GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas fluorescens GW456-L13

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate PfGW456L13_2872 Acetoacetyl-CoA synthetase (EC 6.2.1.16)

Query= BRENDA::Q9Z3R3
         (650 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872
           Acetoacetyl-CoA synthetase (EC 6.2.1.16)
          Length = 651

 Score =  705 bits (1820), Expect = 0.0
 Identities = 359/646 (55%), Positives = 440/646 (68%), Gaps = 5/646 (0%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
           LW PD + + ++ M  F  +  +R      DY A H WS+ +R  FW A+ +   +   E
Sbjct: 5   LWQPDAKRIGKTRMEAFRRFINQRHHLKIDDYPALHQWSIDQRPDFWQAIVDFFDIRFHE 64

Query: 66  SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
             +  L++G RM  A++FP A LNFAE+LL++     A+I  GE+     LTW EL   V
Sbjct: 65  QPDAVLLEGPRMPSAQWFPGATLNFAEHLLQRRDDAIAVIAVGENGQREHLTWAELAEQV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           +  Q  L A G+G GDRVAA MPN  +T+  MLAT S+GAIWS  SPDFG QGV+DRFGQ
Sbjct: 125 AGFQNGLIAAGVGVGDRVAACMPNTWQTLVAMLATTSLGAIWSCSSPDFGTQGVVDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPT-VEGGVT 242
           I PK+ + C GY Y GK  D  +KV  + + L +    ++VPYA   A +     +  VT
Sbjct: 185 IEPKVLVTCAGYRYAGKEIDQTAKVNEILQRLPSLQQLIVVPYARPQAHIEEFHTQANVT 244

Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
           L D       G   F  +PF HPLYIL+SSGTTGVPKCI+HS GG LLQH+KEH  H  L
Sbjct: 245 LWDDFYE-PGGEPDFVPVPFAHPLYILYSSGTTGVPKCIIHSTGGVLLQHVKEHGLHGDL 303

Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
             GERLFY+TTCGWMMWNWL S LA G+++ LYDGSPF P+   L D    ER +VFGTS
Sbjct: 304 GPGERLFYYTTCGWMMWNWLVSALATGSSVVLYDGSPFQPEPQRLIDLIDDERISVFGTS 363

Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
            KY+  +   G  P  +HDLSSL+ +  TGS LSP  + FVY   K DV LAS+SGGTDI
Sbjct: 364 PKYLATLESSGIKPRESHDLSSLKTLLCTGSALSPHSYDFVYRDFKADVCLASMSGGTDI 423

Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
           VSCFV GNP+ PV RGEI G  LG+AV+VWNDEG PV GEKGELVCTR FP+MP+  WND
Sbjct: 424 VSCFVNGNPMSPVRRGEIMGKSLGMAVEVWNDEGHPVIGEKGELVCTRHFPAMPIGLWND 483

Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542
           PDG K R +YF  F  VW  GD+AE  PHGG++IHGRSDA LNPGGVRIGTAEIY QVE+
Sbjct: 484 PDGEKLRKSYFSLFPGVWAQGDYAEQLPHGGMMIHGRSDAVLNPGGVRIGTAEIYRQVEK 543

Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602
           + +V + + IGQ W+DDVRVVLFVRL  G+EL EAL ++I+  IR+  +PRHVPAKI+AV
Sbjct: 544 VPQVLDCVAIGQQWQDDVRVVLFVRLRDGLELDEALQQQIRQVIRANTTPRHVPAKIVAV 603

Query: 603 ADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
            DIPRT SGK+VELAVR+VVHG+ VKN +ALANPEAL+ F    EL
Sbjct: 604 TDIPRTISGKVVELAVRNVVHGQKVKNTDALANPEALEQFRDRPEL 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: 1377
Number of extensions: 67
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: 651
Length adjustment: 38
Effective length of query: 612
Effective length of database: 613
Effective search space:   375156
Effective search space used:   375156
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 PfGW456L13_2872 (Acetoacetyl-CoA synthetase (EC 6.2.1.16))
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.32639.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     2e-275  900.9   0.0   2.2e-275  900.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872  Acetoacetyl-CoA synthetase (EC 6


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872  Acetoacetyl-CoA synthetase (EC 6.2.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  900.8   0.0  2.2e-275  2.2e-275       5     650 ..       4     649 ..       1     651 [] 0.98

  Alignments for each domain:
  == domain 1  score: 900.8 bits;  conditional E-value: 2.2e-275
                                               TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefs 59 
                                                             +lw+pda+r+ ++r++ fr ++ +r+ + + dy al++ws+d++ +fw+a+++f+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872   4 ILWQPDAKRIGKTRMEAFRRFINQRHHLKIDDYPALHQWSIDQRPDFWQAIVDFF 58 
                                                             79***************************************************** PP

                                               TIGR01217  60 dvvfssaekev.vddskmlaarffpgarlnyaenllrkkgsedallyvdeekesa 113
                                                             d++f+++ ++v +++ +m++a++fpga+ln+ae+ll++++   a++ v+e+ +  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872  59 DIRFHEQPDAVlLEGPRMPSAQWFPGATLNFAEHLLQRRDDAIAVIAVGENGQRE 113
                                                             ***987766652799**************************************** PP

                                               TIGR01217 114 kvtfeelrrqvaslaaalralGvkkGdrvagylpnipeavaallatasvGaiwss 168
                                                             ++t++el +qva +++ l a Gv+ Gdrva+ +pn+ ++++a+lat+s+Gaiws 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 114 HLTWAELAEQVAGFQNGLIAAGVGVGDRVAACMPNTWQTLVAMLATTSLGAIWSC 168
                                                             ******************************************************* PP

                                               TIGR01217 169 cspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravv 223
                                                             +spdfG++gv+drf+qiepk+l+++ gy+y Gke d++ kv+e+ + lp+l++ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 169 SSPDFGTQGVVDRFGQIEPKVLVTCAGYRYAGKEIDQTAKVNEILQRLPSLQQLI 223
                                                             ******************************************************* PP

                                               TIGR01217 224 lipyvgdreklap..kvegaltledllaaaqaaelvfeqlpfdhplyilfssGtt 276
                                                             ++py+ ++++++   +  +   ++d+      +e+ f  +pf hplyil+ssGtt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 224 VVPYARPQAHIEEfhTQANVTLWDDFYEP--GGEPDFVPVPFAHPLYILYSSGTT 276
                                                             *********99887455566679***998..99********************** PP

                                               TIGR01217 277 GvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGa 331
                                                             Gvpk+i+hs+GG+l+qh+keh+lh+dl++g+rl+yytt+Gwmmwn+lvs+latG+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 277 GVPKCIIHSTGGVLLQHVKEHGLHGDLGPGERLFYYTTCGWMMWNWLVSALATGS 331
                                                             ******************************************************* PP

                                               TIGR01217 332 tlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsal 386
                                                             ++vlydGsp+ p+++ l dl++ e+i+v+Gts ky+ +++ +g+kp ++hdls+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 332 SVVLYDGSPFQPEPQRLIDLIDDERISVFGTSPKYLATLESSGIKPRESHDLSSL 386
                                                             ******************************************************* PP

                                               TIGR01217 387 rlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGei 441
                                                             ++++ tGs l+p+++++vy+ +kadv las+sGGtdivscfv +np+ pv +Gei
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 387 KTLLCTGSALSPHSYDFVYRDFKADVCLASMSGGTDIVSCFVNGNPMSPVRRGEI 441
                                                             ******************************************************* PP

                                               TIGR01217 442 qapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdk 496
                                                              +++lG+ave+w++eG+pv gekGelv+t+ +p+mp+ +wnd+dG k rk+yf+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 442 MGKSLGMAVEVWNDEGHPVIGEKGELVCTRHFPAMPIGLWNDPDGEKLRKSYFSL 496
                                                             ******************************************************* PP

                                               TIGR01217 497 ypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveesl 551
                                                             +pgvwa Gdy+e  p+Gg++ihGrsda lnp+Gvr+G+aeiy +ve++++v +++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 497 FPGVWAQGDYAEQLPHGGMMIHGRSDAVLNPGGVRIGTAEIYRQVEKVPQVLDCV 551
                                                             ******************************************************* PP

                                               TIGR01217 552 vigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievag 606
                                                              igq+++d ++rvvlfv+l  G +ldeal ++i++ ira+ +prhvp+ki++v++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 552 AIGQQWQD-DVRVVLFVRLRDGLELDEALQQQIRQVIRANTTPRHVPAKIVAVTD 605
                                                             ********.********************************************** PP

                                               TIGR01217 607 iprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleel 650
                                                             iprt+sGk ve+av++vv+G+ v+n +al+npeal+ +++ +el
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 606 IPRTISGKVVELAVRNVVHGQKVKNTDALANPEALEQFRDRPEL 649
                                                             ***************************************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (651 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 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 8.14
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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