GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Williamsia sterculiae CPCC 203464

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_076477035.1 BW971_RS04860 AMP-binding protein

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_900156495.1:WP_076477035.1
          Length = 510

 Score =  263 bits (672), Expect = 1e-74
 Identities = 166/489 (33%), Positives = 257/489 (52%), Gaps = 38/489 (7%)

Query: 75  TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134
           TF+E+ + S R    L R G V +G+ V + M +S +L   +LG  ++GA+  PLF AF 
Sbjct: 51  TFRELADRSRRFATGLARCG-VGRGEAVGVLMGKSSDLVVALLGIWRLGAVQVPLFTAFA 109

Query: 135 EGAVKDRLENSEAKVVVTTPELLERI-PVDKLPHLQHVFVVGGEAESGTNIINYDEAAKQ 193
             A++ R+  S A+VV+   +   ++ P D L  ++     GG   +G   +  D    +
Sbjct: 110 TPAIELRVRASGAQVVIADADQAVKLDPFDDLTVIR-----GGTEFAG---LIADNEPYE 161

Query: 194 ESTRLDIEWMDKKDGFLLH-YTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWC 252
            S  +        DG ++  +TSG+TGTPKGV     A+   +    + LD+ +ED++W 
Sbjct: 162 ASVAVG------GDGTMVQLFTSGTTGTPKGVPVPVRAIAAFHAYMIYALDVSDEDVFWN 215

Query: 253 TADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMG 312
            ADPGW  G  YG+  P   G  N+++   FSP      +++ GV  +  APT +R L  
Sbjct: 216 AADPGWAYGLYYGLIGPMAIGRPNLLLRAGFSPHLTLDVMQRFGVTNFAGAPTVYRSL-- 273

Query: 313 AGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPC- 371
                       +LR   S GEPL P+V+ W  +     + D +  TE G  ++  +   
Sbjct: 274 ---SKDPAISGVTLRRASSAGEPLTPDVLTWSARALGVEVRDHYGQTELGMLIVNAWHDA 330

Query: 372 --MDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIW-NNPEKYES 428
               + PGSMG P+PG  A + D           G +AI    P      + + PEK   
Sbjct: 331 VRQPVVPGSMGTPLPGFSAELRD-----------GQIAIAADSPLFWFDGYVDAPEKTAE 379

Query: 429 YFMPGG-WYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGV 487
            F     WY++GD+A +D+EG F+F  R DDVI+ +G R+GPF+VES LV HP + +  V
Sbjct: 380 RFSEDRTWYLTGDTAKVDDEGRFFFTARDDDVIIMAGYRIGPFDVESVLVTHPQVIDVAV 439

Query: 488 IGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRS 547
           +G PD +RGE+++A++ L +G + + +L+ E++  VK   AAHA PR + F D LPKT S
Sbjct: 440 VGTPDELRGEVLEAYVVLADGVDGTAELEAELQRLVKTQFAAHAYPRRVHFVDGLPKTPS 499

Query: 548 GKIMRRVLK 556
           GK+ R +L+
Sbjct: 500 GKVQRFLLR 508


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: 693
Number of extensions: 30
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: 510
Length adjustment: 35
Effective length of query: 537
Effective length of database: 475
Effective search space:   255075
Effective search space used:   255075
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: 52 (24.6 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