GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Dinoroseobacter shibae DFL-12

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate 3610436 Dshi_3817 beta-ketoadipyl CoA thiolase (RefSeq)

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__Dino:3610436
          Length = 400

 Score =  320 bits (821), Expect = 3e-92
 Identities = 180/399 (45%), Positives = 251/399 (62%), Gaps = 10/399 (2%)

Query: 4   EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62
           + V+    RTP+G +GG L  V +  L A+ +   + R  G+   ++DEVI+G   QAG 
Sbjct: 2   DAVICDGVRTPIGRYGGALSSVRADDLAALPIAALMARNPGVDWARVDEVIYGAANQAGE 61

Query: 63  -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121
             +NVAR   + AG+P+EV   T+N++C SG+ AV  AA+ IKAG+ D+ +AGG E+M +
Sbjct: 62  DNRNVARMAALLAGLPEEVPGLTVNRLCASGMDAVGAAARGIKAGEYDLAIAGGIESMSR 121

Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITREE 177
           APF++P A   +  +    D    + W  +       H    M  TA+ +   Y I+R +
Sbjct: 122 APFVMPKAESAFTRAATVHDTT--IGWRFVNPKIAAMHGIDTMPQTADTVAAAYEISRAD 179

Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGK-KGDIVFDTDEHPRKSTPEA-MAKLAP 235
           QDAF  RSQ   A A  +G F DEIVPV +  +    I+ D DEHPR  T  A +A L  
Sbjct: 180 QDAFAARSQARWAAADAAGLFADEIVPVPVPQRGSAPILVDRDEHPRPGTDAARLAGLKG 239

Query: 236 AFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPI 295
               G SVTAGNASG+ND AAA+++ S   A   G+ PMA+VV  AS GV P VMG+GP+
Sbjct: 240 INGPGLSVTAGNASGVNDGAAALLIASAAAARAHGLTPMARVVGMASAGVAPRVMGIGPV 299

Query: 296 PASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIG 355
           PASRK L++AGLT+D +D+IE NEAFA+QS+A  R LG AD   +VN NGGAIA+GHP+G
Sbjct: 300 PASRKLLDRAGLTLDQMDVIELNEAFASQSLATLRQLGLADDDVRVNPNGGAIAMGHPLG 359

Query: 356 SSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
            SGAR+++T  +++++ G +  L T+C+G G GTALI+E
Sbjct: 360 MSGARLVLTAAHQLRRTGGRYALCTMCVGVGQGTALILE 398


Lambda     K      H
   0.317    0.135    0.387 

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: 487
Number of extensions: 25
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: 396
Length of database: 400
Length adjustment: 31
Effective length of query: 365
Effective length of database: 369
Effective search space:   134685
Effective search space used:   134685
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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