GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Shewanella loihica PV-4

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate 5209189 Shew_1667 acetyl-CoA acetyltransferase (RefSeq)

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__PV4:5209189
          Length = 396

 Score =  269 bits (687), Expect = 1e-76
 Identities = 162/401 (40%), Positives = 236/401 (58%), Gaps = 15/401 (3%)

Query: 2   SREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQA 61
           ++E+ I  A RTP+G F GSL++V +  LAA  +K L++    V    ++EV +GC   A
Sbjct: 7   NQEIVIVAAKRTPMGGFQGSLSSVPSPTLAATAIKGLMDA-AGVQGGDVNEVLMGCVLPA 65

Query: 62  GEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESM 121
           G   +  AR A L A LP SV   T+N++C SGM  V  A   I +G A++VIAGG+ESM
Sbjct: 66  GL-GQAPARQATLGADLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSADVVIAGGMESM 124

Query: 122 SRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRAD 181
           S+APY++ KA      G       +   F++ L  A  G  AM   A   ADD+ ++R  
Sbjct: 125 SQAPYLLDKARGGMRMGH---GKVLDHMFLDGLEDAYTG-GAMGTFAQKTADDFGITREA 180

Query: 182 QDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADE---HLRPDTTLEALAKL 238
            D FAL S Q A  A  +G F  EIVPV +  +KG+ VVD DE   + RP    E +  L
Sbjct: 181 MDNFALSSLQKANAAIESGAFKAEIVPVTVASRKGDLVVDTDEQPGNARP----EKIPTL 236

Query: 239 KPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIG 298
           +P    D T+TA N+S ++DG+  L++ SA+   K GL+  A + G  +    P +    
Sbjct: 237 RPAFAKDGTITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSMFTTA 296

Query: 299 PVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHP 358
           PV A+ KLL+++N S  + D+ E+NEAFA   +    ELG+  D+A+VN NGGA ALGHP
Sbjct: 297 PVGAMNKLLDKVNWSKDEVDLFEINEAFAMVTMLAISELGL--DEAKVNVNGGACALGHP 354

Query: 359 LGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399
           +G SGAR+++T +H L+  G +RG+ ++C+G G+  A+A+E
Sbjct: 355 IGCSGARVLVTLIHALKARGLKRGVASLCIGGGEATAMAIE 395


Lambda     K      H
   0.317    0.134    0.379 

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: 398
Number of extensions: 23
Number of successful extensions: 4
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: 401
Length of database: 396
Length adjustment: 31
Effective length of query: 370
Effective length of database: 365
Effective search space:   135050
Effective search space used:   135050
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 (21.6 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