GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Ruegeria conchae TW15

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_010437861.1 G7G_RS0102215 3-oxoadipyl-CoA thiolase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_000192475.1:WP_010437861.1
          Length = 400

 Score =  541 bits (1394), Expect = e-158
 Identities = 274/399 (68%), Positives = 317/399 (79%)

Query: 3   EAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGE 62
           +AFICD  RTPIGRYGG+LS VR DDLAAIP+  L+ RNP++D   IDDVI G ANQAGE
Sbjct: 2   DAFICDAQRTPIGRYGGSLSQVRTDDLAAIPIAALIARNPQVDWTGIDDVIYGDANQAGE 61

Query: 63  DNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSR 122
            NRNVARMA LLAGLP  V GTTINRLC SG+DA+G AARAI+AGD D+ IAGGVESMSR
Sbjct: 62  SNRNVARMAALLAGLPVDVPGTTINRLCASGMDAVGMAARAIRAGDYDMAIAGGVESMSR 121

Query: 123 APFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQD 182
           APFVM KA SAFSR   ++DTTIGWRFVNP M Q+FG DSMPETA+NVAE   I+R DQD
Sbjct: 122 APFVMPKATSAFSRANSVYDTTIGWRFVNPKMKQEFGIDSMPETADNVAEAYGINRSDQD 181

Query: 183 SFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPF 242
           +FA RSQ R A A  +G+  EEI PV +  +KG    +  DEH RP TT E+L GLK   
Sbjct: 182 AFAERSQARWAAAHQTGVFREEITPVTIPQRKGDPVVVDTDEHPRPGTTAEKLSGLKGIN 241

Query: 243 RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPA 302
             +  +TAGNASGVNDGAAA+++A+E  AA   LTP AR+V M+ AGVEPR+MG+GPVPA
Sbjct: 242 GLDKTVTAGNASGVNDGAAAILMANESAAAKNDLTPIARVVGMSVAGVEPRVMGIGPVPA 301

Query: 303 TRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMS 362
           +R+VL RAGLSI  MDVIELNEAFA+Q L  LRELG+PDDAPHVNPNGGAIA+GHPLGMS
Sbjct: 302 SRKVLARAGLSIDQMDVIELNEAFASQGLATLRELGVPDDAPHVNPNGGAIAIGHPLGMS 361

Query: 363 GARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           GARL + A+++L R  GRYALCTMC+GVGQG A+ILERV
Sbjct: 362 GARLVMTAAYQLRRTGGRYALCTMCVGVGQGAALILERV 400


Lambda     K      H
   0.319    0.135    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: 550
Number of extensions: 11
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: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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 WP_010437861.1 G7G_RS0102215 (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.1052942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-213  694.8   9.9     2e-213  694.6   9.9    1.0  1  NCBI__GCF_000192475.1:WP_010437861.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010437861.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.6   9.9    2e-213    2e-213       2     400 .]       2     400 .]       1     400 [] 1.00

  Alignments for each domain:
  == domain 1  score: 694.6 bits;  conditional E-value: 2e-213
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           +++i+da rtpiGrygGsls+vr+ddlaa+p++al+arnp++d++ iddvi+G anqaGe nrnvarmaalla
  NCBI__GCF_000192475.1:WP_010437861.1   2 DAFICDAQRTPIGRYGGSLSQVRTDDLAAIPIAALIARNPQVDWTGIDDVIYGDANQAGESNRNVARMAALLA 74 
                                           69*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glpv+vpgtt+nrlc+sg+da+g+aarai+aG+ d+ iaGGvesmsrapfv+ ka safsr + + dttiGwr
  NCBI__GCF_000192475.1:WP_010437861.1  75 GLPVDVPGTTINRLCASGMDAVGMAARAIRAGDYDMAIAGGVESMSRAPFVMPKATSAFSRANSVYDTTIGWR 147
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnpk+k+ +G+dsmpeta+nvae +g++r+dqdafa rsq+r+aaa+++G+f eei+pv+i+q+kG+++vvd
  NCBI__GCF_000192475.1:WP_010437861.1 148 FVNPKMKQEFGIDSMPETADNVAEAYGINRSDQDAFAERSQARWAAAHQTGVFREEITPVTIPQRKGDPVVVD 220
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           +deh+r+ tt e+l+ lk+++  d+tvtaGnasGvndGaaa+l+a e a+++++ltp ar+++++ aGveprv
  NCBI__GCF_000192475.1:WP_010437861.1 221 TDEHPRPGTTAEKLSGLKGINGLDKTVTAGNASGVNDGAAAILMANESAAAKNDLTPIARVVGMSVAGVEPRV 293
                                           ************************************************************************* PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gpvpa +k+laragls++++dvielneafa+q+la+lrelg++dd+ +vnpnGGaia+GhplG+sGarlv
  NCBI__GCF_000192475.1:WP_010437861.1 294 MGIGPVPASRKVLARAGLSIDQMDVIELNEAFASQGLATLRELGVPDDAPHVNPNGGAIAIGHPLGMSGARLV 366
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                           +ta +ql+++ggryal+t+c+GvGqG al++erv
  NCBI__GCF_000192475.1:WP_010437861.1 367 MTAAYQLRRTGGRYALCTMCVGVGQGAALILERV 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.24
//
[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:

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