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

GapMind for catabolism of small carbon sources

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

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate Ac3H11_2303 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2303
          Length = 392

 Score =  560 bits (1444), Expect = e-164
 Identities = 281/392 (71%), Positives = 330/392 (84%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M D+VIVSAARTAVGKFGG+LAK PA ELGA+VI+ A+ RAG+  +Q+ EVIMGQVL AG
Sbjct: 1   MEDIVIVSAARTAVGKFGGALAKTPASELGAIVIREAIARAGLSSDQIGEVIMGQVLAAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQNPARQA++KAG+    PA+TIN VCGSGLKAVMLAA A+  GD++IVVAGGQENMS 
Sbjct: 61  VGQNPARQASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENMSL 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           APHVL GSRDG RMGD K+VD+MIVDGLWDVYNQYHMGITAENVAK YGITR+ QD  A+
Sbjct: 121 APHVLNGSRDGQRMGDWKMVDSMIVDGLWDVYNQYHMGITAENVAKAYGITRDMQDALAL 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
           GSQ KA AAQ AGKF +EIV V + Q+KGDP+ F  DE++ +    ++++GL+PAFDKAG
Sbjct: 181 GSQQKAAAAQDAGKFADEIVGVSLAQKKGDPILFNADEYLNRKTNAEALAGLRPAFDKAG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTA NASGLNDGAAAVVVMSA KA  LGL PLA I ++  +G+DP  MGMGPVPAS++A
Sbjct: 241 SVTAGNASGLNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATMGMGPVPASRKA 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L RA W   D+DL E+NEAFAAQA AV++++  D +KVNVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LQRAGWNAADVDLFELNEAFAAQACAVNKELAIDPAKVNVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM+RRDAKKGLA+LCIGGGMGV+LA+ER
Sbjct: 361 TLLHEMQRRDAKKGLAALCIGGGMGVSLALER 392


Lambda     K      H
   0.315    0.131    0.369 

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: 532
Number of extensions: 15
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate Ac3H11_2303 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.1117.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   5.4e-145  469.1  14.7   6.1e-145  468.9  14.7    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.9  14.7  6.1e-145  6.1e-145       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.9 bits;  conditional E-value: 6.1e-145
                                        TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaR 62 
                                                      iv+a+Rt++gk+gg+l++++a++L+a vi+e+++ragl+ ++i evi+G+vl ag ++n+aR
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303   6 IVSAARTAVGKFGGALAKTPASELGAIVIREAIARAGLSSDQIGEVIMGQVLAAGVGQNPAR 67 
                                                      8************************************************************* PP

                                        TIGR01930  63 eaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkasl 124
                                                      +a ++ag+ +++palt+n vC+Sgl+Av+laaq+++ G+ d+vvaGG E+mS +p++l+ s 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303  68 QASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENMSLAPHVLNGS- 128
                                                      ***********************************************************98. PP

                                        TIGR01930 125 rreslklgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakA 183
                                                       r++ ++g+ k+ d+++ d+   v+++++mg+tAen+ak ygi+R++qD++al S+qkaa+A
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 129 -RDGQRMGDWKMVDSMIVDGlwdVYNQYHMGITAENVAKAYGITRDMQDALALGSQQKAAAA 189
                                                      .8*****************9***99************************************* PP

                                        TIGR01930 184 ieegkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssq 242
                                                      +++gkf+deiv v++ +k   +  ++ De + ++t++e+La+L+paf++ +gs vtAgN+s+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 190 QDAGKFADEIVGVSLAQKkgdPILFNADEYLNRKTNAEALAGLRPAFDK-AGS-VTAGNASG 249
                                                      ***************99999999************************95.9*7.******** PP

                                        TIGR01930 243 lnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdi 304
                                                      lnDGAaa+++ms ++a++lgl+plari +++++g+dp++mg+gpvpA++kaL++ag+++ d+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 250 LNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATMGMGPVPASRKALQRAGWNAADV 311
                                                      ************************************************************** PP

                                        TIGR01930 305 dlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkk 366
                                                      dl+E+nEAFAaq+ av+kel+ +d++kvNvnGGAiA+GHP+GasG+ri++tll+e+++r++k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 312 DLFELNEAFAAQACAVNKELA-IDPAKVNVNGGAIAIGHPIGASGCRILVTLLHEMQRRDAK 372
                                                      *********************.88************************************** PP

                                        TIGR01930 367 yGlatlCvggGqGaAvile 385
                                                       Gla+lC+ggG+G+++ le
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 373 KGLAALCIGGGMGVSLALE 391
                                                      **************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.07
//
[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