GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Klebsiella michiganensis M5al

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate BWI76_RS23705 BWI76_RS23705 3-oxoacyl-ACP reductase

Query= uniprot:Q8EGC1
         (252 letters)



>FitnessBrowser__Koxy:BWI76_RS23705
          Length = 244

 Score =  154 bits (390), Expect = 1e-42
 Identities = 94/254 (37%), Positives = 140/254 (55%), Gaps = 12/254 (4%)

Query: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL 60
           M L  K  ++TG A G+G  +A   A+ GA++ + D D      A +   S  +    + 
Sbjct: 1   MKLASKTAIVTGAARGIGFGIAQVLAREGARVIIADRDAHGEAAAASLRESGAQALFISC 60

Query: 61  DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120
           +I D+  V A F+   E FG ++++VNNAGI RD ML K  +           + +VI+V
Sbjct: 61  NIGDKAQVEALFSQAEEAFGAVDIVVNNAGINRDAMLHKLSEA---------DWDTVIDV 111

Query: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKEL 180
           NL GTFLC ++AA  M E G AG I+NI+S +  GNVGQ+NY+ASKAGV  M+    +EL
Sbjct: 112 NLKGTFLCMQQAAIRMRERG-AGRIINIASASWLGNVGQTNYSASKAGVVGMTKTACREL 170

Query: 181 ARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND--Y 238
           A+  +   A+ PG I T+MT  +     + +   +P G  G A+++   V F+  +   Y
Sbjct: 171 AKKGVTVNAICPGFIDTDMTRGVPENVWQIMINKIPAGYAGEAKDVGECVAFLASDGARY 230

Query: 239 VNGRVFEVDGGIRL 252
           +NG V  V GG+ L
Sbjct: 231 INGEVINVGGGMVL 244


Lambda     K      H
   0.317    0.134    0.369 

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: 175
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: 252
Length of database: 244
Length adjustment: 24
Effective length of query: 228
Effective length of database: 220
Effective search space:    50160
Effective search space used:    50160
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