GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; 2-hydroxymuconic semialdehyde hydrolase; EC 3.7.1.9 (characterized)
to candidate Pf1N1B4_4192 Hydrolase, alpha/beta fold family functionally coupled to Phosphoribulokinase

Query= SwissProt::P23106
         (281 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4192
          Length = 288

 Score = 74.3 bits (181), Expect = 3e-18
 Identities = 68/233 (29%), Positives = 108/233 (46%), Gaps = 18/233 (7%)

Query: 55  SQTRRVIAPDMLGFGYSERPADGKYSQARWVEHAIGVLDALGIQQGDIVGNSFGGGLALA 114
           ++ RRVI  D  G G S   A    +     + A+G++ ALG  + D++G S GG +A  
Sbjct: 65  AKNRRVITTDYRGIGGSGGAAP--LTVGEMADDAVGLIRALGFDKVDLLGFSLGGFVAQD 122

Query: 115 LAIRHPERVRRLVLMGSVGVSFPITAGLETAWGYTPSLANMRRLLDL-----FAHDRTLV 169
           +A++ PERVRRL+L G+         G+++    T  L  ++ LL L     +    T  
Sbjct: 123 IAMKAPERVRRLILTGTGPAG---GTGIDSVGSVTWPLM-IKGLLTLRDPKFYLFFTTTA 178

Query: 170 NDELAELRYQASIRPGFQESFAAMFPPPRQNGVDDLAS----NETDIRALPNETLVIHGR 225
           N + A   Y   ++   Q+      P      +  + +       ++  L   TL+ +G 
Sbjct: 179 NGQRAASEYLQRLKERQQDRDKGPTPRAFLRQLKAITAWGKQAPQELGRLRMPTLIANGD 238

Query: 226 EDRIIPLQASLTLAQWIPNAQLHVFGQCGHWTQIEHAERFARLVENFLAEADA 278
            D ++P   SL LA+ IPNAQL ++   GH +  +H   F   V N LA  DA
Sbjct: 239 NDIMVPTVNSLELAKRIPNAQLIIYQDAGHGSIFQHHTDF---VANALAFLDA 288


Lambda     K      H
   0.320    0.137    0.416 

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: 183
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 281
Length of database: 288
Length adjustment: 26
Effective length of query: 255
Effective length of database: 262
Effective search space:    66810
Effective search space used:    66810
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: 47 (22.7 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