GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Nocardioides daejeonensis MJ31

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_110208807.1 DNK54_RS20110 AMP-binding protein

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_003194585.1:WP_110208807.1
          Length = 545

 Score =  303 bits (777), Expect = 9e-87
 Identities = 189/491 (38%), Positives = 272/491 (55%), Gaps = 13/491 (2%)

Query: 75  TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134
           ++ ++ E S R   VL   G V  GDRV   M +S +    +LG  + GA+  PLF AF 
Sbjct: 49  SYGDLGESSRRMAAVLTELG-VRPGDRVATLMGKSADFVTTVLGIWRAGAVHVPLFTAFA 107

Query: 135 EGAVKDRLENSEAKVVVTTPELLERI-PVDKLP-HLQHVFVVGGEAESGTNIINYDEAAK 192
             A+  RL  S+A+VVV  P    ++ P + LP       VV G+A +  ++   +  A 
Sbjct: 108 PPAIGLRLAGSDARVVVVDPGQRSKLDPSEDLPADPSRRIVVAGDAVAEGDLALSELLAA 167

Query: 193 QESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWC 252
            +            D  +  +TSG+TGTPKGV    +A+       ++ LD+  ED+YW 
Sbjct: 168 ADPASAPAVVRAGSDELVRLFTSGTTGTPKGVPIPVKALAAFVIYLEYGLDVTAEDVYWN 227

Query: 253 TADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMG 312
            ADPGW  G  YGI AP   G  N+++   F+PE+ +  I+ LGV    +APT +R L  
Sbjct: 228 AADPGWAYGLYYGIAAPLALGRRNILLQAGFTPETTWKVIQDLGVTNLAAAPTVYRSLRS 287

Query: 313 AGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYP-- 370
           A     A     +LR   S GEPLNP+V++WG +V    IHDT+  TE G  ++  +   
Sbjct: 288 ATTPAPAGI---ALRRASSAGEPLNPDVVQWGAEVLGSEIHDTYGQTELGMSIVNGWHPE 344

Query: 371 -CMDIKPGSMGKPIPGVEAAIVDNQGNELPPY-RMGNLAIK-KGWPSMMHTIW-NNPEKY 426
              +++ GSMG+ +PG  A ++ +  +E+     +G + I   G P M  T + + PEK 
Sbjct: 345 IAAEVRHGSMGRAMPGWAATVLKDDADEVADAGELGRVVIDLAGSPLMWFTGYVDAPEKT 404

Query: 427 -ESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEA 485
            E +   G WY +GD+  MD++G+ +F  R DDVI+ +G R+GPFEVES LV  P +AEA
Sbjct: 405 AERFSADGRWYYTGDAGQMDDDGFLYFSARDDDVIIMAGYRIGPFEVESVLVGDPRVAEA 464

Query: 486 GVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKT 545
            V+G PD +RGE+++AF+ L  G EPS +L EE++  VK  LAAH  PREI F   LPKT
Sbjct: 465 AVVGVPDALRGEVVEAFVVLAPGTEPSVELAEELKQRVKTKLAAHLYPREIHFVASLPKT 524

Query: 546 RSGKIMRRVLK 556
            SGKI R  L+
Sbjct: 525 PSGKIQRFELR 535


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: 801
Number of extensions: 40
Number of successful extensions: 6
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: 545
Length adjustment: 36
Effective length of query: 536
Effective length of database: 509
Effective search space:   272824
Effective search space used:   272824
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