Alignments for a candidate for acs in Bacillus altitudinis 41KF2b

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Bacillus altitudinis 41KF2b

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_017367863.1 BA79_RS07825 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000691145.1:WP_017367863.1
          Length = 574

 Score = 1014 bits (2622), Expect = 0.0
 Identities = 474/574 (82%), Positives = 531/574 (92%), Gaps = 2/574 (0%)

Query: 1   MNLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNK 60
           M ++ LP+++GD++L +YE+ Y+ F W EA K+FSW+ETGK+NAAYEAIDRHA+SFRKNK
Sbjct: 1   MKVETLPSVKGDYHLNDYEQAYKEFSWEEARKNFSWYETGKVNAAYEAIDRHADSFRKNK 60

Query: 61  VALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAI 120
           VAL+YKD++RDEKYTF++MK ++N+AGN+LR   +V+KGDRVFIFMPRSPELYF++LGA+
Sbjct: 61  VALHYKDSQRDEKYTFRDMKIKTNKAGNLLREQAHVQKGDRVFIFMPRSPELYFLLLGAV 120

Query: 121 KIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAES 180
           KIGAI GPLFEAFMEGAVKDRLENSEAKV+VTTP+LLERIP  +LP L+ V +VGGE E 
Sbjct: 121 KIGAIVGPLFEAFMEGAVKDRLENSEAKVIVTTPDLLERIPFAELPKLESVIIVGGEKED 180

Query: 181 --GTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTG 238
             G   I+++EA +Q +  L+IEWMD+KDG+LLHYTSGSTGTPKGVLHVH AM+QQ QTG
Sbjct: 181 ADGVRTIHFEEAFEQAAKELEIEWMDEKDGYLLHYTSGSTGTPKGVLHVHGAMVQQGQTG 240

Query: 239 KWVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVN 298
           KWVLDLKEED+YWCTADPGWVTGTVYGIF+PWLNGATNVI+GGRF+P++WY TIE LGV 
Sbjct: 241 KWVLDLKEEDVYWCTADPGWVTGTVYGIFSPWLNGATNVILGGRFNPDTWYETIESLGVT 300

Query: 299 VWYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWM 358
           VWYSAPTAFRMLMGAGD++  KYDL+SLRHVLSVGEPLNPEVIRWG  VF KRIHDTWWM
Sbjct: 301 VWYSAPTAFRMLMGAGDDLIQKYDLSSLRHVLSVGEPLNPEVIRWGDAVFGKRIHDTWWM 360

Query: 359 TETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHT 418
           TETG+QLICNYPCMDIKPGSMGKPIPGVEAAIVDN GNELPPYRMGNLAIKKGWPSMMHT
Sbjct: 361 TETGAQLICNYPCMDIKPGSMGKPIPGVEAAIVDNAGNELPPYRMGNLAIKKGWPSMMHT 420

Query: 419 IWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVE 478
           IWNNPEKYESYFMPG WYVSGDSAYMDE+GYFWFQGRVDDVIMTSGERVGPFEVESKLVE
Sbjct: 421 IWNNPEKYESYFMPGDWYVSGDSAYMDEDGYFWFQGRVDDVIMTSGERVGPFEVESKLVE 480

Query: 479 HPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEF 538
           HPAIAEAGVIGKPDPVRGEIIKAFIALR G+EP+D+LKEEIR FVK+GLAAHAAPREIEF
Sbjct: 481 HPAIAEAGVIGKPDPVRGEIIKAFIALRSGYEPTDELKEEIRTFVKKGLAAHAAPREIEF 540

Query: 539 KDKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572
           KDKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED
Sbjct: 541 KDKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED 574


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: 1315
Number of extensions: 49
Number of successful extensions: 3
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: 574
Length adjustment: 36
Effective length of query: 536
Effective length of database: 538
Effective search space:   288368
Effective search space used:   288368
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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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 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