GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Mesorhizobium ciceri WSM1271

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase

Query= SwissProt::P50174
         (393 letters)



>NCBI__GCF_000185905.1:YP_004140539.1
          Length = 392

 Score =  636 bits (1641), Expect = 0.0
 Identities = 315/389 (80%), Positives = 350/389 (89%)

Query: 5   SIVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEG 64
           SIVIASAART VGSFNGAF  T AHELGA  I+ +L RAGVE GEVDEVILGQVL A +G
Sbjct: 4   SIVIASAARTPVGSFNGAFAATPAHELGAVVIRELLSRAGVEPGEVDEVILGQVLTAAQG 63

Query: 65  QNPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAP 124
           QNPARQA++ AGLP+E TAWG+NQ+CGSGLRA+ALGMQQIA GDA+VI+AGG ESMS++ 
Sbjct: 64  QNPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQESMSLST 123

Query: 125 HCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQ 184
           H  HLR GVKMGD+K+IDTMIKDGL DAF GYHMG TAENVAR++Q+TRE+QD+FALASQ
Sbjct: 124 HAQHLRAGVKMGDFKLIDTMIKDGLWDAFNGYHMGNTAENVARQFQITREDQDQFALASQ 183

Query: 185 NKAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTA 244
           NKAEAAQKAG+F DEIV   +K +KGD  VDQDEYIRHGAT+D++ KL+PAFDK+GTVTA
Sbjct: 184 NKAEAAQKAGKFKDEIVAVTIKGKKGDTIVDQDEYIRHGATIDAMTKLKPAFDKDGTVTA 243

Query: 245 GNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 304
            NASG+NDGAA ALLM+EAEA RRGI PLARIVSWATAGVDPQIMGTGPIPASRKALEKA
Sbjct: 244 ANASGINDGAAGALLMSEAEAVRRGITPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 303

Query: 305 GWSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 364
           GWSV D++LVEANEAFAAQACAVNKD+GWDPSIVNVNGGAIAIGHPIGASGARV NTL+F
Sbjct: 304 GWSVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVFNTLVF 363

Query: 365 EMKRRGVSKGLATLCIGGGMGVAMCVERL 393
           EM+RRG  KGLATLCIGGGMGVAMCVE L
Sbjct: 364 EMRRRGAKKGLATLCIGGGMGVAMCVEAL 392


Lambda     K      H
   0.317    0.132    0.381 

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: 526
Number of extensions: 12
Number of successful extensions: 1
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: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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