GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Cupriavidus basilensis 4G11

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate RR42_RS32485 RR42_RS32485 3-keto-5-aminohexanoate cleavage protein

Query= reanno::acidovorax_3H11:Ac3H11_1849
         (381 letters)



>FitnessBrowser__Cup4G11:RR42_RS32485
          Length = 627

 Score =  150 bits (378), Expect = 1e-40
 Identities = 113/331 (34%), Positives = 157/331 (47%), Gaps = 15/331 (4%)

Query: 35  GFEFVEFTSPQPGVLE--AVFEKLGFTLVAKHRSKDVVLYRQNGINFILNREPHSQAAYF 92
           G +F+EF        E  A    LGF    +HRSK V LYRQ G+N ILN E  S AA  
Sbjct: 288 GVDFLEFAVDYVTGRELGARLRSLGFGHAGRHRSKAVELYRQGGVNIILNAEQDSAAAEH 347

Query: 93  GAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTGPMELRLPAIKGIGGAPLYLIDR 152
              HGPS C L  +V DA +A  RA  L  +      GP E  +PA++   G   YLID 
Sbjct: 348 FQLHGPSVCALGLKVDDAQRAVTRARALLCKEWRERIGPHERSIPALRAPDGMLFYLIDE 407

Query: 153 FEDGKSIYDIDFEFIEGVDRRPAGHGLNLIDHLTHNVYRGRMGFWANFYEKLFGFREIRY 212
               +SIY+ DF  +E      AG GL  IDH+   +   R+  +  FY+ +FG +    
Sbjct: 408 QGSDRSIYESDF-VLEPGGADSAGAGLMAIDHIAQALPPHRLDSFVLFYKTVFGLQAQAL 466

Query: 213 FDIQGEYTGLTSKAMTAPDGKIRIPLN--EESKQGGGQIEEFLMQFNGEGIQHIALICDN 270
            +I   Y  + S+AM + +  +RIPLN  E S+   G+   F+  + G GI HIA    +
Sbjct: 467 HEIADPYGLVKSRAMVSAEQSLRIPLNVSESSRTATGR---FITAYAGSGIHHIAFRTPD 523

Query: 271 LLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPELQSRGILLDGTTADGTPRLL 330
           L   +D+   A   +   P+  YY+ +  RL      +  L+   +L D   A G     
Sbjct: 524 LCATLDQAVPAEAAMLHVPDN-YYDDVGARLGLDDAALEHLRQHQLLYD-RDAGGE---F 578

Query: 331 LQIFSTPMLGPVFFEFIQREGDYRDGFGEGN 361
           L  ++ P     FFE +QR+G    GFG  N
Sbjct: 579 LHAYTEPFHDRFFFELVQRDGYL--GFGAAN 607


Lambda     K      H
   0.322    0.142    0.431 

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: 625
Number of extensions: 37
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 381
Length of database: 627
Length adjustment: 34
Effective length of query: 347
Effective length of database: 593
Effective search space:   205771
Effective search space used:   205771
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 (21.9 bits)
S2: 52 (24.6 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