Alignments for a candidate for aacS in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Pseudomonas putida KT2440

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_3071 PP_3071 acetoacetyl-coenzyme A synthetase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__Putida:PP_3071
          Length = 650

 Score =  694 bits (1791), Expect = 0.0
 Identities = 366/648 (56%), Positives = 440/648 (67%), Gaps = 6/648 (0%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66
           LW P    +E S M  F      R+     DY A H WS+ +R AFW  + E+ +V   +
Sbjct: 5   LWRPSTTQIEASRMDAFRRRVNLRYNLQLNDYQALHGWSIEQRPAFWQTLAEYFQVHWHT 64

Query: 67  G-EKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
              + L +G +M DA++F  A LNFAE+LLR+     A++   ED      T  EL A V
Sbjct: 65  PPSQVLSEGPQMPDAQWFANATLNFAEHLLRRRDDRPAVVAVREDGQREVFTHAELAAQV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           + LQ A +A GI  GDRVAA+MPN  +T+  MLA  S+GA+WS+ SP+FG  G++DRFGQ
Sbjct: 125 AGLQTAFKAVGIVPGDRVAAIMPNTWQTLVAMLACTSLGAVWSTSSPEFGVHGIIDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVTL 243
           I PKL IVC GY Y GK  D  +KV  V   L      ++VP+              V+L
Sbjct: 185 IEPKLLIVCAGYQYAGKAIDQVTKVNQVCAQLPGLEHLIVVPHTRKGTRADEFQAANVSL 244

Query: 244 -ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
             DF      G   F  LPF HPLYIL+SSGTTGVPKCIVH AGG LLQHLKEH  H  L
Sbjct: 245 WNDFFQ--PGGEPRFTPLPFDHPLYILYSSGTTGVPKCIVHRAGGVLLQHLKEHGLHNDL 302

Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
           +  + LFY+TTCGWMMWNWLASGLAVGATL LYDGSPF P    L D   AE    FGTS
Sbjct: 303 KADDVLFYYTTCGWMMWNWLASGLAVGATLVLYDGSPFHPGPERLLDLIEAEGIHAFGTS 362

Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
           AKY+ A+ + G  PA +H L+SLRL+ STGSPLSP  + +VY+ IK D+ L S+SGGTDI
Sbjct: 363 AKYLAALEQAGLEPANSHCLTSLRLLLSTGSPLSPHSYDYVYDKIKADLWLVSMSGGTDI 422

Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
           VSCFVLGNP  PV RGEIQ  GLG+AV+VWN++G+PV  EKGELVCTR FPSMP+ FWND
Sbjct: 423 VSCFVLGNPTLPVRRGEIQCKGLGMAVEVWNEQGQPVVDEKGELVCTRNFPSMPLGFWND 482

Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542
           PDG +Y  AYF +F  VW  GD+AE    GG+VIHGRSDA LNPGGVRIGTAEIY QVE+
Sbjct: 483 PDGRRYHDAYFSQFPGVWAQGDYAEQRASGGMVIHGRSDAVLNPGGVRIGTAEIYRQVEK 542

Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602
           +++V E++ IGQDW  DVRVVLFVRL  G++L EAL + I+  IR   +PRHVPA I  V
Sbjct: 543 VEQVVESVAIGQDWNGDVRVVLFVRLQDGLQLDEALRQHIRQVIRQYTTPRHVPAVIAQV 602

Query: 603 ADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
           +DIPRT SGK+VELA+RDVVHGRPVKN +ALANPEAL+ F    ELKS
Sbjct: 603 SDIPRTISGKLVELAIRDVVHGRPVKNTDALANPEALEQFRDRAELKS 650


Lambda     K      H
   0.322    0.139    0.441 

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: 1340
Number of extensions: 60
Number of successful extensions: 3
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: 650
Length of database: 650
Length adjustment: 38
Effective length of query: 612
Effective length of database: 612
Effective search space:   374544
Effective search space used:   374544
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 (21.9 bits)
S2: 54 (25.4 bits)

Align candidate PP_3071 PP_3071 (acetoacetyl-coenzyme A synthetase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

# 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/TIGR01217.hmm
# target sequence database:        /tmp/gapView.14139.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01217  [M=652]
Accession:   TIGR01217
Description: ac_ac_CoA_syn: acetoacetate-CoA ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.4e-271  887.0   0.0   3.8e-271  886.8   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3071  PP_3071 acetoacetyl-coenzyme A s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3071  PP_3071 acetoacetyl-coenzyme A synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  886.8   0.0  3.8e-271  3.8e-271       4     652 .]       3     650 .]       1     650 [] 0.98

  Alignments for each domain:
  == domain 1  score: 886.8 bits;  conditional E-value: 3.8e-271
                           TIGR01217   4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd.dskml 77 
                                         +vlw+p + +++ +r++ fr  v  r+ + l dy+al+ ws++++ afw+ + e+++v  +++ ++v+  + +m+
  lcl|FitnessBrowser__Putida:PP_3071   3 DVLWRPSTTQIEASRMDAFRRRVNLRYNLQLNDYQALHGWSIEQRPAFWQTLAEYFQVHWHTPPSQVLSeGPQMP 77 
                                         59************************************************************99999861679** PP

                           TIGR01217  78 aarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipea 152
                                         +a++f +a+ln+ae+llr+++  +a++ v e+ +    t++el +qva l++a++a+G+ +Gdrva+++pn+ ++
  lcl|FitnessBrowser__Putida:PP_3071  78 DAQWFANATLNFAEHLLRRRDDRPAVVAVREDGQREVFTHAELAAQVAGLQTAFKAVGIVPGDRVAAIMPNTWQT 152
                                         *************************************************************************** PP

                           TIGR01217 153 vaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipy 227
                                         ++a+la++s+Ga+ws++sp+fG++g++drf+qiepkll+++ gy+y Gk  d+  kv++v  +lp l++ +++p+
  lcl|FitnessBrowser__Putida:PP_3071 153 LVAMLACTSLGAVWSTSSPEFGVHGIIDRFGQIEPKLLIVCAGYQYAGKAIDQVTKVNQVCAQLPGLEHLIVVPH 227
                                         *************************************************************************** PP

                           TIGR01217 228 vgdreklap.kvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhc 301
                                           +  + +  +  +   ++d+      +e+ f  lpfdhplyil+ssGttGvpk+ivh aGG+l+qhlkeh+lh 
  lcl|FitnessBrowser__Putida:PP_3071 228 TRKGTRADEfQAANVSLWNDFFQP--GGEPRFTPLPFDHPLYILYSSGTTGVPKCIVHRAGGVLLQHLKEHGLHN 300
                                         997777766577888899***988..89*********************************************** PP

                           TIGR01217 302 dltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglk 376
                                         dl+  d+l+yytt+Gwmmwn+l+sgla+GatlvlydGsp+ p ++ l dl+e+egi  +Gtsaky+ a++++gl+
  lcl|FitnessBrowser__Putida:PP_3071 301 DLKADDVLFYYTTCGWMMWNWLASGLAVGATLVLYDGSPFHPGPERLLDLIEAEGIHAFGTSAKYLAALEQAGLE 375
                                         *************************************************************************** PP

                           TIGR01217 377 parthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlave 451
                                         pa++h l++lrl++stGspl+p++++yvy++ikad++l s+sGGtdivscfv++np+lpv +Geiq++glG+ave
  lcl|FitnessBrowser__Putida:PP_3071 376 PANSHCLTSLRLLLSTGSPLSPHSYDYVYDKIKADLWLVSMSGGTDIVSCFVLGNPTLPVRRGEIQCKGLGMAVE 450
                                         *************************************************************************** PP

                           TIGR01217 452 awdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatln 526
                                         +w+e+G+pv +ekGelv+t+ +psmp+ fwnd+dG +y++ayf+++pgvwa Gdy+e  + Gg+vihGrsda ln
  lcl|FitnessBrowser__Putida:PP_3071 451 VWNEQGQPVVDEKGELVCTRNFPSMPLGFWNDPDGRRYHDAYFSQFPGVWAQGDYAEQRASGGMVIHGRSDAVLN 525
                                         *************************************************************************** PP

                           TIGR01217 527 pnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpski 601
                                         p+Gvr+G+aeiy +ve++++v es+ igq+++ g++rvvlfv+l  G +ldeal ++i++ ir   +prhvp+ i
  lcl|FitnessBrowser__Putida:PP_3071 526 PGGVRIGTAEIYRQVEKVEQVVESVAIGQDWN-GDVRVVLFVRLQDGLQLDEALRQHIRQVIRQYTTPRHVPAVI 599
                                         *******************************7.6***************************************** PP

                           TIGR01217 602 ievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelks 652
                                          +v++iprt+sGk ve+a++dvv+G+pv+n +al+npeal+ +++ +elks
  lcl|FitnessBrowser__Putida:PP_3071 600 AQVSDIPRTISGKLVELAIRDVVHGRPVKNTDALANPEALEQFRDRAELKS 650
                                         *********************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (650 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: 00:00:00.03
# Mc/sec: 12.43
//
[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