GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872
          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.18804.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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 9.40
//
[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