GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Pseudomonas fluorescens GW456-L13

Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; EC 1.13.11.27 (uncharacterized)
to candidate PfGW456L13_1425 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

Query= curated2:Q9I576
         (357 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1425
          Length = 633

 Score =  174 bits (442), Expect = 4e-48
 Identities = 109/325 (33%), Positives = 161/325 (49%), Gaps = 8/325 (2%)

Query: 16  DGFEFVEFTAPDAKGIEQLRQLFNMMGFTETAKHRSKEVFLFQQNDINIVLNGSPTGHVH 75
           +G EF+EF   ++ G + L      +GF +  +HRSK V L +Q DIN++LN  P    H
Sbjct: 295 NGIEFLEFAVDESLGAK-LSHWLERLGFVKAGQHRSKSVSLMRQGDINLILNSEPYSFGH 353

Query: 76  EFALKHGPSACAMAFRVKNASQAAAYAESQGAKLVGSHANFGELNIPSLEGIGGSLLYLV 135
            F   HGPS CA A RVK+++ A A A +   +         EL + ++    GSL+YLV
Sbjct: 354 SFFEAHGPSLCATAVRVKDSASALARAVAYKGQPYRGLVGPNELELAAVRAPDGSLIYLV 413

Query: 136 DRYGDRSIYDVDFEFIEGRSANDNSVGLTYIDHLTHNVKRGQMDVWSGFYERIANFREIR 195
           D+  D  +Y  DF  +        S GL  IDH+   +    +D W  FY+ + +F    
Sbjct: 414 DQ--DADVYGTDFNLLADAPV---SGGLKRIDHMAMALPADSLDSWVLFYKSLLDFEADD 468

Query: 196 YFDIEGKLTGLFSRAMTAPCGKIRIPINESADDTSQIEEFIREYHGEGIQHIALTTDDIY 255
              +      + SRA+ +    IR+P+N S +  + I   +  Y G G+ HIA   DDI+
Sbjct: 469 EVVLPDPYGLVKSRALRSRDSSIRLPLNISENRNTAISHALSSYRGSGVHHIAFDCDDIF 528

Query: 256 ATVRKLRDNGVKFMSTPDTYYEKVDTRVAGHGEPLEQLRELNLLIDGAPGDDGILLQIFT 315
           A V + ++ GV  +  P  YY+ +  R     E L +L   N+L D      G L  ++T
Sbjct: 529 AQVSRAKEAGVPLLDIPLNYYDDLAARFDFDDEFLSELAYYNVLYD-RDAQGGELFHVYT 587

Query: 316 DTVIGPIFFEIIQRK-GNQGFGEGN 339
           +   G  FFEIIQRK G  G+G  N
Sbjct: 588 EPFEGRFFFEIIQRKNGYAGYGAAN 612


Lambda     K      H
   0.320    0.139    0.406 

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: 572
Number of extensions: 32
Number of successful extensions: 5
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: 357
Length of database: 633
Length adjustment: 33
Effective length of query: 324
Effective length of database: 600
Effective search space:   194400
Effective search space used:   194400
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: 51 (24.3 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