GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kce in Dinoroseobacter shibae DFL-12

Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate 3610094 Dshi_3475 protein of unknown function DUF849 (RefSeq)

Query= BRENDA::Q8RHX2
         (272 letters)



>FitnessBrowser__Dino:3610094
          Length = 279

 Score =  169 bits (429), Expect = 5e-47
 Identities = 104/271 (38%), Positives = 140/271 (51%), Gaps = 7/271 (2%)

Query: 6   IITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVREDDGTPTQDKERFR 65
           II  AI G+  TK  NPAVP TV E       A++AGASI H HVR DD TP+ D E+F 
Sbjct: 7   IICVAITGSVATKSANPAVPITVAEQVESTHEAFEAGASICHAHVRNDDETPSSDPEKFA 66

Query: 66  KCIEAIREKCPDVIIQPSTGGAVGMTDLERLQPTELHPEMATLDCGTCNFGGDEIFVNTE 125
           +  E +++ CP +IIQ STGG  G    ER     L P+MA+L  G+ NF    ++ N  
Sbjct: 67  RLQEGLQKHCPGMIIQFSTGGRSG-AGRERGGMLPLRPDMASLTVGSNNF-PTRVYENPP 124

Query: 126 NTIKNFGKILIERGVKPEIEVFDKGMIDYAIRYQKQGFIQKPMHFDFVLGVQMSASARDL 185
           + +      +    V PEIE FD   I +A    + G +    +  FV+GV+ +      
Sbjct: 125 DLVDWLASEMRAHEVIPEIEAFDLSHIHHAALMHRDGRLATRPYIQFVMGVKNAMPVDRE 184

Query: 186 VF-----MSESIPEGSTWTVAGVGRHQFQMAALAIVMGGHVRVGFEDNVYIDKGILAKSN 240
            F       E +  G+ W  A +G  Q  M    +  GGH R G EDNV +D+  LA SN
Sbjct: 185 TFDFYRATVERLLPGAEWCGAAIGASQIVMNEWCVAEGGHARTGLEDNVRLDRETLAPSN 244

Query: 241 GELVERVVRLAKELGREIATPDEARQILSLK 271
             LV RVV L  +  R +A P +AR+IL L+
Sbjct: 245 AALVRRVVELCNQYERPVADPAQAREILGLR 275


Lambda     K      H
   0.319    0.137    0.394 

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: 200
Number of extensions: 11
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: 272
Length of database: 279
Length adjustment: 25
Effective length of query: 247
Effective length of database: 254
Effective search space:    62738
Effective search space used:    62738
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: 47 (22.7 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