GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Marinobacter algicola DG893

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 WP_007153301.1 MDG893_RS08275 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_000170835.1:WP_007153301.1
          Length = 542

 Score =  612 bits (1577), Expect = e-179
 Identities = 292/545 (53%), Positives = 383/545 (70%), Gaps = 16/545 (2%)

Query: 17  ANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTVA 76
           AN   LTPL FL R A V+P   +VIHG+    W+QTY+RCRRLASALADR +G G TVA
Sbjct: 14  ANNATLTPLDFLARTASVYPEYPAVIHGATRRNWQQTYERCRRLASALADRGVGKGDTVA 73

Query: 77  IIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAEDS 136
            + PNIP M E HFG+PM GAVLN +N RL+A  +AF+L H ++ V++ D+EF  +  ++
Sbjct: 74  AMLPNIPPMLECHFGIPMLGAVLNALNTRLDAKAIAFMLEHGEAKVLIADREFGDVINEA 133

Query: 137 LRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPADE 196
           + +++         P +I + D    PE          ++Y+ F+A+GDP + WQ PADE
Sbjct: 134 VGMLDNP-------PQVIDVND----PEFSGAGTQVSDLDYDAFVASGDPAFDWQMPADE 182

Query: 197 WQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCFP 256
           W +I+L YTSGTT +PKGVV HHRGAY  A+ N  +W M    VYLWTLPMFHCNGWCFP
Sbjct: 183 WDAISLCYTSGTTGNPKGVVYHHRGAYENAMGNQAVWSMGMHPVYLWTLPMFHCNGWCFP 242

Query: 257 WSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTVH 316
           W++   +GT +CLR+V  +++  +I+++KV+H C AP+VLN ++ A  E       HTV 
Sbjct: 243 WTITAFAGTHVCLRKVEPEKILQLISEHKVSHMCGAPIVLNTLLGA-SEAAKSSFSHTVQ 301

Query: 317 VMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNARQ 376
            MTAGAAPP  V+ ++   GFRV H YGL+E YGP TVCAWK EWD LP E +A++ ARQ
Sbjct: 302 AMTAGAAPPAKVIEAIENMGFRVTHVYGLTEVYGPVTVCAWKSEWDDLPVEDRARIKARQ 361

Query: 377 GVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFHS 436
           GVRY  +  + V D +T + VP DG T GEI  RGN VMKGYLKNP+A +E F GGWFH+
Sbjct: 362 GVRYHTLAGMMVGDPETMEAVPKDGNTIGEIFLRGNTVMKGYLKNPKATEEAFRGGWFHT 421

Query: 437 GDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQES 496
           GD+AV H D Y EIKDR KD+IISGGENIS++EVE+V+Y HP +LEA+VVARPDE+W E+
Sbjct: 422 GDLAVWHADGYAEIKDRLKDIIISGGENISTIEVEDVLYRHPDILEAAVVARPDEKWGET 481

Query: 497 PCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILRT 556
           PCAFVTLK +  +  ++    DI+ FCRE++  + VPK++VF  LPKT+TGKIQK +LR 
Sbjct: 482 PCAFVTLKPEAGEVSED----DIIAFCRERMAKFKVPKTIVFSELPKTSTGKIQKFVLRD 537

Query: 557 KAKEM 561
            AK++
Sbjct: 538 DAKKL 542


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: 930
Number of extensions: 39
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: 542
Length adjustment: 36
Effective length of query: 533
Effective length of database: 506
Effective search space:   269698
Effective search space used:   269698
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 24 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