GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Pseudomonas fluorescens FW300-N1B4

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate Pf1N1B4_4463 FIG00958979: hypothetical protein

Query= SwissProt::Q88JY0
         (361 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4463
          Length = 360

 Score =  323 bits (828), Expect = 4e-93
 Identities = 176/348 (50%), Positives = 225/348 (64%), Gaps = 3/348 (0%)

Query: 5   RIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKVAI 64
           RIPC+LMRGGTSKG  FL  DLP     RD +LLAVMGS    +IDGIGG    TSKVAI
Sbjct: 3   RIPCVLMRGGTSKGPVFLAWDLPVSIEERDELLLAVMGSGHELEIDGIGGGSPQTSKVAI 62

Query: 65  IRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVRIF 124
           +  S   DADVDYLF QV+V + RVD   NCGN+L  VGPFA+E+GLV A G  T VRI 
Sbjct: 63  VSPSLHPDADVDYLFVQVMVSQRRVDTAPNCGNMLCAVGPFAIEQGLVKAVGELTRVRIR 122

Query: 125 MENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNSRD 184
             NTG    + V T +G+V Y GDT IDGVPG AA + +TF D AG+  G L PTG+++D
Sbjct: 123 NLNTGTFVTSDVQTPNGKVSYEGDTAIDGVPGSAAPVQLTFLDAAGSKTGKLFPTGSTQD 182

Query: 185 CVEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMNLGD 244
             + + VTCID  MP++++ A  LG  G E    L+AD     RLEA+RL+ G  M LGD
Sbjct: 183 WFDDIPVTCIDMAMPMLIIEARHLGKRGDETPAELDADKDFMRRLEALRLRAGMAMGLGD 242

Query: 245 VSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGS-VAQGLAS 303
           VS + +PK  L++  + GGT+  R F+PH CH ++ + G++ +ATAC+ EGS VAQ L +
Sbjct: 243 VSDKVIPKPVLVAPAKAGGTLQVRYFMPHNCHRALAITGSIGLATACVSEGSVVAQMLGN 302

Query: 304 TSGGDRQRLAVEHPSGEFTVEISL--EHGVIKGCGLVRTARLLFDGVV 349
           T G   Q++ +EHPSG   V +S   ++G      +VRTAR LF G V
Sbjct: 303 TGGPRLQQVRIEHPSGGIDVVLSYTGKNGDTIRASVVRTARRLFSGFV 350


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: 443
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: 360
Length adjustment: 29
Effective length of query: 332
Effective length of database: 331
Effective search space:   109892
Effective search space used:   109892
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