GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_2808
          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 (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