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.31023.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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.84
//
[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