GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Synechococcus elongatus PCC 7942

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate Synpcc7942_1573 Synpcc7942_1573 3-oxoacyl-(acyl-carrier protein) reductase

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>FitnessBrowser__SynE:Synpcc7942_1573
          Length = 266

 Score =  132 bits (331), Expect = 1e-35
 Identities = 82/267 (30%), Positives = 145/267 (54%), Gaps = 16/267 (5%)

Query: 18  RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVI--------SDIQAQKVEAVAAHW---R 66
           +L +++ L+TG++QGIG+ I    AS+ A +VI        ++   ++VEA  A     +
Sbjct: 3   KLDNQIALVTGSSQGIGQEIAIRLASEGASVVIDYRSHPEGAEETRKQVEAAGAQCHLAK 62

Query: 67  ERGADVHALQADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCF 126
           +   + + +QAD+     ++ +   +++  G++D+LVN AG+       E+TE D+    
Sbjct: 63  DHAPEGYVVQADLGDVTQVRNLVAESIKHFGKLDILVNNAGMERRAPFWEVTEADYDMVL 122

Query: 127 AIDLDGAWYGCKAVLPQMIE-QGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALG 185
            ++L GA++  +A++  ++E +  G IINI+SVH     P    Y ++K G+  +TR L 
Sbjct: 123 NVNLKGAFFAAQALVQHLLETKRPGKIINISSVHEELPFPNFASYCLSKGGIKMMTRDLA 182

Query: 186 IEYAPKGVRVNAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAV 245
           +E    G+ +N +APG IET +N +  N       E    L   P +R+G+P ++A   +
Sbjct: 183 VELGEYGITINNVAPGAIETPINTNLLNN----PTELNALLGNIPLKRLGKPKDIASLVL 238

Query: 246 FLASDEAPFINASCITIDGGRSVMYHD 272
           FLAS +A +I  + I  DGG    YH+
Sbjct: 239 FLASPDADYITGTTIFADGGLLWNYHE 265


Lambda     K      H
   0.321    0.137    0.419 

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: 160
Number of extensions: 6
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: 272
Length of database: 266
Length adjustment: 25
Effective length of query: 247
Effective length of database: 241
Effective search space:    59527
Effective search space used:    59527
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: 47 (22.7 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