GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Burkholderia phytofirmans PsJN

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate BPHYT_RS06760 BPHYT_RS06760 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q0AVM2
         (279 letters)



>FitnessBrowser__BFirm:BPHYT_RS06760
          Length = 521

 Score =  216 bits (551), Expect = 6e-61
 Identities = 112/278 (40%), Positives = 166/278 (59%), Gaps = 1/278 (0%)

Query: 3   IMVLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDKA 62
           I ++G G MG GI Q AA AG  V + D     +      + +  +K   KG++      
Sbjct: 11  IGIVGTGAMGRGIAQIAALAGLTVRLYDTNPAAIGAARDYLAETFAKLTAKGKLDQARSL 70

Query: 63  AVMGRISGTVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSVTE 122
           A +  +SG   +G  A CDLV+EA +E +D+K+A+F+EL+++    C+LASNTS+LS+T 
Sbjct: 71  AALANVSGAQSIGELAGCDLVVEAIVEKLDVKQALFRELETVVSGRCVLASNTSSLSITA 130

Query: 123 IAAATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEAP 182
           IAA      +V+G HFFNPVP MK+VEVI G  +  A  DA+ +L+ +MG +PV   + P
Sbjct: 131 IAAGCSDPSRVVGYHFFNPVPLMKVVEVIDGLRSDPAAGDALMNLARRMGHTPVRAKDMP 190

Query: 183 GFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIME 242
           GF+VN     M  EG+    EGVA+ ADID  ++  AG  +GP  L D+  LD+   +ME
Sbjct: 191 GFIVNHAGRGMNTEGLRVAGEGVASFADIDRIVREQAGFRLGPFELLDLTALDVSHPVME 250

Query: 243 TLYKEF-GDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279
           ++Y +F  +P++ P P+    +    +GRKTGEGF+ Y
Sbjct: 251 SIYHQFYEEPRFTPSPITGTRLAGGLIGRKTGEGFYRY 288



 Score = 72.4 bits (176), Expect = 2e-17
 Identities = 38/132 (28%), Positives = 65/132 (49%)

Query: 130 ADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEAPGFVVNRL 189
           A +V+ +    P+   +   ++   +T++   D    L    G     I ++ GFV  R+
Sbjct: 365 ATRVVAIDALFPLVGAQRRTLMTTPATTRTARDTAHALFAADGVPVTVIRDSTGFVAQRV 424

Query: 190 LIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIMETLYKEFG 249
           +  ++N G     + +A   DID ++  G G+P GPL L D +G    L I+  ++   G
Sbjct: 425 VATIVNIGCDIAQKQIATPQDIDLAVTLGLGYPRGPLGLGDALGSTTILTILRNMFSVLG 484

Query: 250 DPKYRPCPLLAK 261
           DP+YRP P LA+
Sbjct: 485 DPRYRPSPWLAR 496


Lambda     K      H
   0.321    0.137    0.389 

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: 376
Number of extensions: 20
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 279
Length of database: 521
Length adjustment: 30
Effective length of query: 249
Effective length of database: 491
Effective search space:   122259
Effective search space used:   122259
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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