Aligments for a candidate for atoB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Aligments for a candidate for atoB in Shewanella loihica PV-4

Align acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized)
to candidate 5207484 Shew_0018 3-ketoacyl-CoA thiolase (RefSeq)

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



>lcl|FitnessBrowser__PV4:5207484 Shew_0018 3-ketoacyl-CoA thiolase
           (RefSeq)
          Length = 387

 Score =  287 bits (734), Expect = 4e-82
 Identities = 180/400 (45%), Positives = 239/400 (59%), Gaps = 22/400 (5%)

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

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

Query: 118 MSLAPYLLDAKARSGYRLGDGQVYDVILRDGLMCATHGYHMGITAENVAKEYGITREMQD 177
           M   P         G     G   +V    G+M        G+TAE + K +GITR+ QD
Sbjct: 121 MGHVPM------NHGVDFHPGLATNVAKASGMM--------GLTAEMLGKMHGITRQQQD 166

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

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

Query: 296 ATQKALQLAGLQLADIDLIEANEAFAAQFLAVGKNLG---FDSEKVNVNGGAIALGHPIG 352
           ATQKALQ AGL + DIDLIE NEAFAAQ L   K+LG      EKVN+NGGAIALGHP+G
Sbjct: 287 ATQKALQRAGLTMNDIDLIELNEAFAAQSLPCVKDLGLMDLVDEKVNLNGGAIALGHPLG 346

Query: 353 ASGARILVTLLHAMQARDKTLGLATLCIGGGQGIAMVIER 392
            SGARI  TL++ M+++D TLGLAT+CIG GQGIA V ER
Sbjct: 347 CSGARISTTLINLMESKDATLGLATMCIGLGQGIATVFER 386


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: 374
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the preprint on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources