GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__ANA3:7022768 Shewana3_0023 3-ketoacyl-CoA
           thiolase (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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