GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Thermoactinomyces daqus H-18

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_033099083.1 JG50_RS0100120 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000763315.1:WP_033099083.1
          Length = 572

 Score =  857 bits (2214), Expect = 0.0
 Identities = 400/571 (70%), Positives = 470/571 (82%), Gaps = 1/571 (0%)

Query: 2   NLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKV 61
           N + +P     +NL+NYEETY  FDW + E+ FSW++TGK+NAAYEAIDRH E  +  K 
Sbjct: 3   NTERIPVQTNGNNLQNYEETYASFDWKQVEQEFSWYKTGKVNAAYEAIDRHVEQGKGEKT 62

Query: 62  ALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIK 121
           AL Y    R+E YTF+++KE+SN+  ++L+R G + KGDRVFIFMPR+P+LY   LG IK
Sbjct: 63  ALIYSAPDREETYTFRQLKEKSNQFAHLLKRIG-IHKGDRVFIFMPRTPDLYVSFLGTIK 121

Query: 122 IGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAESG 181
           IGAI GPLFEAFME AV+DRLENSEA  +VTTP LLER+PVD LPHL+H+ +VG + E  
Sbjct: 122 IGAIVGPLFEAFMEAAVRDRLENSEAVALVTTPTLLERVPVDDLPHLKHIILVGAKGELT 181

Query: 182 TNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWV 241
               ++++   +  T L+  W+D++D  L+HYTSGSTG PKGV+H H AMIQ YQTGKWV
Sbjct: 182 DGYYSFEKELAKSPTELEPVWVDREDPMLIHYTSGSTGKPKGVVHAHNAMIQHYQTGKWV 241

Query: 242 LDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWY 301
           LDL+E DIYWCT DPGWVTGT YGIFAPWLNG TNV+ GGRFSP+ WY T+E+  V VWY
Sbjct: 242 LDLQEGDIYWCTVDPGWVTGTSYGIFAPWLNGVTNVVRGGRFSPDDWYQTLEKYKVTVWY 301

Query: 302 SAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTET 361
           SAPTAFRMLM AG+++  KYD++S+RHVLSVGEPLNPEV+RWG +V+ KRIHD WWMTET
Sbjct: 302 SAPTAFRMLMAAGEDLVKKYDISSVRHVLSVGEPLNPEVVRWGLQVYGKRIHDNWWMTET 361

Query: 362 GSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWN 421
           G  LI NYP M+IKPGSMGKP PG+ AAI+D+QGNELPPY MGNLAIK  WPS+M  IW 
Sbjct: 362 GGILISNYPQMEIKPGSMGKPFPGIYAAILDDQGNELPPYEMGNLAIKTPWPSIMRKIWK 421

Query: 422 NPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPA 481
           NPEKY+ YF   GWYVSGDSAY DE+GYFWFQGR+DDVI TSGERVGPFEVESKLVEHPA
Sbjct: 422 NPEKYQEYFRIPGWYVSGDSAYKDEDGYFWFQGRLDDVINTSGERVGPFEVESKLVEHPA 481

Query: 482 IAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDK 541
           +AEAGVIGKPDP+RGEIIKAFI+LR G++PS++LKEEIR FVK  LAAHAAPREIEFKDK
Sbjct: 482 VAEAGVIGKPDPLRGEIIKAFISLRAGYKPSEELKEEIRQFVKTRLAAHAAPREIEFKDK 541

Query: 542 LPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572
           LPKTRSGKIMRRVLKAWEL+LP GDLSTMED
Sbjct: 542 LPKTRSGKIMRRVLKAWELDLPVGDLSTMED 572


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: 1206
Number of extensions: 45
Number of successful extensions: 2
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: 572
Length adjustment: 36
Effective length of query: 536
Effective length of database: 536
Effective search space:   287296
Effective search space used:   287296
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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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