GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Shewanella oneidensis MR-1

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 201911 SO2776 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)

Query= SwissProt::Q1NEI6
         (249 letters)



>FitnessBrowser__MR1:201911
          Length = 248

 Score =  146 bits (369), Expect = 3e-40
 Identities = 85/239 (35%), Positives = 134/239 (56%), Gaps = 4/239 (1%)

Query: 9   AGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEI--DATHVVALDVSD 66
           AG+ A+VTG + G+G+ +A  ++ E GAV +     +  AA   E   D    + L+V+D
Sbjct: 8   AGKVALVTGASRGIGRAIAETLV-EAGAVVIGTATSEKGAAAIQEYLGDKGFGLVLNVTD 66

Query: 67  HAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREV 126
             +V           G VDIL+ +AGIT   + +     D +  +ID NL  LF  ++ V
Sbjct: 67  SQSVTDLFDSIKEKAGDVDILVNNAGITRDNL-LMRMKDDEWNDIIDTNLTSLFRLSKPV 125

Query: 127 VPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTP 186
           +  M++  +GRI+N+ SV G  GN     YSA+KAG+IGFTKSL +E+A + +  NA+ P
Sbjct: 126 MRTMMKKRFGRIINIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLAREVASRQITVNAIAP 185

Query: 187 ATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245
              ++ + D+L + Q   + S++PM RLG  +E A  V F+AS+  ++ T  T   +GG
Sbjct: 186 GFIQTDMTDELTEDQQKAIMSQVPMERLGQAQEIANAVLFLASDSAAYITGETLHVNGG 244


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: 148
Number of extensions: 7
Number of successful extensions: 3
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: 248
Length adjustment: 24
Effective length of query: 225
Effective length of database: 224
Effective search space:    50400
Effective search space used:    50400
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