GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucA in Haloterrigena daqingensis JX313

Align L-fuculose phosphate aldolase; EC 4.1.2.17; L-fuculose-1-phosphate aldolase (uncharacterized)
to candidate WP_076580931.1 BB347_RS09575 class II aldolase/adducin family protein

Query= curated2:Q8FEF0
         (215 letters)



>NCBI__GCF_001971705.1:WP_076580931.1
          Length = 213

 Score =  133 bits (334), Expect = 3e-36
 Identities = 77/209 (36%), Positives = 122/209 (58%), Gaps = 10/209 (4%)

Query: 8   RQIIDTCLEMTRLGLNQGTAGNVSVRYQ---DGMLITPTGIPYEKLTESHIVFIDGNGKH 64
           RQ+++   E+  L       GN+SVR     D   ITPTG+PY+    +    +  +G+ 
Sbjct: 8   RQVVEHAAELAEL--TPARTGNLSVRESTDGDAFAITPTGVPYDSFDVAETPVVGVDGEQ 65

Query: 65  EEGKL-PSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRPIPAIHYMIAAAGGNSI 123
            +G++ PSSE   H A Y+ R D  A+VH H+   TA++  ++P+P IHYMI A  G  +
Sbjct: 66  RDGEMAPSSEVPMHSAIYR-REDVGAIVHTHSPWSTAMATAHQPLPPIHYMIVAV-GKRV 123

Query: 124 PCAPYATFGTRELSEHV--ALALKNRKATLLQHHGLIACEANLEKALWLAHEVEVLAQLY 181
           P A YA +GT +L+E++  A++  +  A  +++HGL+    +LE AL   H VE LA+LY
Sbjct: 124 PVASYAPYGTDKLAENIVEAMSAADSTAAFIENHGLVVTAPDLETALENTHHVESLARLY 183

Query: 182 LTTLAITDPVPVLSDEEIAVVLEKFKTYG 210
           L   + +     L+DE++  VLE+F++YG
Sbjct: 184 LEIRSASLEPRPLTDEQLETVLEQFESYG 212


Lambda     K      H
   0.319    0.134    0.397 

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: 114
Number of extensions: 5
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: 215
Length of database: 213
Length adjustment: 22
Effective length of query: 193
Effective length of database: 191
Effective search space:    36863
Effective search space used:    36863
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: 45 (21.9 bits)

This GapMind analysis is from Sep 24 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