GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Klebsiella michiganensis M5al

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 BWI76_RS23705 BWI76_RS23705 3-oxoacyl-ACP reductase

Query= SwissProt::Q1NEI6
         (249 letters)



>FitnessBrowser__Koxy:BWI76_RS23705
          Length = 244

 Score =  132 bits (333), Expect = 5e-36
 Identities = 85/242 (35%), Positives = 130/242 (53%), Gaps = 5/242 (2%)

Query: 7   RYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWD--LNGDALAATQAEIDATHV-VALD 63
           + A + AIVTG A G+G  +A  +  EG  V + D   +G+A AA+  E  A  + ++ +
Sbjct: 2   KLASKTAIVTGAARGIGFGIAQVLAREGARVIIADRDAHGEAAAASLRESGAQALFISCN 61

Query: 64  VSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCN 123
           + D A V A    +  A G VDI++ +AGI    + + +     +  VID+NL G F C 
Sbjct: 62  IGDKAQVEALFSQAEEAFGAVDIVVNNAGINRDAM-LHKLSEADWDTVIDVNLKGTFLCM 120

Query: 124 REVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANA 183
           ++    M E G GRI+N+AS A   GN   + YSASKAGV+G TK+  +ELA KGV  NA
Sbjct: 121 QQAAIRMRERGAGRIINIAS-ASWLGNVGQTNYSASKAGVVGMTKTACRELAKKGVTVNA 179

Query: 184 LTPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTS 243
           + P   ++ +   +P++    M +KIP G  G  ++    V F+AS+   +      +  
Sbjct: 180 ICPGFIDTDMTRGVPENVWQIMINKIPAGYAGEAKDVGECVAFLASDGARYINGEVINVG 239

Query: 244 GG 245
           GG
Sbjct: 240 GG 241


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: 152
Number of extensions: 10
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: 249
Length of database: 244
Length adjustment: 24
Effective length of query: 225
Effective length of database: 220
Effective search space:    49500
Effective search space used:    49500
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