GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Amantichitinum ursilacus IGB-41

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_053939433.1 WG78_RS19070 acetyl-CoA C-acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_001294205.1:WP_053939433.1
          Length = 393

 Score =  319 bits (817), Expect = 1e-91
 Identities = 185/400 (46%), Positives = 256/400 (64%), Gaps = 9/400 (2%)

Query: 3   REVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAG 62
           +E+ I  A RT IG FGG+LA+V A DL A  +K L++R+  +   Q+ EV +G    AG
Sbjct: 2   QEIAIVAAGRTAIGNFGGALASVSAPDLGATVIKGLLQRSG-ISADQISEVMMGNVLTAG 60

Query: 63  EDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMS 122
              +N AR A   AG+PD+VPG+T+N++C SG+ AV    ++I +G+ ++VIAGG E+MS
Sbjct: 61  L-GQNPARQASRKAGVPDAVPGLTVNQVCGSGLKAVALGVQSILAGDNQIVIAGGQENMS 119

Query: 123 RAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQ 182
            AP+++  +   F  G    + T+    +   +   Y    M  TA+N+A  Y +SRA+Q
Sbjct: 120 AAPHLLPGSRDGFRMG----NATLVDSMVYDGLTDVYHQYHMGVTAENIARKYGISRAEQ 175

Query: 183 DAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDA-DEHLRPDTTLEALAKLKPV 241
           D  A  SQ  A  A+ AG FA+EI+ V +  +KG+ +    DE +RP TT+E LA+L+P 
Sbjct: 176 DELAATSQMRAAAAREAGRFADEIIAVPVPQRKGDPIAFLEDEFIRPGTTVETLARLRPA 235

Query: 242 NGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVP 301
              + TVTAGNASG+NDG+  +IL S E   + GL   A +   ASAGV P +MG+GPVP
Sbjct: 236 FDKEGTVTAGNASGINDGAAGVILMSRERAAELGLPILAIIRAAASAGVDPALMGMGPVP 295

Query: 302 AVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGA 361
           A ++ L R   S+   D+IE NEAFAAQ L V REL    D  RVN NGGAIALGHP+GA
Sbjct: 296 ATQRALARAGWSLDSLDLIEGNEAFAAQALGVAREL--RWDMQRVNVNGGAIALGHPIGA 353

Query: 362 SGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           SGAR+++T +H++ +   QRGL T+C+G G GVALAVERV
Sbjct: 354 SGARVLVTLLHEMARRDAQRGLATLCIGGGMGVALAVERV 393


Lambda     K      H
   0.317    0.134    0.379 

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: 464
Number of extensions: 19
Number of successful extensions: 5
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
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 (21.6 bits)
S2: 50 (23.9 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