Alignments for a candidate for acs in Methylocapsa aurea KYG

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methylocapsa aurea KYG

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_036264504.1 DL86_RS18225 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000746085.1:WP_036264504.1
          Length = 585

 Score =  526 bits (1356), Expect = e-154
 Identities = 270/570 (47%), Positives = 367/570 (64%), Gaps = 17/570 (2%)

Query: 14  NLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEK 73
           N+++YE +   F WA  +        G LN A+EA+DRH  + R +K+AL +    RD++
Sbjct: 17  NIQDYEASIAAFSWAREQAQLDGLPKGGLNIAHEALDRHVLAGRGDKLALRW--IGRDDR 74

Query: 74  ---YTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLF 130
              +++ +++  +NR  NVL R G V KG+RVF  + R+PELY   LGA+K G++  PLF
Sbjct: 75  VHDFSYADLQAAANRFANVLARRG-VGKGERVFSLLGRTPELYMAALGALKNGSVFSPLF 133

Query: 131 EAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPH----LQHVFVVGGEAESGTNIIN 186
            AF    +K R+    AK ++T+ E   R  ++ + H    L+HVF+     +      N
Sbjct: 134 SAFGPEPIKARMTIGAAKALITS-ETFYRRKIEPIRHELSSLEHVFLTDCSDDPPVGATN 192

Query: 187 YDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKE 246
              A   E    +  W   +D  LLH+TSG+TG PKG +HVH++++  + TGK  LDL  
Sbjct: 193 LTAAMAMEQDSFETVWTVPEDMALLHFTSGTTGRPKGAVHVHQSVVAHHVTGKLALDLHP 252

Query: 247 EDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTA 306
            DI+WCTADPGWVTG  YGI +P  NGAT ++    F  E WY  +E   VNVWY+APTA
Sbjct: 253 GDIFWCTADPGWVTGASYGIISPLTNGATLIVDQAEFDAERWYRILEAQKVNVWYTAPTA 312

Query: 307 FRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLI 366
            RMLM AG  +A ++DL++LR + SVGEPLNPE + WG + F K  HD WW TETG  +I
Sbjct: 313 IRMLMKAGAGLAKQFDLSNLRFMASVGEPLNPEAVIWGVEAFGKPFHDNWWQTETGGIMI 372

Query: 367 CNYPCMDIKPGSMGKPIPGVEAAIV----DNQGNEL-PPYRMGNLAIKKGWPSMMHTIWN 421
            NY  MD+KPGSMG+P+PGV A+IV    D +  E+  P  MG LA++ GWPSMM    N
Sbjct: 373 ANYRSMDVKPGSMGRPLPGVTASIVERSRDGKIREVGKPMAMGELALRPGWPSMMRAYLN 432

Query: 422 NPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPA 481
             E+Y   F  GGWY++GD A  D +GY+WF GR DDVI ++G  +GPFEVES L+EH A
Sbjct: 433 EEERYRKCF-AGGWYLTGDLAMRDADGYYWFVGRADDVIKSAGHLIGPFEVESALMEHAA 491

Query: 482 IAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDK 541
           +AEAGVIG PD + GE++KAF+AL+EG EP++ L++E+    ++ L    AP++I F+  
Sbjct: 492 VAEAGVIGIPDAIAGEVVKAFVALKEGAEPTEALRKELLGHARKRLGPAIAPKDIAFRKN 551

Query: 542 LPKTRSGKIMRRVLKAWELNLPAGDLSTME 571
           LPKTRSGKIMRR+LKA EL LP GDLST+E
Sbjct: 552 LPKTRSGKIMRRLLKARELGLPEGDLSTLE 581


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: 1035
Number of extensions: 55
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: 585
Length adjustment: 36
Effective length of query: 536
Effective length of database: 549
Effective search space:   294264
Effective search space used:   294264
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources