GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Paraburkholderia phymatum STM815

Align 2-oxoisovalerate dehydrogenase subunit alpha; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_012403064.1 BPHY_RS18995 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha

Query= SwissProt::Q5SLR4
         (367 letters)



>NCBI__GCF_000020045.1:WP_012403064.1
          Length = 327

 Score =  159 bits (403), Expect = 8e-44
 Identities = 103/323 (31%), Positives = 164/323 (50%), Gaps = 4/323 (1%)

Query: 33  LEGEKLRRLYRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWV 91
           L  EKL   YR M   R  +ER  +   TG+   F+   AG EA+ V     +    D+V
Sbjct: 7   LSREKLLDAYRLMRTIREFEERLHVEFATGEIPGFVHLYAGEEASAVGTMLHLNDK-DYV 65

Query: 92  FPYYRDHGLALALGIPLKELLGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVP 151
              +R HG  +A G+ +  ++ ++   +    KG+    H    +         + +  P
Sbjct: 66  ATTHRGHGHCIAKGVDVHGMMAEIYGRQTGVCKGKGGSMHIADLSKGMLGANGIVGAGGP 125

Query: 152 PAAGAAISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFIAENNFYAISVD 211
              GAA++ KL +TG V VC FGDGA+++G  +  +N A+V   PA+F+AENN YA +  
Sbjct: 126 LVCGAALAAKLKKTGGVGVCFFGDGASNQGVIFESMNLASVWRLPAIFVAENNGYAEATS 185

Query: 212 YRHQTHSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYG 271
                 S  IAD+A  FG+PG +VDG D  A +  + EA+ERAR G GP+LVE+++ RY 
Sbjct: 186 STWSVSSDNIADRASGFGMPGVIVDGFDFFAVHEALGEAIERARGGGGPTLVEVKLSRYF 245

Query: 272 PHSSADDDSRYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLK 331
            H   D  +   P E      +KD + RF+  +    + N +    +  +++A ++  + 
Sbjct: 246 GHFEGDAQTYRAPGEVQKLREEKDCLKRFQERVVRAEMLNTDDLRKIDSDVKALIDDSVL 305

Query: 332 EAEEAGPVPPEW-MFEDVFAEKP 353
           +A +A P+P E  +  DV+   P
Sbjct: 306 KA-KAAPLPAEADLLTDVYVSYP 327


Lambda     K      H
   0.320    0.137    0.421 

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: 267
Number of extensions: 16
Number of successful extensions: 2
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: 367
Length of database: 327
Length adjustment: 29
Effective length of query: 338
Effective length of database: 298
Effective search space:   100724
Effective search space used:   100724
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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