GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HPD in Pseudomonas fluorescens FW300-N1B4

Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; EC 1.13.11.27 (uncharacterized)
to candidate Pf1N1B4_2747 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

Query= curated2:Q9I576
         (357 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2747
           4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
          Length = 633

 Score =  180 bits (457), Expect = 8e-50
 Identities = 111/325 (34%), Positives = 163/325 (50%), 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-LSHWLERLGFVKAGQHRSKSVSLLRQGDINLILNSEPYSFAH 353

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

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

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

Query: 256 ATVRKLRDNGVKFMSTPDTYYEKVDTRVAGHGEPLEQLRELNLLIDGAPGDDGILLQIFT 315
           A V + ++ GV  +  P  YY+ +  R   + E L +L   N+L D      G L  ++T
Sbjct: 529 AEVSRAKEAGVPLLDIPLNYYDDLAARFDFNDEFLSELAYFNVLYD-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: 578
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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