GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Shewanella sp. ANA-3

Align acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized)
to candidate 7022768 Shewana3_0023 3-ketoacyl-CoA thiolase (RefSeq)

Query= ecocyc::ACETYL-COA-ACETYLTRANSFER-MONOMER
         (394 letters)



>FitnessBrowser__ANA3:7022768
          Length = 387

 Score =  281 bits (718), Expect = 3e-80
 Identities = 176/401 (43%), Positives = 239/401 (59%), Gaps = 22/401 (5%)

Query: 1   MKNCVIVSAVRTAIG-SFNGSLASTSAIDLGATVIKAAIER-AKIDSQHVDEVIMGNVLQ 58
           MK  VIV  +RT +G S  G   +  A  L A ++K  + R  ++D   +++VI G V Q
Sbjct: 1   MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60

Query: 59  A-GLGQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMEN 117
               G N AR A L +G+ +T    TVN++CGS ++++  AA+AI  G   + + GG+E+
Sbjct: 61  TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120

Query: 118 MSLAPYLLDAKARSGYRLGDGQVYDVILRDGLMCATHGYHMGITAENVAKEYGITREMQD 177
           M   P         G     G   +V    G+M        G+TAE + K +GITRE QD
Sbjct: 121 MGHVPM------NHGVDFHPGLANNVAKASGMM--------GLTAEMLGKLHGITREQQD 166

Query: 178 ELALHSQRKAAAAIESGAFTAEIVPVNVVTRKKTFV-FSQDEFPKANSTAEALGALRPAF 236
             A+ S ++A AA   G F  EI  +         +    DE  +  ++ E+L ALRP F
Sbjct: 167 AFAVRSHQRAHAATVEGRFAKEIYGIEGHDANGALIKVLHDEVIRPETSMESLAALRPVF 226

Query: 237 DKA-GTVTAGNASGINDGAAALVIMEESAALAAGLTPLARIKSYASGGVPPALMGMGPVP 295
           D A GTVTAG +S ++DGA+A+++MEES A A GL   ARI+S A  G   A+MG GPVP
Sbjct: 227 DPANGTVTAGTSSALSDGASAMLVMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVP 286

Query: 296 ATQKALQLAGLQLADIDLIEANEAFAAQFLAVGKNLGF---DSEKVNVNGGAIALGHPIG 352
           ATQKAL  AG+ + D+D+IE NEAFAAQ L   K+LG      +K+N+NGGAIALGHP+G
Sbjct: 287 ATQKALARAGITVNDLDVIELNEAFAAQSLPCVKDLGLLDVVEDKINLNGGAIALGHPLG 346

Query: 353 ASGARILVTLLHAMQARDKTLGLATLCIGGGQGIAMVIERL 393
            SGARI  TL++ M+ +D TLGLAT+CIG GQGIA V ER+
Sbjct: 347 CSGARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.317    0.132    0.364 

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: 365
Number of extensions: 16
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: 394
Length of database: 387
Length adjustment: 31
Effective length of query: 363
Effective length of database: 356
Effective search space:   129228
Effective search space used:   129228
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