GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Dyella japonica UNC79MFTsu3.2

Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate N515DRAFT_2292 N515DRAFT_2292 4-hydroxy-2-oxoheptanedioate aldolase

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2292
          Length = 242

 Score =  108 bits (269), Expect = 1e-28
 Identities = 78/236 (33%), Positives = 118/236 (50%), Gaps = 9/236 (3%)

Query: 21  IGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNE 80
           IG   ++ +P+  E+LG AG+D+++LD EH           + A +    AP VRVP  +
Sbjct: 5   IGLLQSVPSPLLCEMLGHAGYDFVLLDLEHVLLSPDQLQHAIRACELGGCAPWVRVPEVD 64

Query: 81  PVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANMFGTVA--DY 138
             +I R+LD G    +I  +ET E+AE AVA+ R+PP G RG++   R   FG  A  DY
Sbjct: 65  EKLIGRVLDAGARGVVISRLETVEQAERAVAAARFPPLGRRGIT-GGRVTGFGKTALPDY 123

Query: 139 FAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKA 198
             Q+N+ I ++  IES+ GV  +  I A  G+  +  G  DLA  LG      H DV + 
Sbjct: 124 IEQANREIHVVPMIESEAGVRALPQILAVPGISLVMEGALDLALDLGLGPQPLHADVWQR 183

Query: 199 IQHIFNRASAHGKPSGILAPVEADARRYLEWGA---TFVAVGSDLGVFRSATQKLA 251
           +Q I +     G P     P   + ++   W A    ++  G D G+  +A +  A
Sbjct: 184 LQDIADCCDTAGIP---FCPNPRNEQQLRYWAAREVRWMLAGEDRGLLLAALRDRA 236


Lambda     K      H
   0.318    0.134    0.392 

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: 137
Number of extensions: 8
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: 256
Length of database: 242
Length adjustment: 24
Effective length of query: 232
Effective length of database: 218
Effective search space:    50576
Effective search space used:    50576
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