GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catA in Paraburkholderia bryophila 376MFSha3.1

Align Catechol 1,2-dioxygenase; EC 1.13.11.1 (characterized)
to candidate H281DRAFT_02578 H281DRAFT_02578 hydroxyquinol 1,2-dioxygenase

Query= SwissProt::P86029
         (303 letters)



>FitnessBrowser__Burk376:H281DRAFT_02578
          Length = 288

 Score =  178 bits (451), Expect = 2e-49
 Identities = 91/248 (36%), Positives = 140/248 (56%), Gaps = 3/248 (1%)

Query: 6   TESVKTSLGPNATPRAKKLIASLVQHVHDFARENHLTTEDWLWGVDFINRIGQMSDSRRN 65
           T +V   L  + + R  ++  +LV+H+H F +E   T ++W   + F+ + GQM    R 
Sbjct: 10  TAAVIERLAGSTSKRVHQISDALVRHLHAFVKEIEPTEDEWAAAIRFLTQTGQMCTDTRQ 69

Query: 66  EGILVCDIIGLETLVDALTNESEQSNHTSSAILGPFYLPDSPVYPNGGSIVQKAIPTDVK 125
           E IL+ D +G+  LVDA+ N     + T + +LGPFY+ ++   P G SI        + 
Sbjct: 70  EFILLSDTLGVSMLVDAI-NHRYPGDATQTTVLGPFYVEEAAELPLGASIADGEPGEPL- 127

Query: 126 CFVRGKVTDTEGKPLGGAQLEVWQCNSAGFYSQQADHDGPEFNLRGTFITDDEGNYSFEC 185
             V G V D  GKP+ GA +E W  +S GFY  Q      E ++R  F+TD +G + +  
Sbjct: 128 -LVEGTVRDLNGKPIAGALVETWHADSHGFYDVQKAAGKTELHMRARFLTDADGAFWYRS 186

Query: 186 LRPTSYPIPYDGPAGDLLKIMDRHPNRPSHIHWRVSHPGYHTLITQIYDAECPYTNNDSV 245
           + P +YPIP DGP G +L    RHP RP+H+H+RVS PG+ TL+T ++ +   Y ++D V
Sbjct: 187 IVPAAYPIPNDGPVGRMLDAQGRHPYRPAHVHFRVSAPGFETLVTHVFVSGDVYLDSDVV 246

Query: 246 YAVKDDII 253
           + VKD +I
Sbjct: 247 FGVKDALI 254


Lambda     K      H
   0.316    0.134    0.407 

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: 245
Number of extensions: 13
Number of successful extensions: 3
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: 303
Length of database: 288
Length adjustment: 26
Effective length of query: 277
Effective length of database: 262
Effective search space:    72574
Effective search space used:    72574
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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