Alignments for a candidate for paaJ2 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Acidovorax sp. GW101-3H11

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate Ac3H11_3920 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3920
          Length = 403

 Score =  593 bits (1529), Expect = e-174
 Identities = 301/397 (75%), Positives = 337/397 (84%)

Query: 4   AYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGED 63
           A+ICDAIRTP GRYGGAL  VR DDLGA+PIKAL+ RNPGVDW AV DV YGCANQAGED
Sbjct: 7   AFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAGED 66

Query: 64  NRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRA 123
           NRNVA MS+LLAGLP +  GATINRLCGSG+DAVGTAARAIKAGEA LMIAGGVESM+RA
Sbjct: 67  NRNVAHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMSRA 126

Query: 124 PFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDA 183
           PFVM KA SAF+R + ++DTTIGWRFVN LMK +YGVDSMPETAENVA  F I R  QD 
Sbjct: 127 PFVMPKAESAFSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQDQ 186

Query: 184 FALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRP 243
            AL SQ  A  A + G LA+EIV V I QKKGDAI V+ DEHPRETSLE+LA+LKGVVRP
Sbjct: 187 MALRSQLNAVAAIKAGHLAREIVPVHIPQKKGDAIIVSQDEHPRETSLEALAKLKGVVRP 246

Query: 244 DGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQ 303
           DGTVTAGNASGVNDGACALL+A +  A +YGL+ RARVVGMA AGV PRIMG GP PATQ
Sbjct: 247 DGTVTAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPATQ 306

Query: 304 KLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGA 363
           K+L Q G+T+D +DVIELNEAFA+QGLAVLR LGL+DDD RVN  GGAIALGHPLGASGA
Sbjct: 307 KVLAQTGLTIDHMDVIELNEAFAAQGLAVLRALGLKDDDGRVNAWGGAIALGHPLGASGA 366

Query: 364 RLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           RLVTTA+++L    G++ALCTMCIGVGQGIA+++ER+
Sbjct: 367 RLVTTAVNRLHEHAGQYALCTMCIGVGQGIAVILERV 403


Lambda     K      H
   0.319    0.134    0.386 

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: 529
Number of extensions: 8
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: 400
Length of database: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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.25136.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  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  Acetyl-CoA acetyltransferase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thio
   #    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 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGed 62 
                                                      ++++i+dairtp+GrygG+lssvr+ddl+a+p+kal++rnp +d+aa+ dv++GcanqaGed
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920   5 RQAFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAGED 66 
                                                      689*********************************************************** PP

                                        TIGR02430  63 nrnvarmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapf 124
                                                      nrnva m+ llaGlp +v+g+t+nrlcgsglda+g+aaraikaGea l+iaGGvesmsrapf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  67 NRNVAHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMSRAPF 128
                                                      ************************************************************** PP

                                        TIGR02430 125 vlGkadsafsrsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalr 186
                                                      v+ ka+safsr+  + dttiGwrfvn  +k+ yGvdsmpetaenva++f+++re qd++alr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 129 VMPKAESAFSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQDQMALR 190
                                                      ************************************************************** PP

                                        TIGR02430 187 sqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvt 248
                                                      sq ++ aa ++G++a+eivpv+i+qkkG++ +v++deh+r et+lealaklk+vvr+dgtvt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 191 SQLNAVAAIKAGHLAREIVPVHIPQKKGDAIIVSQDEHPR-ETSLEALAKLKGVVRPDGTVT 251
                                                      ****************************************.********************* PP

                                        TIGR02430 249 aGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpavkkllarag 310
                                                      aGnasGvndGa+allla e  ++++gl+prar++++a aGv+pr+mG+gp+pa++k+la++g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 252 AGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPATQKVLAQTG 313
                                                      ************************************************************** PP

                                        TIGR02430 311 lsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkq 372
                                                      l+++++dvielneafaaq+lavlr+lgl+ddd rvn+ GGaialGhplGasGarlv+ta+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 314 LTIDHMDVIELNEAFAAQGLAVLRALGLKDDDGRVNAWGGAIALGHPLGASGARLVTTAVNR 375
                                                      ************************************************************** PP

                                        TIGR02430 373 leksggryalatlciGvGqGialvierv 400
                                                      l+++ g+yal+t+ciGvGqGia+++erv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 376 LHEHAGQYALCTMCIGVGQGIAVILERV 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.08
//
[ok]

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

Downloads

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

Related tools

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