GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29235
          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.

Links

Downloads

Related tools

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