GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Cupriavidus basilensis 4G11

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate RR42_RS23050 RR42_RS23050 4-oxalomesaconate tautomerase

Query= SwissProt::Q88JY0
         (361 letters)



>FitnessBrowser__Cup4G11:RR42_RS23050
          Length = 359

 Score =  310 bits (795), Expect = 3e-89
 Identities = 171/356 (48%), Positives = 218/356 (61%), Gaps = 5/356 (1%)

Query: 6   IPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKVAII 65
           IPC+LMRGGTS+G  F  D LP     RD+VLL+ MGSP A Q+DG+GG  SLTSK AI+
Sbjct: 5   IPCVLMRGGTSRGPLFRADWLPDDPARRDQVLLSAMGSPHALQVDGLGGGSSLTSKAAIV 64

Query: 66  RASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVRIFM 125
             S+R   D+DYLFAQV VD+ RVD   NCGN+LA V PFA+E GLV A   +T +RIF 
Sbjct: 65  SCSRRPGCDIDYLFAQVAVDKHRVDTRPNCGNMLAAVAPFAIEEGLVRAGQCATTLRIFN 124

Query: 126 ENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNSRDC 185
            NT  +  A V T  GQV YAG TRIDGV G AA +++ F D  G   GA+ PTGN+ D 
Sbjct: 125 VNTSSVVEAVVQTPGGQVTYAGATRIDGVAGTAAPIMLNFLDAWGRVTGAMFPTGNTIDV 184

Query: 186 VEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMNLGDV 245
           ++ V VTCID  MP+V++ A  LGV G E    L+A+  +  RLE++R Q G RM LGDV
Sbjct: 185 IDAVPVTCIDAAMPLVVVHAASLGVRGDETPAALDANREMLARLESVRRQAGRRMGLGDV 244

Query: 246 SQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTS 305
           S   +PK  L+S       + +R F P RCH +  V GAV +A A    G+VA GLAST 
Sbjct: 245 SHSVIPKPVLVSGCGRANEITSRYFTPLRCHTAHAVTGAVGIAAAYCTPGTVANGLASTP 304

Query: 306 GGDRQRLAVEHPSGEFTVEISLEH----GVIKGCGLVRTARLLFDGVVCIGRDTWG 357
              + R+ V HP+G   V +  E        +  GLVRTAR +  G++ +  +  G
Sbjct: 305 -SPQGRIVVRHPAGSIEVHVEPERDGGPSPFRRIGLVRTARRIMKGLLSVPGEVMG 359


Lambda     K      H
   0.320    0.138    0.412 

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: 432
Number of extensions: 16
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: 361
Length of database: 359
Length adjustment: 29
Effective length of query: 332
Effective length of database: 330
Effective search space:   109560
Effective search space used:   109560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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