Alignments for a candidate for paaJ2 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Pseudomonas putida KT2440

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PP_3280 PP_3280 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase

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



>FitnessBrowser__Putida:PP_3280
          Length = 406

 Score =  703 bits (1815), Expect = 0.0
 Identities = 353/399 (88%), Positives = 377/399 (94%)

Query: 3   EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62
           +ALIIDAVRTPIGRYAGAL+SVRADDL AIPLKALI RHP+LDW A+DDVI+GCANQAGE
Sbjct: 8   DALIIDAVRTPIGRYAGALSSVRADDLAAIPLKALIQRHPELDWKAIDDVIFGCANQAGE 67

Query: 63  DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122
           DNRNVA MA+LLAGLP+ VPGTT+NRLCGSGLDA+G+AARALRCGEAGLMLAGGVESMSR
Sbjct: 68  DNRNVAHMASLLAGLPLEVPGTTINRLCGSGLDAIGNAARALRCGEAGLMLAGGVESMSR 127

Query: 123 APFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQD 182
           APFVMGKSEQAFGR+AE+FDTTIGWRFVN LM+  +GIDSMPETAENVA QF ISRADQD
Sbjct: 128 APFVMGKSEQAFGRAAELFDTTIGWRFVNPLMKAAYGIDSMPETAENVAEQFGISRADQD 187

Query: 183 AFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTPF 242
           AFALRSQHKAAAA A GRLA+EIV VEI QRKGPAK+VEHDEHPRGDTTLEQLA+LGTPF
Sbjct: 188 AFALRSQHKAAAAQARGRLAREIVPVEIPQRKGPAKVVEHDEHPRGDTTLEQLARLGTPF 247

Query: 243 RQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVPA 302
           R+GGSVTAGNASGVNDGACALLLASS AA+RHGLKAR R+VGMA AGVEPR+MGIGPVPA
Sbjct: 248 REGGSVTAGNASGVNDGACALLLASSAAARRHGLKARGRIVGMAVAGVEPRLMGIGPVPA 307

Query: 303 TRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGMS 362
           TRKVL LTGLALAD+DVIELNEAFAAQGLAVLRELGLADDD RVN NGGAIALGHPLGMS
Sbjct: 308 TRKVLALTGLALADLDVIELNEAFAAQGLAVLRELGLADDDPRVNRNGGAIALGHPLGMS 367

Query: 363 GARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           GARLVTTALHELEE  GRYALCTMCIGVGQGIA+IIER+
Sbjct: 368 GARLVTTALHELEETAGRYALCTMCIGVGQGIAMIIERL 406


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: 665
Number of extensions: 18
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: 406
Length adjustment: 31
Effective length of query: 370
Effective length of database: 375
Effective search space:   138750
Effective search space used:   138750
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 PP_3280 PP_3280 (3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-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.493.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.2e-222  722.5   9.5   8.2e-222  722.3   9.5    1.0  1  lcl|FitnessBrowser__Putida:PP_3280  PP_3280 3-oxoadipyl-CoA/3-oxo-5,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3280  PP_3280 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.3   9.5  8.2e-222  8.2e-222       2     400 .]       8     406 .]       7     406 .] 1.00

  Alignments for each domain:
  == domain 1  score: 722.3 bits;  conditional E-value: 8.2e-222
                           TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaGl 76 
                                         ++ i+da+rtpiGry+G+lssvraddlaa+plkal++r+p+ld++aiddvi+GcanqaGednrnva ma llaGl
  lcl|FitnessBrowser__Putida:PP_3280   8 DALIIDAVRTPIGRYAGALSSVRADDLAAIPLKALIQRHPELDWKAIDDVIFGCANQAGEDNRNVAHMASLLAGL 82 
                                         578************************************************************************ PP

                           TIGR02430  77 pvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnp 151
                                         p +vpgtt+nrlcgsglda+g aara+++Gea l++aGGvesmsrapfv+Gk++ af+r a+l+dttiGwrfvnp
  lcl|FitnessBrowser__Putida:PP_3280  83 PLEVPGTTINRLCGSGLDAIGNAARALRCGEAGLMLAGGVESMSRAPFVMGKSEQAFGRAAELFDTTIGWRFVNP 157
                                         *************************************************************************** PP

                           TIGR02430 152 klkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehlr 226
                                          +ka yG+dsmpetaenvae+fg+sr+dqdafalrsq+++aaaqa+G +a+eivpvei+q+kG ++vv++deh+r
  lcl|FitnessBrowser__Putida:PP_3280 158 LMKAAYGIDSMPETAENVAEQFGISRADQDAFALRSQHKAAAAQARGRLAREIVPVEIPQRKGPAKVVEHDEHPR 232
                                         *************************************************************************** PP

                           TIGR02430 227 aettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpa 301
                                          +ttle+la+l +++re+g+vtaGnasGvndGa+alllas  a++rhgl++r+ri+++a aGvepr+mG+gpvpa
  lcl|FitnessBrowser__Putida:PP_3280 233 GDTTLEQLARLGTPFREGGSVTAGNASGVNDGACALLLASSAAARRHGLKARGRIVGMAVAGVEPRLMGIGPVPA 307
                                         *************************************************************************** PP

                           TIGR02430 302 vkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqleks 376
                                         ++k+la +gl+l+dldvielneafaaq+lavlrelgladdd rvn nGGaialGhplG+sGarlv+tal++le++
  lcl|FitnessBrowser__Putida:PP_3280 308 TRKVLALTGLALADLDVIELNEAFAAQGLAVLRELGLADDDPRVNRNGGAIALGHPLGMSGARLVTTALHELEET 382
                                         *************************************************************************** PP

                           TIGR02430 377 ggryalatlciGvGqGialvierv 400
                                          gryal+t+ciGvGqGia++ier+
  lcl|FitnessBrowser__Putida:PP_3280 383 AGRYALCTMCIGVGQGIAMIIERL 406
                                         **********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (406 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: 9.27
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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