GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Acidovorax sp. GW101-3H11

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Ac3H11_1225 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

Query= reanno::pseudo6_N2E2:Pf6N2E2_456
         (358 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1225
          Length = 299

 Score =  152 bits (383), Expect = 1e-41
 Identities = 102/266 (38%), Positives = 146/266 (54%), Gaps = 16/266 (6%)

Query: 7   NPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN----NE 62
           NP+GL G EFIE+A+  P  L    E +GF  VA HRS++V LYRQG +N+I+N    NE
Sbjct: 17  NPLGLQGIEFIEYATSRPQALGQALERLGFQPVARHRSREVLLYRQGDMNIIVNAHQDNE 76

Query: 63  PHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGG 122
              V +  A    P +  +AFRV ++  A++R LELGA  +H E   MELN+PAI G+G 
Sbjct: 77  RTGVHAPPALTETPVLAAIAFRVGNAAAAFRRVLELGAWAVHTEVEVMELNIPAIHGVGA 136

Query: 123 APLYLIDRFGEGSSIYDIDFVFIEGVD-RNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEK 181
           + +Y +DR+ E  SIYD+DFV I  V+ R P   GL +   +   +  GR A W  FY +
Sbjct: 137 SRIYFVDRWKE-FSIYDVDFVPIPTVNPRPPALQGLHLFG-VVQYIGLGRAADWIHFYSE 194

Query: 182 LFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQH 241
           LF F E+      G  T    + + +P G +   L E        + + L     E +Q 
Sbjct: 195 LFGFAELAPDQSFGVLT--HGRILASPCGTLHWQLIE-------PLVDALDADPEELLQR 245

Query: 242 VAFLTDDLVKTWDHLKSIGMRFMTAP 267
           VAF T D++ T   L++ G+ F+ +P
Sbjct: 246 VAFGTPDVLATVQALRARGVEFVESP 271


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: 308
Number of extensions: 18
Number of successful extensions: 4
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: 299
Length adjustment: 28
Effective length of query: 330
Effective length of database: 271
Effective search space:    89430
Effective search space used:    89430
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: 48 (23.1 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