GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E2

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf6N2E2_2042 Acetoacetyl-CoA synthetase (EC 6.2.1.16)

Query= BRENDA::Q9Z3R3
         (650 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 Acetoacetyl-CoA
           synthetase (EC 6.2.1.16)
          Length = 651

 Score =  687 bits (1774), Expect = 0.0
 Identities = 355/647 (54%), Positives = 439/647 (67%), Gaps = 7/647 (1%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
           LW P  E + +S M  F  +   R      DY A H WS+ +R AFW A+ +  ++   +
Sbjct: 5   LWQPSPERIAQSRMNAFRQFVNARHHLQLHDYPALHAWSIDQREAFWQAIVDFFEIHFHQ 64

Query: 66  SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
           + +  LV+G +M  A++FP A LNFAE+LLR+     A++   E+    +LTW EL A V
Sbjct: 65  APDAVLVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALDENGSQEQLTWAELAAHV 124

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

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP--TVEGGV 241
           I PK+ I C GY Y GK  D  +KV  + + L +    +++PYA   A +    T     
Sbjct: 185 IEPKVLITCAGYRYAGKVIDQRTKVNEILERLPSLQQLIVLPYAQPDACVEDFKTPAAVA 244

Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
              DF      G   F  +PF HPLYIL+SSGTTGVPKCIVH  GG LLQH+KEH  H  
Sbjct: 245 LWNDFYQS--GGEPAFVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVD 302

Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
           L   +RLFY+TTCGWMMWNWL S LAVG+T+ LYDGSPF P    L D    +R +VFGT
Sbjct: 303 LGPEDRLFYYTTCGWMMWNWLVSALAVGSTVVLYDGSPFHPGPERLLDLIDQQRISVFGT 362

Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
           S K++ A+   G  P +TH L SLR + STGS L+P  + +VY  IK DV LAS+SGGTD
Sbjct: 363 SPKFLAALESEGLKPRQTHRLDSLRALLSTGSALAPHSYDYVYRDIKADVCLASMSGGTD 422

Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
           IVSCFV GNPL PV RGE+QG  LG+AV VWN+ G PV GEKGELVCTR FP+MP+  WN
Sbjct: 423 IVSCFVNGNPLSPVSRGEMQGKSLGMAVQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWN 482

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

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
           ++++V + + IGQ W+ DVRVVLFVRL  GV L EAL ++I+  IR+  +PRHVPAKI+A
Sbjct: 543 KVEQVLDCVAIGQRWQGDVRVVLFVRLRDGVTLNEALAQQIRQVIRANTTPRHVPAKILA 602

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
           V+DIPRT SGK+VELAVR+VVHG  VKN +ALANPEAL+ F    EL
Sbjct: 603 VSDIPRTISGKVVELAVRNVVHGEAVKNTDALANPEALEQFRDRPEL 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: 1361
Number of extensions: 70
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 Pf6N2E2_2042 (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.7340.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  886.9   0.0   3.8e-271  886.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042  Acetoacetyl-CoA synthetase (EC 6


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042  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 !  886.8   0.0  3.8e-271  3.8e-271       5     650 ..       4     649 ..       1     651 [] 0.98

  Alignments for each domain:
  == domain 1  score: 886.8 bits;  conditional E-value: 3.8e-271
                                      TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek 68 
                                                    +lw+p  er++++r++ fr++v  r+ + l dy al+ ws+d+++afw+a+++f+++ f++a +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042   4 ILWQPSPERIAQSRMNAFRQFVNARHHLQLHDYPALHAWSIDQREAFWQAIVDFFEIHFHQAPD 67 
                                                    79********************************************************998777 PP

                                      TIGR01217  69 ev.vddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaal 131
                                                    +v v++ +m++a++fpga+ln+ae+llr+++   a++  de+  + ++t++el + va l+++l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042  68 AVlVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALDENGSQEQLTWAELAAHVAGLQTSL 131
                                                    652899********************************************************** PP

                                      TIGR01217 132 ralGvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdg 195
                                                    +a Gv +Gdrva+ +pn+ ++++ +lat+s+Gaiws +spdfG++gv+drf+qiepk+l+++ g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 132 KAAGVTQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTQGVIDRFGQIEPKVLITCAG 195
                                                    **************************************************************** PP

                                      TIGR01217 196 yvynGkehdrrekvrevakelpdlravvlipyvgdreklap.kvegalt.ledllaaaqaaelv 257
                                                    y+y Gk  d+r kv+e+   lp+l++ +++py+ + + ++  k ++a+  ++d+  +   +e+ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 196 YRYAGKVIDQRTKVNEILERLPSLQQLIVLPYAQPDACVEDfKTPAAVAlWNDFYQS--GGEPA 257
                                                    **********************************998766559999986489**999..99*** PP

                                      TIGR01217 258 feqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwn 321
                                                    f  +pfdhplyil+ssGttGvpk+ivh +GG+l+qh+keh+lh dl++ drl+yytt+Gwmmwn
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 258 FVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVDLGPEDRLFYYTTCGWMMWN 321
                                                    **************************************************************** PP

                                      TIGR01217 322 flvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsa 385
                                                    +lvs+la+G+t+vlydGsp+ p ++ l dl+++++i+v+Gts k++ a++ +glkp +th l++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 322 WLVSALAVGSTVVLYDGSPFHPGPERLLDLIDQQRISVFGTSPKFLAALESEGLKPRQTHRLDS 385
                                                    **************************************************************** PP

                                      TIGR01217 386 lrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGla 449
                                                    lr+++stGs l p++++yvy+ ikadv las+sGGtdivscfv +np+ pv +Ge+q+++lG+a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 386 LRALLSTGSALAPHSYDYVYRDIKADVCLASMSGGTDIVSCFVNGNPLSPVSRGEMQGKSLGMA 449
                                                    **************************************************************** PP

                                      TIGR01217 450 veawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
                                                    v++w+e G+pv gekGelv+t+ +p+mp+ +wnd+   k r++yf ++pgvwa Gdy+e  p+G
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 450 VQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWNDPRQEKLRASYFAQFPGVWAQGDYAEELPHG 513
                                                    **************************************************************** PP

                                      TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatld 577
                                                    g +ihGrsda lnp+Gvr+G+aeiy +ve++++v +++ igq ++ g++rvvlfv+l  G+tl+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 514 GFLIHGRSDAVLNPGGVRIGTAEIYRQVEKVEQVLDCVAIGQRWQ-GDVRVVLFVRLRDGVTLN 576
                                                    *******************************************98.5***************** PP

                                      TIGR01217 578 ealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpeal 641
                                                    eal ++i++ ira+ +prhvp+ki++v++iprt+sGk ve+av++vv+G++v+n +al+npeal
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 577 EALAQQIRQVIRANTTPRHVPAKILAVSDIPRTISGKVVELAVRNVVHGEAVKNTDALANPEAL 640
                                                    **************************************************************** PP

                                      TIGR01217 642 dlyeeleel 650
                                                    + +++ +el
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 641 EQFRDRPEL 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: 7.80
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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