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_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase

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



>FitnessBrowser__SynE:Synpcc7942_0684
          Length = 249

 Score =  140 bits (353), Expect = 3e-38
 Identities = 88/249 (35%), Positives = 136/249 (54%), Gaps = 11/249 (4%)

Query: 19  LKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQ-AQKVEAVAAHWRERGADVHALQA 77
           L D++ L+TGA++GIG AI    A+  A++ ++    A   + V A     G +  A++A
Sbjct: 6   LTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKA 65

Query: 78  DVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137
           DVS++ +++A+    +E  GR+DVLVN AG+      L M  +DW+    ++L G +   
Sbjct: 66  DVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCS 125

Query: 138 KAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197
           +A    M++Q  G IINIASV      PG   Y  AK G++GLT+ +  E A +G+ VNA
Sbjct: 126 RAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNA 185

Query: 198 IAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASD-EAPFIN 256
           +APG+I T +  +            ++ L++ P  R G+  EVA    FLA+D  A +I 
Sbjct: 186 VAPGFIATDMTSE---------LAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYIT 236

Query: 257 ASCITIDGG 265
              I IDGG
Sbjct: 237 GQVINIDGG 245


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: 154
Number of extensions: 4
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: 272
Length of database: 249
Length adjustment: 24
Effective length of query: 248
Effective length of database: 225
Effective search space:    55800
Effective search space used:    55800
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