GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Klebsiella michiganensis M5al

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate BWI76_RS04370 BWI76_RS04370 FldA family protein

Query= SwissProt::Q88JY0
         (361 letters)



>FitnessBrowser__Koxy:BWI76_RS04370
          Length = 351

 Score =  320 bits (819), Expect = 5e-92
 Identities = 173/348 (49%), Positives = 220/348 (63%), Gaps = 4/348 (1%)

Query: 6   IPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKVAII 65
           IPC+LMRGGTSKGA+ L DDLP     RD  LLA+MGS    +IDGIGG    TSKVAII
Sbjct: 4   IPCVLMRGGTSKGAFLLADDLPKDIQKRDDCLLAIMGSGHELEIDGIGGGSPQTSKVAII 63

Query: 66  RASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVRIFM 125
             S  ++AD+DYLF QV+V+E RVD   NCGN+L  VG FA+E GLV A+   T VRI  
Sbjct: 64  SQSLSEEADIDYLFVQVIVNERRVDTTPNCGNMLCAVGGFAIEHGLVEAASPVTRVRIRN 123

Query: 126 ENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNSRDC 185
            NT     A V T DG+V Y GD++IDGVPGRAA + +TF + AGA  G L PTGN  D 
Sbjct: 124 VNTNTFIDADVQTPDGKVIYEGDSQIDGVPGRAAPVALTFLNAAGAKSGRLFPTGNRMDV 183

Query: 186 VEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMNLGDV 245
            + V VTCID  MP+V++ A+ LG TGYE    L+ DS L   LE+IR+Q G  M  GDV
Sbjct: 184 FDDVRVTCIDMAMPMVVIPAQSLGKTGYESASELDRDSGLLKSLESIRIQAGKAMGFGDV 243

Query: 246 SQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTS 305
           +   +PK  L+S   +GG++N R F+PH CH S+ + GA+ +A+AC+I  ++A  L   S
Sbjct: 244 TNMVIPKPVLISPALSGGSINVRYFMPHNCHKSLAITGAIGLASACIIPKTIANELTKLS 303

Query: 306 GGDRQRLAVEHPSGEFTVEIS--LEHGVIKGCGLVRTARLLFDGVVCI 351
           G     + VEHPSG   V++S   E        ++RTAR +  G V I
Sbjct: 304 GDG--IIKVEHPSGGIEVDLSQTTERPEDIRASVIRTARKILSGTVYI 349


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: 401
Number of extensions: 13
Number of successful extensions: 2
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: 351
Length adjustment: 29
Effective length of query: 332
Effective length of database: 322
Effective search space:   106904
Effective search space used:   106904
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