Alignments for a candidate for acs in Gracilibacillus halophilus YIM-C55.5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Gracilibacillus halophilus YIM-C55.5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_003462445.1 J416_RS00160 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000359605.1:WP_003462445.1
          Length = 571

 Score =  801 bits (2069), Expect = 0.0
 Identities = 372/573 (64%), Positives = 457/573 (79%), Gaps = 3/573 (0%)

Query: 1   MNLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAES-FRKN 59
           M    +   +GD N+++ E   + F+W E +  FSW+ TGK+N AYEAIDRHAE+  +K+
Sbjct: 1   METTTIDVRQGDFNVEDVETLRKDFNWEEMKATFSWYHTGKVNMAYEAIDRHAENPNKKD 60

Query: 60  KVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGA 119
           ++AL Y   KR+E  TF ++++ SN+  NVL++Y +V KGDRVF+FMPRSPE Y    G 
Sbjct: 61  QIALLYSSPKREESLTFDQLRKRSNQFANVLKKY-HVNKGDRVFLFMPRSPEFYASFFGI 119

Query: 120 IKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAE 179
           +K+GA+AGPLFEAFME AV+DRLE+S+A +++TTPELLER+PVD+LP L+ + +VG    
Sbjct: 120 LKVGAVAGPLFEAFMEQAVRDRLEDSQASMLITTPELLERVPVDELPDLEKIVLVGATGV 179

Query: 180 SGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGK 239
             +N I++D   +  S   DIEW+D +DG ++HYTSGSTG PKGV HVH AMIQ Y TGK
Sbjct: 180 DVSNYIDFDHEMEGASESFDIEWVDLEDGMVMHYTSGSTGKPKGVYHVHHAMIQHYATGK 239

Query: 240 WVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNV 299
           WVLDL E+D+YWCTADPGWVTGT YGIFAPWLNG TNVI GGR+SPESWY T+ +  V V
Sbjct: 240 WVLDLTEDDVYWCTADPGWVTGTSYGIFAPWLNGVTNVIRGGRYSPESWYETLAKYDVTV 299

Query: 300 WYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMT 359
           WY+APTA R LM AG ++A +YDL+ +RH+LSVGEPLNPEVI W    +++RIHDTWWMT
Sbjct: 300 WYTAPTALRKLMSAGKDIAKQYDLSKVRHILSVGEPLNPEVITWALDAYDRRIHDTWWMT 359

Query: 360 ETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTI 419
           ETG+ LI N PCM+I+PGSMGKPIPGVEA+I+D+ GNELPPY+MGNLA+K+GWPSMM  I
Sbjct: 360 ETGAMLIVNLPCMEIRPGSMGKPIPGVEASIIDDDGNELPPYQMGNLAVKEGWPSMMRAI 419

Query: 420 WNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEH 479
           W  PEKY SYF+  GWYVSGDSAYMDE+GYFWFQGR+DDVI TSGERVGPFEVESKL+EH
Sbjct: 420 WKRPEKYNSYFI-NGWYVSGDSAYMDEDGYFWFQGRLDDVINTSGERVGPFEVESKLIEH 478

Query: 480 PAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFK 539
            A++EAGVIGKPD  RGEIIKAFI L  G+E  D L EEIR +VK GL+AHAAPREIE  
Sbjct: 479 HAVSEAGVIGKPDAERGEIIKAFITLNPGYEKDDALLEEIRQYVKTGLSAHAAPREIEIT 538

Query: 540 DKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572
           D +PKTRSGKIMRR+LK+WEL LP GD ST+E+
Sbjct: 539 DTIPKTRSGKIMRRLLKSWELGLPTGDTSTLEE 571


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: 1167
Number of extensions: 49
Number of successful extensions: 4
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: 571
Length adjustment: 36
Effective length of query: 536
Effective length of database: 535
Effective search space:   286760
Effective search space used:   286760
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 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