Alignments for a candidate for aacS in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Pseudomonas simiae WCS417

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF2382 PS417_12145 acetoacetyl-CoA synthetase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__WCS417:GFF2382
          Length = 652

 Score =  682 bits (1760), Expect = 0.0
 Identities = 352/647 (54%), Positives = 442/647 (68%), Gaps = 7/647 (1%)

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

Query: 67  GEKA-LVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
              A L++   M  A++FP A LNFAE+LLR+     A++   ED    +LT+ EL A V
Sbjct: 65  PPTAVLIEDAEMPSAQWFPGATLNFAEHLLRRRDGHPAVVALSEDGQREQLTYAELAAHV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           + LQ +LRA G+  GDRVAA MPN  +T+  MLAT S+GAIWS  SPDFG QGV+DRFGQ
Sbjct: 125 AGLQHSLRAAGVVQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTQGVIDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP-TVEGGVT 242
           I PK+ I C GY Y GK  D  +K+  + + L +    +IVPYA   A ++      GV 
Sbjct: 185 IEPKVLITCAGYRYAGKDIDQSAKLNEILERLPSLEQLIIVPYARPQAQVSDYQTHAGVA 244

Query: 243 L-ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
           L  DF      G   F  +PF HPLYIL+SSGTTGVPKCI+H  GG LL HLKEH  H  
Sbjct: 245 LWQDFYQ--PGGEPQFVAVPFDHPLYILYSSGTTGVPKCIIHGTGGVLLTHLKEHGLHAD 302

Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
           L   + LFY+TTCGWMMWNWL S LA+GAT  LYDGSPF P    L D   AE+ +VFGT
Sbjct: 303 LSRDDCLFYYTTCGWMMWNWLVSVLAIGATAVLYDGSPFHPGPERLIDLIDAEKISVFGT 362

Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
           S K++  + K G  P  +HDL SL+ + STGSPLSP+ + +VY  IK  + L+S+SGGTD
Sbjct: 363 SPKFLATLEKAGLQPRLSHDLGSLKGLISTGSPLSPQSYDYVYREIKAQLCLSSMSGGTD 422

Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
           IVSCFV+GNP+ PV RGE+Q   L +A++VW+D+G+P+ GEKGELVCTR FP+MP+  WN
Sbjct: 423 IVSCFVIGNPVLPVRRGEMQCKSLAMAIEVWDDQGRPLIGEKGELVCTRHFPAMPIGLWN 482

Query: 482 DPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
           DP+  K RA+YF +F  VW  GD+AE  P+G ++IHGRSDA LNPGGVRIGTAEIY QVE
Sbjct: 483 DPECKKLRASYFSQFPGVWAQGDYAEQRPNGSLLIHGRSDAVLNPGGVRIGTAEIYRQVE 542

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
           ++ +V E+L IGQ W++DVRVVLFVRL  GVEL E L ++I+  IR+  +PRHVPAKI+A
Sbjct: 543 KIPQVQESLAIGQRWQEDVRVVLFVRLNEGVELDETLEQQIRQVIRANTTPRHVPAKILA 602

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
           V DIPRT SGKIVELAVR+VVHG PVKN +ALANP+AL+ F    EL
Sbjct: 603 VTDIPRTISGKIVELAVRNVVHGEPVKNTDALANPQALEQFRDRPEL 649


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: 1336
Number of extensions: 62
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: 652
Length adjustment: 38
Effective length of query: 612
Effective length of database: 614
Effective search space:   375768
Effective search space used:   375768
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 GFF2382 PS417_12145 (acetoacetyl-CoA 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.2021.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.4e-270  883.3   0.0     5e-270  883.1   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2382  PS417_12145 acetoacetyl-CoA synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2382  PS417_12145 acetoacetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  883.1   0.0    5e-270    5e-270       5     650 ..       4     649 ..       1     651 [. 0.98

  Alignments for each domain:
  == domain 1  score: 883.1 bits;  conditional E-value: 5e-270
                           TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaeke.vvddskmla 78 
                                         +lw+p  er++++r+++fr  + er+   l+dy al++ws+d + +fw+a+++++dv f s+  + +++d +m++
  lcl|FitnessBrowser__WCS417:GFF2382   4 ILWQPSPERIAHTRMDQFRRHINERYSVQLSDYPALHQWSIDRRPDFWRAIVDYFDVQFRSPPTAvLIEDAEMPS 78 
                                         79********************************************************9887655168999**** PP

                           TIGR01217  79 arffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipeav 153
                                         a++fpga+ln+ae+llr+++ ++a++  +e+ +  ++t++el + va l+ +lra Gv +Gdrva+ +pn+ +++
  lcl|FitnessBrowser__WCS417:GFF2382  79 AQWFPGATLNFAEHLLRRRDGHPAVVALSEDGQREQLTYAELAAHVAGLQHSLRAAGVVQGDRVAACMPNTWQTL 153
                                         *************************************************************************** PP

                           TIGR01217 154 aallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipyv 228
                                         + +lat+s+Gaiws +spdfG++gv+drf+qiepk+l+++ gy+y Gk+ d++ k++e+   lp+l++ +++py+
  lcl|FitnessBrowser__WCS417:GFF2382 154 VGMLATTSLGAIWSCSSPDFGTQGVIDRFGQIEPKVLITCAGYRYAGKDIDQSAKLNEILERLPSLEQLIIVPYA 228
                                         *************************************************************************** PP

                           TIGR01217 229 gdreklap..kvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhc 301
                                          ++++++   +  g   ++d+      +e++f  +pfdhplyil+ssGttGvpk+i+h +GG+l+ hlkeh+lh+
  lcl|FitnessBrowser__WCS417:GFF2382 229 RPQAQVSDyqTHAGVALWQDFYQP--GGEPQFVAVPFDHPLYILYSSGTTGVPKCIIHGTGGVLLTHLKEHGLHA 301
                                         **99987653445555799**988..89*********************************************** PP

                           TIGR01217 302 dltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglk 376
                                         dl+  d l+yytt+Gwmmwn+lvs la+Gat vlydGsp+ p ++ l dl+++e+i+v+Gts k++ +++k+gl+
  lcl|FitnessBrowser__WCS417:GFF2382 302 DLSRDDCLFYYTTCGWMMWNWLVSVLAIGATAVLYDGSPFHPGPERLIDLIDAEKISVFGTSPKFLATLEKAGLQ 376
                                         *************************************************************************** PP

                           TIGR01217 377 parthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlave 451
                                         p  +hdl +l+ ++stGspl+p++++yvy+eika++ l+s+sGGtdivscfv +np+lpv +Ge+q+++l +a+e
  lcl|FitnessBrowser__WCS417:GFF2382 377 PRLSHDLGSLKGLISTGSPLSPQSYDYVYREIKAQLCLSSMSGGTDIVSCFVIGNPVLPVRRGEMQCKSLAMAIE 451
                                         *************************************************************************** PP

                           TIGR01217 452 awdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatln 526
                                         +wd++G+p+ gekGelv+t+ +p+mp+ +wnd++  k r++yf+++pgvwa Gdy+e  p+G+++ihGrsda ln
  lcl|FitnessBrowser__WCS417:GFF2382 452 VWDDQGRPLIGEKGELVCTRHFPAMPIGLWNDPECKKLRASYFSQFPGVWAQGDYAEQRPNGSLLIHGRSDAVLN 526
                                         *************************************************************************** PP

                           TIGR01217 527 pnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpski 601
                                         p+Gvr+G+aeiy +ve++++v+esl igq +++ ++rvvlfv+l +G++lde l ++i++ ira+ +prhvp+ki
  lcl|FitnessBrowser__WCS417:GFF2382 527 PGGVRIGTAEIYRQVEKIPQVQESLAIGQRWQE-DVRVVLFVRLNEGVELDETLEQQIRQVIRANTTPRHVPAKI 600
                                         ********************************9.***************************************** PP

                           TIGR01217 602 ievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleel 650
                                         ++v++iprt+sGk+ve+av++vv+G+pv+n +al+np+al+ +++ +el
  lcl|FitnessBrowser__WCS417:GFF2382 601 LAVTDIPRTISGKIVELAVRNVVHGEPVKNTDALANPQALEQFRDRPEL 649
                                         ********************************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (652 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.42
//
[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