GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HPD in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; Legiolysin; EC 1.13.11.27 (characterized)
to candidate H281DRAFT_03214 H281DRAFT_03214 4-hydroxyphenylpyruvate dioxygenase

Query= SwissProt::P69053
         (348 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03214 H281DRAFT_03214
           4-hydroxyphenylpyruvate dioxygenase
          Length = 627

 Score =  162 bits (409), Expect = 3e-44
 Identities = 105/324 (32%), Positives = 154/324 (47%), Gaps = 10/324 (3%)

Query: 11  GFAFLEFSGPDRNKLH--QQFSEMGFQAVAHHKNQDITLFKQGEIQFIVNAASHCQAEAH 68
           G+ FLEF+  D  + H      ++ F+    H+++D+TL++ G    ++NA     A A 
Sbjct: 293 GYQFLEFAVDDTTRAHLADWLGKLRFRQAGQHRSKDVTLYQHGAASIVLNAEPDSFANAF 352

Query: 69  ASTHGPGACAMGFKVKDAKAAFQHAIAHGGIAFQDAPHANHG-LPAIQAIGGSVIYFVDE 127
              HG   CA  F+V DA  AF+ A   G   F      N   LPA+QA  GS+ YFVDE
Sbjct: 353 FQQHGLSLCASAFRVNDANQAFERAAGFGYAPFSGQIGPNERVLPAVQAPDGSLNYFVDE 412

Query: 128 E-HQPFSHEWNITSSE---PVVGNGLTAIDHLTHNVYRGNMDKWASFYASIFNFQEIRFF 183
              QP   E +   ++   P     LT IDH+   V   ++D W  F  + F FQ     
Sbjct: 413 TPDQPTLFEADFVLTDVNGPFEVGPLTRIDHVCLAVPANSLDTWVLFLRTAFGFQAEPGV 472

Query: 184 NIKGKMTGLVSRALGSPCGKIKIPLNESKDDLSQIEEFLHEYHGEGIQHIALNTNDIYKT 243
            +      + SRAL S  G +++ LN S D  + + E LH YHG G+ H+A +T+DI+  
Sbjct: 473 LVPDPYGLVRSRALRSRDGSVRVVLNASVDHHTAVAEALHTYHGSGLNHVAFSTSDIFSA 532

Query: 244 VNGLRKQGVKFLDVPDTYYEMINDRLPWHKEPLNQLHAEKILIDGEADPKDGLLLQIFTE 303
           +      G+  L +P  YYE +  R     + L  L    IL D   D + G     +TE
Sbjct: 533 IPEFVADGLPVLRIPRNYYEDLAARYELPDDMLEALREHNILYD--RDERGGEFFHAYTE 590

Query: 304 NIFGPVFFEIIQRKGN-QGFGEGN 326
            +    F EI++R+G   G+G  N
Sbjct: 591 QLDQRFFMEIVERRGGYDGYGASN 614


Lambda     K      H
   0.320    0.138    0.421 

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: 583
Number of extensions: 35
Number of successful extensions: 6
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: 348
Length of database: 627
Length adjustment: 33
Effective length of query: 315
Effective length of database: 594
Effective search space:   187110
Effective search space used:   187110
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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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