GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Pedobacter sp. GW460-11-11-14-LB5

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate CA265_RS19580 CA265_RS19580 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= BRENDA::Q72GU1
         (367 letters)



>FitnessBrowser__Pedo557:CA265_RS19580
          Length = 331

 Score =  164 bits (415), Expect = 3e-45
 Identities = 100/314 (31%), Positives = 158/314 (50%), Gaps = 3/314 (0%)

Query: 42  YRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWVFPYYRDHGL 100
           +  ML  R  +E+   L    K   F     G EA       A++ G D +   YRDH  
Sbjct: 15  FESMLLMRKFEEKTGQLYGQQKIRGFCHLYIGQEAVVAGAISAMQKG-DSMITTYRDHAH 73

Query: 101 ALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAAGAAISM 160
           ALALG+    +  +M       +KG+    H  SK  NF+   + +   +P  AG A + 
Sbjct: 74  ALALGVSADSIMAEMYGKATGCSKGKGGSMHMFSKEHNFYGGHAIVGGQIPLGAGVAFAE 133

Query: 161 KLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRHQTHSPT 220
           K   T  V +C  GDGA  +G      N A +   P +FVCENN YA+    +  T+   
Sbjct: 134 KYKGTDNVNICYMGDGAVRQGALNETFNMAMLWKLPVIFVCENNGYAMGTSVQRTTNMTD 193

Query: 221 IADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHSSADDDS 280
           I      F +P   VDGMD +A +  + EA++RAR+GEGP+ +E+R YRY  HS + D +
Sbjct: 194 IYKIGLGFDMPCAPVDGMDPVAVHNAMDEAIQRARKGEGPTFLEMRTYRYRGHSMS-DPA 252

Query: 281 RYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKEAEEAGPVP 340
           +YR KEE+  ++ KDP+   R  +      ++ W E+V  +++A +++ +K AEE+    
Sbjct: 253 KYRTKEELEDYKAKDPVEHARETILKEKYADQAWIEEVEAKVKAIVDQAVKFAEESPWPD 312

Query: 341 PEWMFADVFAEKPW 354
              ++ DV+ ++ +
Sbjct: 313 ASELYKDVYMQQDY 326


Lambda     K      H
   0.320    0.138    0.426 

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: 329
Number of extensions: 15
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: 331
Length adjustment: 29
Effective length of query: 338
Effective length of database: 302
Effective search space:   102076
Effective search space used:   102076
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 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