GapMind for catabolism of small carbon sources

 

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

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_033101535.1 JG50_RS0112880 thiolase family protein

Query= BRENDA::Q0KAI3
         (392 letters)



>NCBI__GCF_000763315.1:WP_033101535.1
          Length = 384

 Score =  331 bits (849), Expect = 2e-95
 Identities = 187/395 (47%), Positives = 256/395 (64%), Gaps = 22/395 (5%)

Query: 2   QQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQA 61
           Q AVI+DA R+P+GR K   + + +   EL A +++ LVERN+LDP  ++D+  GCVTQ 
Sbjct: 4   QDAVIIDAARTPIGRKK--GSLSGIRPDELAAFLLQKLVERNQLDPAEIEDIKMGCVTQT 61

Query: 62  GEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESM 121
           GEQ    GR+A L AGFP  V   +++R C SS + +   A  IMAG  D VIA G+ESM
Sbjct: 62  GEQGYNIGRLAGLIAGFPVEVCGVSVNRMCASSLETLAQGAHAIMAGMSDCVIAAGVESM 121

Query: 122 SRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAA 181
           +RVPMGS       +   +  R+   +V QG++AEL+A K++LSR ++D +S  SH+ A 
Sbjct: 122 NRVPMGS---DGGSFSDQLLNRF--NIVPQGISAELIAEKWQLSREELDQFSLSSHQKAL 176

Query: 182 TARESGAFRREILGIS--TPNG---LVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQ 236
            A+    F+ EI+ +   TP+G    ++ DET RP T++E L +L  SF  D        
Sbjct: 177 KAQSENRFQNEIIPVKAQTPSGETIQLQTDETPRPDTNLEALLSLPPSFLPDG------- 229

Query: 237 IGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPAS 296
               +TAGN+SQISDG +A+LL S   A+ LGLKPRA+  A  + G DP +MLT  IPA+
Sbjct: 230 ---KITAGNSSQISDGVAAVLLASRRKAEELGLKPRAKVRATAIAGVDPEIMLTGIIPAT 286

Query: 297 QRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPLGASGVR 356
           Q+ +K++GL LD ID +E+NEAFA V LAWQR LG    ++NP GGAIALGHPLGASG R
Sbjct: 287 QKVLKRAGLTLDDIDLFEVNEAFASVVLAWQRELGVPSHKINPNGGAIALGHPLGASGAR 346

Query: 357 LMTTMLHALEDSGQRYGLQSMCEAGGMANATIIER 391
           ++ T+L+ LE   +R+GL +MC   GMA+A IIER
Sbjct: 347 IVATLLNELERQEKRFGLIAMCIGFGMASAIIIER 381


Lambda     K      H
   0.318    0.132    0.384 

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: 410
Number of extensions: 21
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: 392
Length of database: 384
Length adjustment: 30
Effective length of query: 362
Effective length of database: 354
Effective search space:   128148
Effective search space used:   128148
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 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