Alignments for a candidate for pcaF in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaF in Phyllobacterium brassicacearum STM 196

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_106711108.1 CU102_RS10795 3-oxoadipyl-CoA thiolase

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



>NCBI__GCF_003010955.1:WP_106711108.1
          Length = 401

 Score =  548 bits (1413), Expect = e-161
 Identities = 274/401 (68%), Positives = 325/401 (81%), Gaps = 1/401 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M +V+ICD IRTPIGRFGGAL+ VRADDL A+PL+AL++ N  V W+ +DEV +GCANQA
Sbjct: 1   MTEVYICDYIRTPIGRFGGALSSVRADDLGAIPLRALVDRNRNVDWEAIDEVIYGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAGLPE++PG T+NRLC SGMDA+ TA RAI +GE+ELAIAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPETVPGTTMNRLCGSGMDAVITAARAIKAGEIELAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAP VM KAES +SR+ ++ DTTIGWRF+NPLM+ QYGVDSMPET +NVA+DY +SRAD
Sbjct: 121 SRAPLVMPKAESAFSRHAEIHDTTIGWRFVNPLMQEQYGVDSMPETGENVAEDYHISRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKP 239
           QDAFA+RSQQKA AA   G  A EI PVRI+ +KG+  IV+RDEH RPETT+E L KL  
Sbjct: 181 QDAFAVRSQQKAGAAMGNGRLAREITPVRISQRKGDPIIVDRDEHPRPETTIEQLAKLPT 240

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
                 +VTAGNASGVNDGAAALI+AS  A +KH LTP AR+LG A+ GV PRVMG+GP+
Sbjct: 241 PFRKGGSVTAGNASGVNDGAAALIIASESAARKHDLTPIARILGGATAGVPPRVMGVGPI 300

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
            A +KL  RLG+   DF ++ELNEAFASQGLA LR LG+ +DA  VNPNGGAIALGHPLG
Sbjct: 301 AATQKLCARLGITPEDFGIVELNEAFASQGLATLRALGIPEDAEFVNPNGGAIALGHPLG 360

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           MSGAR+  TA  +L   G R+ LATMC+GVGQG+A+ +ERV
Sbjct: 361 MSGARITGTAALELGVRGARRALATMCIGVGQGIAIGLERV 401


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: 549
Number of extensions: 21
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: 400
Length of database: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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 WP_106711108.1 CU102_RS10795 (3-oxoadipyl-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.4005061.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-209  681.8   6.8   1.8e-209  681.6   6.8    1.0  1  NCBI__GCF_003010955.1:WP_106711108.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106711108.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  681.6   6.8  1.8e-209  1.8e-209       2     400 .]       3     401 .]       2     401 .] 1.00

  Alignments for each domain:
  == domain 1  score: 681.6 bits;  conditional E-value: 1.8e-209
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           evyi+d irtpiGr+gG+lssvraddl+a+pl+al++rn ++d++aid+vi+GcanqaGednrnvarma+lla
  NCBI__GCF_003010955.1:WP_106711108.1   3 EVYICDYIRTPIGRFGGALSSVRADDLGAIPLRALVDRNRNVDWEAIDEVIYGCANQAGEDNRNVARMALLLA 75 
                                           89*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp++vpgtt+nrlcgsg+da+ +aaraikaGe +l iaGGvesmsrap v+ ka+safsr+a+++dttiGwr
  NCBI__GCF_003010955.1:WP_106711108.1  76 GLPETVPGTTMNRLCGSGMDAVITAARAIKAGEIELAIAGGVESMSRAPLVMPKAESAFSRHAEIHDTTIGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnp ++++yGvdsmpet envae++ +sr+dqdafa+rsqq++ aa  +G +a+ei+pv+i+q+kG++ +vd
  NCBI__GCF_003010955.1:WP_106711108.1 149 FVNPLMQEQYGVDSMPETGENVAEDYHISRADQDAFAVRSQQKAGAAMGNGRLAREITPVRISQRKGDPIIVD 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           +deh+r+ett+e+lakl +++r++g+vtaGnasGvndGaaal++ase a+++h+ltp aril+ a+aGv prv
  NCBI__GCF_003010955.1:WP_106711108.1 222 RDEHPRPETTIEQLAKLPTPFRKGGSVTAGNASGVNDGAAALIIASESAARKHDLTPIARILGGATAGVPPRV 294
                                           ************************************************************************* PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gp+ a++kl ar+g++ ed+ ++elneafa+q+la+lr+lg+++d++ vnpnGGaialGhplG+sGar+ 
  NCBI__GCF_003010955.1:WP_106711108.1 295 MGVGPIAATQKLCARLGITPEDFGIVELNEAFASQGLATLRALGIPEDAEFVNPNGGAIALGHPLGMSGARIT 367
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                            ta  +l  +g r+alat+ciGvGqGia+ +erv
  NCBI__GCF_003010955.1:WP_106711108.1 368 GTAALELGVRGARRALATMCIGVGQGIAIGLERV 401
                                           *********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (401 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.27
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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