRADQDAFALRSQQRAAAAQASGRLAKEIVAVEIPQRKGPAKVVEH 222
                                                             ******************************************************* PP

                                               TIGR02430 222 dehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhglt 276
                                                             deh+r +ttle+lakl +++re+g++taGnasGvndGa+alllas e +kr+glt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 223 DEHPRGDTTLEQLAKLGTPFREGGSITAGNASGVNDGACALLLASPEVAKRQGLT 277
                                                             ******************************************************* PP

                                               TIGR02430 277 prarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqala 331
                                                             +r+r++a+a+aGvepr+mG+gpvpa++k+l+ a+lsl+d+dvielneafaaq+la
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 278 ARGRVVAMATAGVEPRIMGIGPVPATRKVLEVANLSLADMDVIELNEAFAAQGLA 332
                                                             ******************************************************* PP

                                               TIGR02430 332 vlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlc 386
                                                             vlrelgl+d d rvnpnGGaialGhplG+sGarlv+tal++le+++gryal+t+c
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 333 VLRELGLSDTDPRVNPNGGAIALGHPLGMSGARLVTTALHELEERNGRYALCTMC 387
                                                             ******************************************************* PP

                                               TIGR02430 387 iGvGqGialvierv 400
                                                             iGvGqGial+ier+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 388 IGVGQGIALIIERL 401
                                                             ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (403 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: 00:00:00.01
# Mc/sec: 12.21
//
[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