GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Flavobacterium glycines Gm-149

Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_066329720.1 BLR17_RS09410 SDR family oxidoreductase

Query= SwissProt::Q8P3K4
         (300 letters)



>NCBI__GCF_900100165.1:WP_066329720.1
          Length = 255

 Score =  132 bits (331), Expect = 1e-35
 Identities = 81/252 (32%), Positives = 140/252 (55%), Gaps = 12/252 (4%)

Query: 56  RLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAESDAITTQLL---- 111
           R + K CL+T A +GIGR +A++ A+ GA+V+ +D++ AA + +  E  A+  +      
Sbjct: 3   RFENKVCLVTGASSGIGRATAISFAKEGANVVVSDVNEAAGELVVNEIKALGKEAFFVKC 62

Query: 112 DVTDAAAITAL----VAAHGPFDVLFNCAGYVHQGSI--LDCDEPAWRRSFSINVDAMYY 165
           D++  A +  +    V   G  D   N AG     S+   +  E AW +  +IN+   +Y
Sbjct: 63  DISQRAEVENMIQKTVKTFGRLDCAVNSAGIAGTLSLPTHEYPEDAWLQQININLTGTWY 122

Query: 166 TCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVR 225
             K  L  ML++G G+I+ +SS A+ + G P+   Y  +K  VIG+ K+ A +   + +R
Sbjct: 123 CVKYQLIEMLKQGGGNIVCVSS-AAGLVGQPDNVPYCASKHGVIGIVKSAAIENATKNIR 181

Query: 226 CNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESS 285
            NAICP  I+TP + +  + L  + +A+ ++  + Q M R+G P E+A + +++ SD+S+
Sbjct: 182 INAICPTAIETPMIMEGRRKLAHNPEAL-EAAINLQRMKRMGQPLEVADVALWMCSDQST 240

Query: 286 FTTGQTHIIDGG 297
           F TG    +DGG
Sbjct: 241 FITGHAMAVDGG 252


Lambda     K      H
   0.320    0.133    0.395 

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: 142
Number of extensions: 9
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: 300
Length of database: 255
Length adjustment: 25
Effective length of query: 275
Effective length of database: 230
Effective search space:    63250
Effective search space used:    63250
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: 47 (22.7 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