GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Marinobacter algicola DG893

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_007152779.1 MDG893_RS05680 AMP-binding protein

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000170835.1:WP_007152779.1
          Length = 549

 Score =  330 bits (845), Expect = 1e-94
 Identities = 206/554 (37%), Positives = 303/554 (54%), Gaps = 26/554 (4%)

Query: 14  NLKNYEETYRHFDWAEAEKHF-SWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDE 72
           +L +Y+  Y +FD A  E      +    LN   E  D+ A  +   +VALYY+ A    
Sbjct: 2   SLPDYQSVYDNFDPASLEAEILEGNLQDGLNVCTEICDKWA--YDPQRVALYYEKADGGS 59

Query: 73  -KYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131
            K TF E+KE+S R  N L   G + KGDRV   +PRSPEL  ++ GA++ GA+  PLF 
Sbjct: 60  GKLTFAELKEQSARFANYLTSQG-IGKGDRVAALLPRSPELLIVIAGALRAGAVYQPLFT 118

Query: 132 AFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHV--FVVGGEAESGTNIINYDE 189
           AF  GA++ R E +  K+VVT P     +   KL  ++     V    AE   ++ ++D+
Sbjct: 119 AFGPGAIEYRFERASTKLVVTDP-----VNYPKLTEVKDCAPVVCVNAAEVSGDVPDFDK 173

Query: 190 AAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDI 249
              ++S + +   +   D FL  +TSG+ G  KGV    +A++  Y   K+ +DL+++D+
Sbjct: 174 TLAEQSGQFEPVLIKGGDPFLQMFTSGTVGKSKGVAVPAKALLAFYVYMKYAIDLRDDDV 233

Query: 250 YWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRM 309
           +W  ADPGW  G  Y +  P L G       G F+PE+ Y  I +  +    +APTA+R+
Sbjct: 234 FWNVADPGWAYGLYYAVVGPLLMGHATHFNPGAFTPETTYDMIRKYKITNLAAAPTAYRL 293

Query: 310 LMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNY 369
           L  A D +  + +   LR   S GEPLNPEV+ W  K     + D +  TETG    CN+
Sbjct: 294 LK-ANDHVLPEGENLGLRVASSAGEPLNPEVVSWIEKRHFCPVKDHYGQTETG-MTCCNF 351

Query: 370 PCMD--IKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHT---IWNNPE 424
             +D  ++ GSMG   PG     ++ +  E+    +G +A+      + H     W   +
Sbjct: 352 HGLDHPVRQGSMGYSSPGHRVVALNEKNEEVGEGEIGQVAVDVKASPLFHFDGYTWGEKD 411

Query: 425 KYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAE 484
            +       G+Y++GD A    +G F F GR DD+I T+G RVGP +VES L+EH A+AE
Sbjct: 412 PFVK-----GYYLTGDMAVCHGDGCFSFSGRDDDIITTAGYRVGPADVESTLLEHKAVAE 466

Query: 485 AGVIGKPDPVRGEIIKAFIALREGFEP--SDKLKEEIRLFVKQGLAAHAAPREIEFKDKL 542
           +GV+ KPD  RG IIKA++ ++   EP   D LK+E++  V+  L+AHA PREIEF D+L
Sbjct: 467 SGVVAKPDEKRGSIIKAYVVIKGDQEPESEDALKDELQELVRHRLSAHAYPREIEFVDEL 526

Query: 543 PKTRSGKIMRRVLK 556
           PKT SGKI R VL+
Sbjct: 527 PKTPSGKIQRFVLR 540


Lambda     K      H
   0.318    0.136    0.425 

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: 899
Number of extensions: 46
Number of successful extensions: 7
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: 572
Length of database: 549
Length adjustment: 36
Effective length of query: 536
Effective length of database: 513
Effective search space:   274968
Effective search space used:   274968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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