Alignments for a candidate for acs in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Geotalea uraniireducens Rf4

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011938514.1 GURA_RS08185 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000016745.1:WP_011938514.1
          Length = 584

 Score =  515 bits (1326), Expect = e-150
 Identities = 267/568 (47%), Positives = 366/568 (64%), Gaps = 13/568 (2%)

Query: 14  NLKNYEETYRHFDWAEAEKHFSWHETGK-LNAAYEAIDRHAESFRKNKVALYY--KDAKR 70
           +L +YE+T   F W       S    GK LN A+EA+DR A    ++++A  +  KD   
Sbjct: 18  HLLDYEKTCAGFSWEAVRSELSGLPEGKGLNIAHEAVDRQAAGPLRDRLAFRWLGKDGAV 77

Query: 71  DEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLF 130
            + +TF ++KE+S+R  NVL+R G VEKG+RVF+   R P LY   LG +K  ++  PLF
Sbjct: 78  QD-FTFCDLKEQSSRFANVLKRLG-VEKGERVFVLAGRIPPLYIAALGCLKNISVFCPLF 135

Query: 131 EAFMEGAVKDRLENSEAKVVVTTPELLERIPV---DKLPHLQHVFVVGGEAESGTNIINY 187
            AF    ++ RL   +A+++VTT     +      + LP L+HV +   + +    +++ 
Sbjct: 136 SAFGPDPIRQRLSRGDARLLVTTERQYAKKIAGIRESLPQLRHVLLTDIDDDLDETVLSL 195

Query: 188 DEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEE 247
                + S    I   D +D  +LH+TSG+TG PKG + VH+A++    TG++V+D    
Sbjct: 196 PRLMAEASADFTIPPTDPEDMAVLHFTSGTTGMPKGAVLVHDAVLTHLVTGRYVMDFHSA 255

Query: 248 DIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAF 307
           DI+WCTADPGWVTG+ YGI AP L+G T++I    F  E WY  +E+  V VWY+APTA 
Sbjct: 256 DIFWCTADPGWVTGSSYGIIAPLLHGITSIIDEADFDAERWYRILEEQRVTVWYTAPTAI 315

Query: 308 RMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLIC 367
           RMLM A  E   ++DL+ LR + SVGEPLNPE + WG +V    IHD WW TETG  +I 
Sbjct: 316 RMLMRAAIEPLKRFDLSPLRLIHSVGEPLNPEAVVWGERVLGLPIHDNWWQTETGGIMIA 375

Query: 368 NYPCMDIKPGSMGKPIPGVEAAIV----DNQGNELPPYRMGNLAIKKGWPSMMHTIWNNP 423
           NY  M+I+PGSMG+P+PG+EAAIV    D+      P   G+LA++ GWPSM     ++ 
Sbjct: 376 NYAAMEIRPGSMGRPLPGIEAAIVRRVDDSVDVLTEPDVEGDLALRPGWPSMFRAYLHDE 435

Query: 424 EKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIA 483
           E+Y   F+  GWY++GD A  D +GY+WF GR DD+I TSG  VGPFEVES L+EHPA+A
Sbjct: 436 ERYRKCFV-SGWYITGDLAKRDADGYYWFVGRGDDIIKTSGHMVGPFEVESALMEHPAVA 494

Query: 484 EAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLP 543
           EAGVIGKP+P+ GEI+KAF+ L+ GFEP+DKL+ E+  F +  L +  AP+E+EF D LP
Sbjct: 495 EAGVIGKPEPIIGEIVKAFVCLKPGFEPTDKLRLELIGFGRTRLGSAVAPKEMEFVDSLP 554

Query: 544 KTRSGKIMRRVLKAWELNLPAGDLSTME 571
           +TRSGKIMRR+LKA EL LP GD ST+E
Sbjct: 555 RTRSGKIMRRLLKARELGLPEGDTSTLE 582


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: 1026
Number of extensions: 45
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: 584
Length adjustment: 36
Effective length of query: 536
Effective length of database: 548
Effective search space:   293728
Effective search space used:   293728
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