Alignments for a candidate for pcaF in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaF in Acidovorax sp. GW101-3H11

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate Ac3H11_3920 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_3920
          Length = 403

 Score =  558 bits (1437), Expect = e-163
 Identities = 286/399 (71%), Positives = 326/399 (81%), Gaps = 1/399 (0%)

Query: 3   EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62
           +A I DA+RTP GRY GAL+SVR DDLGAIP+KAL+ R+P +DW+AV DV YGCANQAGE
Sbjct: 6   QAFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAGE 65

Query: 63  DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122
           DNRNVA M++LLAGLP+ V G T+NRLCGSGLDAVG+AARA++ GEAGLM+AGGVESMSR
Sbjct: 66  DNRNVAHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMSR 125

Query: 123 APFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQD 182
           APFVM K+E AF R++ ++DTTIGWRFVNKLM++ +G+DSMPETAENVA  F I R  QD
Sbjct: 126 APFVMPKAESAFSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQD 185

Query: 183 AFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTPF 242
             ALRSQ  A AAI  G LA+EIV V I Q+KG A IV  DEHPR +T+LE LAKL    
Sbjct: 186 QMALRSQLNAVAAIKAGHLAREIVPVHIPQKKGDAIIVSQDEHPR-ETSLEALAKLKGVV 244

Query: 243 RQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVPA 302
           R  G+VTAGNASGVNDGACALLLA    A ++GLK RARVVGMA AGV PRIMG GP PA
Sbjct: 245 RPDGTVTAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPA 304

Query: 303 TRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGMS 362
           T+KVL  TGL +  MDVIELNEAFAAQGLAVLR LGL DDD RVN  GGAIALGHPLG S
Sbjct: 305 TQKVLAQTGLTIDHMDVIELNEAFAAQGLAVLRALGLKDDDGRVNAWGGAIALGHPLGAS 364

Query: 363 GARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           GARLVTTA++ L E  G+YALCTMCIGVGQGIA+I+ER+
Sbjct: 365 GARLVTTAVNRLHEHAGQYALCTMCIGVGQGIAVILERV 403


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: 537
Number of extensions: 16
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: 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 Ac3H11_3920 (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.1435529.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-213  695.0  10.6   1.8e-213  694.8  10.6    1.0  1  FitnessBrowser__acidovorax_3H11:Ac3H11_3920  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__acidovorax_3H11:Ac3H11_3920  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.8  10.6  1.8e-213  1.8e-213       1     400 []       5     403 .]       5     403 .] 1.00

  Alignments for each domain:
  == domain 1  score: 694.8 bits;  conditional E-value: 1.8e-213
                                    TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnv 66 
                                                  ++++i+dairtp+GrygG+lssvr+ddl+a+p+kal++rnp +d+aa+ dv++GcanqaGednrnv
  FitnessBrowser__acidovorax_3H11:Ac3H11_3920   5 RQAFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAGEDNRNV 70 
                                                  689*************************************************************** PP

                                    TIGR02430  67 armaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsa 132
                                                  a m+ llaGlp +v+g+t+nrlcgsglda+g+aaraikaGea l+iaGGvesmsrapfv+ ka+sa
  FitnessBrowser__acidovorax_3H11:Ac3H11_3920  71 AHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMSRAPFVMPKAESA 136
                                                  ****************************************************************** PP

                                    TIGR02430 133 fsrsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakG 198
                                                  fsr+  + dttiGwrfvn  +k+ yGvdsmpetaenva++f+++re qd++alrsq ++ aa ++G
  FitnessBrowser__acidovorax_3H11:Ac3H11_3920 137 FSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQDQMALRSQLNAVAAIKAG 202
                                                  ****************************************************************** PP

                                    TIGR02430 199 ffaeeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalll 264
                                                  ++a+eivpv+i+qkkG++ +v++deh+r et+lealaklk+vvr+dgtvtaGnasGvndGa+alll
  FitnessBrowser__acidovorax_3H11:Ac3H11_3920 203 HLAREIVPVHIPQKKGDAIIVSQDEHPR-ETSLEALAKLKGVVRPDGTVTAGNASGVNDGACALLL 267
                                                  ****************************.************************************* PP

                                    TIGR02430 265 aseeavkrhgltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqal 330
                                                  a e  ++++gl+prar++++a aGv+pr+mG+gp+pa++k+la++gl+++++dvielneafaaq+l
  FitnessBrowser__acidovorax_3H11:Ac3H11_3920 268 ADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPATQKVLAQTGLTIDHMDVIELNEAFAAQGL 333
                                                  ****************************************************************** PP

                                    TIGR02430 331 avlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialv 396
                                                  avlr+lgl+ddd rvn+ GGaialGhplGasGarlv+ta+++l+++ g+yal+t+ciGvGqGia++
  FitnessBrowser__acidovorax_3H11:Ac3H11_3920 334 AVLRALGLKDDDGRVNAWGGAIALGHPLGASGARLVTTAVNRLHEHAGQYALCTMCIGVGQGIAVI 399
                                                  ****************************************************************** PP

                                    TIGR02430 397 ierv 400
                                                  +erv
  FitnessBrowser__acidovorax_3H11:Ac3H11_3920 400 LERV 403
                                                  ***8 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.62
//
[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