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_RS32440 RR42_RS32440 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::pseudo5_N2C3_1:AO356_22845
         (358 letters)



>FitnessBrowser__Cup4G11:RR42_RS32440
          Length = 346

 Score =  256 bits (654), Expect = 6e-73
 Identities = 147/345 (42%), Positives = 203/345 (58%), Gaps = 17/345 (4%)

Query: 12  MGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHSVASYFA 71
           MG+EF+EFASP P  L   FE  GF  +A HR K+V L+RQG +N I++ EP S A+ +A
Sbjct: 1   MGYEFVEFASPDPAALGRTFERFGFHAIAQHRHKNVKLFRQGEMNFIVDAEPDSFATRYA 60

Query: 72  AEHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIET-GPMELNLPAIKGIGGAPLYLIDR 130
           +E+G S+C +  RV D+  A+ RA++ GA P    T GPMELN+PAI+GIG + +Y IDR
Sbjct: 61  SEYGLSICAVGIRVNDAATAFARAVDAGAWPFEAGTVGPMELNIPAIQGIGRSIIYFIDR 120

Query: 131 F--GEGS-------SIYDIDFVFL----EGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAG 177
           +   EG        SIYD+DF  L            GAGL  +DH+T  V  G +  W  
Sbjct: 121 WRGKEGRPGDVGDISIYDVDFRALAHAATDTAATTAGAGLARVDHVTQAVDPGHLEEWLD 180

Query: 178 FYEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGE 237
           FY K+  FREI   +  G +    S+ + +P G+IRIP+ E+ ++   Q+E +L   +GE
Sbjct: 181 FYRKVLGFREIHEVN-AGWHVASDSRVLLSPCGLIRIPIYEKGTQRHDQMEHYLSGHHGE 239

Query: 238 GIQHVAFLTDDLIKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQSRGILLD 297
           GIQH+A  TDDL+ +   L   G+RF+  PP  YY+ ++ R+P HG  +  L+  GIL+D
Sbjct: 240 GIQHIALATDDLVASAAALARNGVRFV-EPPAAYYDTVDARVPGHGLDLAALRRYGILVD 298

Query: 298 GA-SEQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKAL 341
           GA    G +   LQ F+    G  FFE +QR    GFGEGN  AL
Sbjct: 299 GALRADGTREAFLQAFARREAGEFFFEIVQRDNYHGFGEGNLPAL 343


Lambda     K      H
   0.321    0.141    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: 378
Number of extensions: 23
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: 358
Length of database: 346
Length adjustment: 29
Effective length of query: 329
Effective length of database: 317
Effective search space:   104293
Effective search space used:   104293
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: 49 (23.5 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