GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas fluorescens FW300-N2C3

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate AO356_29235 AO356_29235 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29235 AO356_29235 acyl-CoA
           synthetase
          Length = 550

 Score =  546 bits (1407), Expect = e-160
 Identities = 275/555 (49%), Positives = 358/555 (64%), Gaps = 19/555 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L +  ANY  LTPL FLDRAA+VHP R +V+HG    TWRQT +RC RLASAL++  +G 
Sbjct: 10  LEQSKANYLPLTPLGFLDRAALVHPDRVAVVHGDLRRTWRQTRERCYRLASALSNEGMGA 69

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TV+I++PN PAM EAHFGVP+CGAVLN VN RL+A  VAF+L H +  +++VD+EF  
Sbjct: 70  GDTVSILSPNTPAMLEAHFGVPLCGAVLNTVNYRLDAEGVAFILRHGECKLLLVDREFAA 129

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191
           LA  +L  +E         P++I I DH     S     S G ++YE F+  G P++   
Sbjct: 130 LAVAALERLEHP-------PVVIDINDHLAPLGS-----SIGDVDYETFIGRGSPDFQGV 177

Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251
            P+DEWQ IAL YTSGTT  PKGVV  HRG Y+M++     W +     YLWTLPMFH N
Sbjct: 178 WPSDEWQPIALNYTSGTTGDPKGVVASHRGTYLMSMLQMTNWPLSRAPRYLWTLPMFHAN 237

Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311
           GWCF W++   +GT +CLR+V+A+ V+  I    V HFCAAP+V+  I N+       PL
Sbjct: 238 GWCFTWAITAAAGTHVCLRKVSAEAVFDAIDTQGVDHFCAAPIVMAMIANSADRP---PL 294

Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371
              V V+TAG+ PP +VL ++   GF V H YG++E  G    C W+  W++L    Q  
Sbjct: 295 ETPVRVLTAGSPPPATVLDAVVSLGFDVDHVYGITEVSGTPISCVWQDGWNALAQSDQGA 354

Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431
           L  RQG R  G E L V D  T +PVP DG T GE++ +GN VM GYLKN  A ++ F G
Sbjct: 355 LRVRQGARAAGFEGLMVADADTLQPVPKDGHTTGELLLKGNTVMMGYLKNENATRKAFEG 414

Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491
           GWFH+GD+AV HP+ YI+I DR KDVIISGGENISSVE+E  ++ HPAVL A+VVA+PD+
Sbjct: 415 GWFHTGDVAVVHPNGYIQITDRCKDVIISGGENISSVEIEEAIHCHPAVLHAAVVAQPDD 474

Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551
            W E PCAF+ LK   E+  +     D++ FC+ +L  +  P+ V+F  LPKTATGKIQK
Sbjct: 475 IWGEVPCAFIELKGGAERPTE----ADMIAFCQARLARFKCPRRVIFMELPKTATGKIQK 530

Query: 552 HILRTKAKEMGPVPR 566
            +LR +A     + R
Sbjct: 531 FLLREQAGSRDAIVR 545


Lambda     K      H
   0.319    0.134    0.422 

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: 879
Number of extensions: 48
Number of successful extensions: 5
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: 569
Length of database: 550
Length adjustment: 36
Effective length of query: 533
Effective length of database: 514
Effective search space:   273962
Effective search space used:   273962
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 (21.8 bits)
S2: 53 (25.0 bits)

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