GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Burkholderia phytofirmans PsJN

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate BPHYT_RS28250 BPHYT_RS28250 3-oxoacyl-ACP reductase

Query= SwissProt::Q1NEI6
         (249 letters)



>FitnessBrowser__BFirm:BPHYT_RS28250
          Length = 250

 Score =  245 bits (626), Expect = 5e-70
 Identities = 125/243 (51%), Positives = 168/243 (69%), Gaps = 3/243 (1%)

Query: 10  GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQ---AEIDATHVVALDVSD 66
           GR   +TGGA G+G  VA R +  G +VALWD++ + LA +Q   +E+     V ++++ 
Sbjct: 8   GRVVAITGGARGIGYAVAQRALNSGSSVALWDVDAERLARSQRELSELGKVTAVCVELTQ 67

Query: 67  HAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREV 126
            AAVA A   + A  G +D+LI  AGITG     WE   D ++RVID+NL G +   R V
Sbjct: 68  EAAVAQAVAQTVADHGAIDVLINCAGITGGNGTTWELEPDVWRRVIDVNLIGPYLTCRAV 127

Query: 127 VPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTP 186
           VP ML+ GYGRIVN+ASVAGKEGNPNAS YSASKAG+IG TKSLGKELA K ++ NA+TP
Sbjct: 128 VPQMLKQGYGRIVNIASVAGKEGNPNASHYSASKAGLIGLTKSLGKELATKNILVNAVTP 187

Query: 187 ATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGR 246
           A  ++ I D + Q  +DYM SKIPM R  + EE+A+++ +++SE+C+F+T S FD SGGR
Sbjct: 188 AAAKTEIFDSMSQQHIDYMLSKIPMNRFLMPEEAASLILWLSSEDCAFSTGSVFDLSGGR 247

Query: 247 TTF 249
            T+
Sbjct: 248 ATY 250


Lambda     K      H
   0.318    0.132    0.381 

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: 211
Number of extensions: 12
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: 249
Length of database: 250
Length adjustment: 24
Effective length of query: 225
Effective length of database: 226
Effective search space:    50850
Effective search space used:    50850
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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