GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Nocardioides daejeonensis MJ31

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_110204929.1 DNK54_RS00015 acetyl-CoA C-acetyltransferase

Query= SwissProt::P45855
         (393 letters)



>NCBI__GCF_003194585.1:WP_110204929.1
          Length = 395

 Score =  354 bits (909), Expect = e-102
 Identities = 197/395 (49%), Positives = 260/395 (65%), Gaps = 6/395 (1%)

Query: 1   MRKTVIVSAARTPFGKFGGVLKEVKAAELGGIVMKEALQQAGVSGDDVEGNVMGMVVQAG 60
           M  +VIV+ ARTP G+  G LK++ AA+LGG+ +K AL++AG+SGD V+  VMG V+QAG
Sbjct: 1   MSGSVIVAGARTPVGRLLGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAG 60

Query: 61  SGQIPSRQAARLAGMPWSVPSETLNKVCASGLRAVTLCDQMIRAQDADILVAGGMESMSN 120
           +GQI +RQAA   G+P  VPS T+NKVC SG+ A+ L DQ+IRA + +I+VAGGMESM+ 
Sbjct: 61  AGQITARQAAVKGGIPMGVPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQ 120

Query: 121 IPYAVPAGRWGARMGDGELRDLMVYDGLTCAFDEVHMA---VHGNTAAKEYAISRREQDE 177
            P+ +P  R G + GD +L D M YD L   F +  M       N A     ++R EQD 
Sbjct: 121 APHLLPKSREGFKYGDTKLVDSMAYDALYDQFTDQAMGNLTEQCNVAGGN--LTREEQDA 178

Query: 178 WALRSHARAAKAADEGKFQDEIVPVNWIGRKGKPNVVDKDEAIRRDTSLDQLAKLAPIYA 237
           ++ RSH  AA A   G F DEIVPV    R+G   VV  DE +R DT+ + L  L P +A
Sbjct: 179 FSARSHQLAAAAQKNGVFDDEIVPVTISSRRGDV-VVSVDEGVRGDTTAESLGGLRPAFA 237

Query: 238 SDGSITAGNAPGVNDGAGAFVLMSEEKAAELGKRPLATILGFSTTGMPAHELAAAPGFAI 297
            DG+ITAG++  ++DGA A V+MS+ KA ELG   LA I        P   L   P  AI
Sbjct: 238 KDGTITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQPARAI 297

Query: 298 NKLLKKNGLTVQDIDLFEVNEAFASVVLTCEKIVGFDLEKVNVNGGAIALGHPIGASGAR 357
            K ++K G+ V DIDLFE+NEAFA+V +   + +G   +KVNVNGGAIA+GHP+G SGAR
Sbjct: 298 AKAVEKEGIAVSDIDLFELNEAFAAVGIESARELGVSEDKVNVNGGAIAIGHPVGMSGAR 357

Query: 358 ILMTLVYELKRRGGGLGVAAICSGAAQGDAVLVQV 392
           I++ L  ELKRRGGG+G AA+C G  QGDA++V+V
Sbjct: 358 IVLHLALELKRRGGGIGAAALCGGGGQGDALIVRV 392


Lambda     K      H
   0.317    0.134    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: 516
Number of extensions: 28
Number of successful extensions: 3
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: 393
Length of database: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
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