GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Dechlorosoma suillum PS

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 Dsui_2808 Dsui_2808 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II

Query= SwissProt::Q8VZF1
         (569 letters)



>lcl|FitnessBrowser__PS:Dsui_2808 Dsui_2808 acyl-CoA synthetase
           (AMP-forming)/AMP-acid ligase II
          Length = 552

 Score =  575 bits (1483), Expect = e-168
 Identities = 286/554 (51%), Positives = 379/554 (68%), Gaps = 19/554 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L K  ANY  L+PL F+ R+A ++P R SVIHG R YTW +T++R RRLASAL  R I  
Sbjct: 16  LEKNAANYVPLSPLTFIARSAYIYPERVSVIHGQRRYTWLETFNRARRLASALEARGIKE 75

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TVA++  N P MYE HFGVP+ GAVLN +N RL+   VAF+L+H ++ +++ D+E+  
Sbjct: 76  GDTVAVMLNNTPEMYECHFGVPVTGAVLNTLNTRLDPEAVAFMLNHGEAKILITDKEYSH 135

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHT-CAPESLNRALSKGAIEYEDFLATGDPNYPW 190
           +   +L    EK G S    ++I + D     P  L      G  +YE  LA G P+Y W
Sbjct: 136 IVGPAL----EKLGRSI---VVIDVNDSEYTGPGDL-----LGEKDYEALLAEGTPDYEW 183

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
           + P DEW +I+L YTSGTT +PKGVV HHRGAY+ A+SN + WGM   +VYLWTLPMFHC
Sbjct: 184 KGPQDEWDAISLNYTSGTTGNPKGVVYHHRGAYLNAMSNIVSWGMPPHSVYLWTLPMFHC 243

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGWCFPW++A  +GT++CLR+V  K +   I + KVTH+C AP+V + + NAP E     
Sbjct: 244 NGWCFPWTMAANAGTNVCLRRVDPKLILQSIRENKVTHYCGAPIVHSMLANAPAEWRE-G 302

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
           + H V  + A A PP +V+  M + GF++ H YGL+ETYGP++VCA +PEW  LP   Q 
Sbjct: 303 INHGVSGLIAAAPPPAAVIEGMAKIGFKITHVYGLTETYGPASVCAQQPEWFDLPVGEQV 362

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
            LN RQGVRY   E + V+D  T + VP D +T GEI+FRGN+VMKGYLKNP+A +E+FA
Sbjct: 363 NLNGRQGVRYHAQEAITVLDPATMEAVPWDNETMGEIMFRGNLVMKGYLKNPKATEESFA 422

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
           GG++H+GD+AV   D Y++IKDRSKDVIISGGENISS+EVE+ +Y HPAV+ A+VVA PD
Sbjct: 423 GGYYHTGDLAVMQADGYVKIKDRSKDVIISGGENISSIEVEDTLYRHPAVMAAAVVATPD 482

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550
            +W E P AF+ LK      +      +I++FCRE +  + VPK V+FGPLPKT+TGKIQ
Sbjct: 483 PKWGEVPAAFIELKDGVSITE-----VEIIEFCREHMARFKVPKKVIFGPLPKTSTGKIQ 537

Query: 551 KHILRTKAKEMGPV 564
           K++LR  AK    +
Sbjct: 538 KYVLREMAKSTAAI 551


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: 921
Number of extensions: 47
Number of successful extensions: 4
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: 552
Length adjustment: 36
Effective length of query: 533
Effective length of database: 516
Effective search space:   275028
Effective search space used:   275028
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, 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