GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Synechococcus elongatus PCC 7942

Align Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; Cmo2DD; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; EC 1.3.1.20; EC 1.1.1.179 (characterized)
to candidate Synpcc7942_1665 Synpcc7942_1665 probable oxidoreductase

Query= SwissProt::Q9TQS6
         (334 letters)



>FitnessBrowser__SynE:Synpcc7942_1665
          Length = 371

 Score = 79.0 bits (193), Expect = 2e-19
 Identities = 59/193 (30%), Positives = 90/193 (46%), Gaps = 7/193 (3%)

Query: 3   LRWGIVSVGLISSDFTAVLQTLPRSEHQVVAVAARDLSRAKEFAQKHDIPKAYGSYEELA 62
           LR  ++  G  S      LQ    SE  V AV  R   RA   A +  IP AY   ++L 
Sbjct: 10  LRVAVLGTGFGSKVHIPALQH--HSETTVQAVYHRQPDRAAAIAVQFGIPNAYSDLDQLL 67

Query: 63  KDPNVEVAYVGTQHPQHKAAVMLCLAAGKAVLCEKPMGVNAAEVREMVTEARSRGLFLME 122
            DP +E   + +    H       L+AGK+VL EKP  +N  E R +   A S+GL +  
Sbjct: 68  ADPAIEAVTIASPPFLHYPMAWAALSAGKSVLLEKPTTLNVEEARALWKLASSQGLTVTL 127

Query: 123 AIWTRFFPASEALRSVLAQGTLGDLRVARAEF-GKNLTHVPRAVDW----AQAGGALLDL 177
               RF PA + +  +LA+G +G   + + ++   +     R  +W    +Q GGAL  L
Sbjct: 128 DFEYRFVPAWQYVAELLAEGVIGQPWLVKLDWLMSSRADASRPWNWYALRSQGGGALGAL 187

Query: 178 GIYCVQFISMVFG 190
           G +   +++ +FG
Sbjct: 188 GSHSFDYLAWLFG 200


Lambda     K      H
   0.320    0.134    0.401 

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: 227
Number of extensions: 9
Number of successful extensions: 2
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: 334
Length of database: 371
Length adjustment: 29
Effective length of query: 305
Effective length of database: 342
Effective search space:   104310
Effective search space used:   104310
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