GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Shewanella loihica PV-4

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 5211109 Shew_3525 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= SwissProt::Q1NEI6
         (249 letters)



>FitnessBrowser__PV4:5211109
          Length = 241

 Score =  116 bits (290), Expect = 5e-31
 Identities = 78/241 (32%), Positives = 123/241 (51%), Gaps = 16/241 (6%)

Query: 14  IVTGGASGLGKQVAARIIAEGGAVAL-WDLNGDALAATQAEIDATHV----VALDVSDHA 68
           ++TG + G+GK +A ++   G  +AL +  N  A  ATQ E++A       +  DV+D A
Sbjct: 6   LITGASRGIGKAIALKLAETGYDIALHFHSNQAAADATQTELEALGAKVSRLQFDVADRA 65

Query: 69  AVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPV---DSFQRVIDINLNGLFYCNRE 125
            V AA +      G    ++ +AGIT  T     FP    + +  VI  NL+G +     
Sbjct: 66  GVKAAIEADIYQHGAYYGVVLNAGITRDTA----FPAMSDEEWDGVIHTNLDGFYNVIHP 121

Query: 126 -VVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANAL 184
             +P +     GRI+ +ASV+G  GN     YSASKAG+IG TK+L  ELA + +  N +
Sbjct: 122 CTMPMIQSRQGGRIITMASVSGIAGNRGQVNYSASKAGIIGATKALSLELAKRKITVNCI 181

Query: 185 TPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSG 244
            P   E+ +++  PQ  V   +  +PM R+G   E A +  F+ S++ ++ T      +G
Sbjct: 182 APGLIETDMVESFPQEMV---KELVPMRRMGKASEIAGLANFLMSDDAAYITRQVISVNG 238

Query: 245 G 245
           G
Sbjct: 239 G 239


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: 144
Number of extensions: 6
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: 241
Length adjustment: 24
Effective length of query: 225
Effective length of database: 217
Effective search space:    48825
Effective search space used:    48825
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.

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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