GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Paraburkholderia bryophila 376MFSha3.1

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate H281DRAFT_05723 H281DRAFT_05723 acetyl-CoA acyltransferase

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



>FitnessBrowser__Burk376:H281DRAFT_05723
          Length = 400

 Score =  592 bits (1526), Expect = e-174
 Identities = 302/401 (75%), Positives = 341/401 (85%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+A I DA+RTPIGRY GAL  VRADDLGA+P+KALI R+P +DW AVDDVIYGCANQA
Sbjct: 1   MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRAVDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLP   PG T+NRLCGSG+DAVG+AARA++ GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           +RAPFVMGK+  AF R AEI DTTIGWRFVN LM++ +G+DSMPETAENVA QF ISRAD
Sbjct: 121 TRAPFVMGKAASAFARQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFAL SQ KAA A  +G LA+EIV VEIAQ+KG A  V  DEHPR +T+LE LAKL  
Sbjct: 181 QDAFALVSQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLAKLKG 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
             R  G+VTAGNASGVNDGACALL+AS +AA ++GL+ RARVVGMATAGVEPRIMGIGP 
Sbjct: 240 VVRPDGTVTAGNASGVNDGACALLIASQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PAT+K+L   G+ L  +DVIELNEAFA+QGLAVLR LGL DDD RVNPNGGAIALGHPLG
Sbjct: 300 PATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
            SGARLVTTALH+LE   GR+ALCTMCIGVGQGIAL+IER+
Sbjct: 360 ASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400


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: 577
Number of extensions: 17
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: 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 H281DRAFT_05723 H281DRAFT_05723 (acetyl-CoA acyltransferase)
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.129346.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.6e-224  730.5  12.6   2.9e-224  730.3  12.6    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05723  H281DRAFT_05723 acetyl-CoA acylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05723  H281DRAFT_05723 acetyl-CoA acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.3  12.6  2.9e-224  2.9e-224       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 730.3 bits;  conditional E-value: 2.9e-224
                                    TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnva 67 
                                                  ++yi+dairtpiGrygG+l  vraddl+avp+kal++rnp +d+ a+ddvi+GcanqaGednrnva
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723   3 DAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRAVDDVIYGCANQAGEDNRNVA 68 
                                                  79**************************************************************** PP

                                    TIGR02430  68 rmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsaf 133
                                                  rm+allaGlp++ pg+t+nrlcgsg+da+g+aaraikaGea+l+iaGGvesm+rapfv+Gka+saf
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723  69 RMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKAASAF 134
                                                  ****************************************************************** PP

                                    TIGR02430 134 srsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGf 199
                                                  +r+a+++dttiGwrfvnp +k++yGvdsmpetaenvae+fg+sr+dqdafal sqq++a+aq  G 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 135 ARQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALVSQQKAARAQRDGT 200
                                                  ****************************************************************** PP

                                    TIGR02430 200 faeeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaallla 265
                                                  +a+eiv vei+qkkG++  v  deh+r et+le+laklk+vvr+dgtvtaGnasGvndGa+all+a
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 201 LAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLAKLKGVVRPDGTVTAGNASGVNDGACALLIA 265
                                                  ***************************.************************************** PP

                                    TIGR02430 266 seeavkrhgltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqala 331
                                                  s++a+ ++gl+ rar++++a+aGvepr+mG+gp+pa++kll+++g++l++ldvielneafa+q+la
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 266 SQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLA 331
                                                  ****************************************************************** PP

                                    TIGR02430 332 vlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvi 397
                                                  vlr lgl+ddd rvnpnGGaialGhplGasGarlv+tal+qle+s+gr+al+t+ciGvGqGialvi
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 332 VLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVI 397
                                                  ****************************************************************** PP

                                    TIGR02430 398 erv 400
                                                  er+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 398 ERL 400
                                                  *96 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: 31.71
//
[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:

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