GapMind for catabolism of small carbon sources

 

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

Align Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate 7024268 Shewana3_1460 3-ketoacyl-CoA thiolase (RefSeq)

Query= curated2:P44873
         (393 letters)



>FitnessBrowser__ANA3:7024268
          Length = 436

 Score =  224 bits (572), Expect = 3e-63
 Identities = 146/424 (34%), Positives = 229/424 (54%), Gaps = 36/424 (8%)

Query: 2   ENVVIVSAVRTPIGSFNGALSSVSAVDLGAIVIQEAIKRANIESALVNEVIMGNVLQAGL 61
           E + IV+ +RTP      A   VSA+D+G +V+ E + R+ ++  L+ +++ G V+Q   
Sbjct: 13  ERIAIVAGLRTPFAKQATAFHGVSALDMGKMVVNELLARSELDPKLIEQLVYGQVVQMPA 72

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

Query: 122 PYLLDSKVRQ-----------GVKM---GNLTLRDTM-IEDGLTCASNHYHMGITAENIA 166
           P  +  K+             G K+     L ++D + +   +   S    MG TAE +A
Sbjct: 133 PIGVSKKLAHALVDLNKARSFGQKLQIFRRLGIKDLLPVPPAVAEYSTGLSMGQTAEQMA 192

Query: 167 EQYGISRQAQDELALRSQTLASQAVQLGVFDKEIVPVMVKTRKGDIIVSRDEYPKADTTA 226
           + Y ISR  QD LA RS TLAS+    G    E++   V   K    + RD   + ++  
Sbjct: 193 KTYNISRADQDALAHRSHTLASETWASGHLRDEVMVAHVPPYKQ--FIERDNNIRENSDL 250

Query: 227 EGLAKLKPAF-KKEGTVTAGNASGINDGAAALILVSESKAHALGLKAIAKIRSYASGGVD 285
              AKL+PAF KK G+VTA N++ + DGA+A+IL+SE +A ALG + I  I+SYA   +D
Sbjct: 251 SSYAKLRPAFDKKHGSVTAANSTPLTDGASAIILMSEGRAKALGYQPIGYIKSYAFTAID 310

Query: 286 P-SVMGLGPVPATQKALKKAGINLDDIDLIEANEAFASQFLG--------------VGKD 330
               M +GP  AT  ALK+AG+ L+D+ LIE +EAFA+Q L               +G++
Sbjct: 311 VWQDMLMGPSYATPLALKRAGMELEDLTLIEMHEAFAAQTLANMQMFASKKFAEEKLGRN 370

Query: 331 L---NLDMNKTNIHGGAIALGHPIGASGARILVTLLHNLIEKDKKLGLATLCIGGGQGIS 387
                +DM+K N+ GG++A GHP  A+G R++  +   L  +    GLAT C  GG G +
Sbjct: 371 RAIGEIDMSKFNVLGGSLAYGHPFAATGTRLITQVCRELKRRGGGTGLATACAAGGLGAA 430

Query: 388 MIVE 391
           MIVE
Sbjct: 431 MIVE 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: 414
Number of extensions: 15
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: 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