GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Shewanella amazonensis SB2B

Align Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate 6938035 Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)

Query= curated2:P44873
         (393 letters)



>FitnessBrowser__SB2B:6938035
          Length = 436

 Score =  223 bits (567), Expect = 1e-62
 Identities = 143/424 (33%), Positives = 226/424 (53%), Gaps = 36/424 (8%)

Query: 2   ENVVIVSAVRTPIGSFNGALSSVSAVDLGAIVIQEAIKRANIESALVNEVIMGNVLQAGL 61
           E + IVS +RTP      A   VSA+D+G +V+ E + R+ ++  LV +++ G V+Q   
Sbjct: 13  ERIAIVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKLVEQLVYGQVVQMPA 72

Query: 62  GQNPARQAALKAGIEKEIPSLTINKVCGSGLKSVALGAQSIISGDADIVVVGGMENMSQA 121
             N AR+  L  G+     + ++ + C +  +S    A+SI++G+ +I + GG ++ S  
Sbjct: 73  APNIAREIVLGTGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSSVL 132

Query: 122 PYLLDSKVRQ-----------GVKMG---NLTLRDTM-IEDGLTCASNHYHMGITAENIA 166
           P  +  K+             G K+     L ++D + +   +   S    MG TAE +A
Sbjct: 133 PIGVSKKLAHALVDLTKARTFGQKLAIFRRLGIKDLLPVPPAVAEYSTGLSMGQTAEQMA 192

Query: 167 EQYGISRQAQDELALRSQTLASQAVQLGVFDKEIVPVMVKTRKGDIIVSRDEYPKADTTA 226
           + +GISR  QD +A RS TLA+Q    GV   E++   V     +  + +D   +  +  
Sbjct: 193 KTHGISRADQDAMAHRSHTLAAQTWASGVMKNEVMVAHVPPY--NQFIEKDNNIRESSDL 250

Query: 227 EGLAKLKPAF-KKEGTVTAGNASGINDGAAALILVSESKAHALGLKAIAKIRSYASGGVD 285
              AKL+P F +K G+VTA N++ + DGA+AL+L+SE +A ALG   I  I+SYA   +D
Sbjct: 251 ASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAID 310

Query: 286 P-SVMGLGPVPATQKALKKAGINLDDIDLIEANEAFASQFLGVGKDL------------- 331
               M +GP  AT  ALK+AG+ L+D+ LIE +EAFA+Q L   K               
Sbjct: 311 VWEDMLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQN 370

Query: 332 ----NLDMNKTNIHGGAIALGHPIGASGARILVTLLHNLIEKDKKLGLATLCIGGGQGIS 387
                +DM+K N+ GG++A GHP  A+GAR++  + + L  +   +GL T C  GG G +
Sbjct: 371 RAIGEIDMSKFNVLGGSLAYGHPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGAA 430

Query: 388 MIVE 391
           MI+E
Sbjct: 431 MILE 434


Lambda     K      H
   0.315    0.133    0.360 

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: 405
Number of extensions: 17
Number of successful extensions: 5
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: 436
Length adjustment: 31
Effective length of query: 362
Effective length of database: 405
Effective search space:   146610
Effective search space used:   146610
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: 42 (22.0 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