GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Gallaecimonas xiamenensis 3-C-1

Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= SwissProt::Q8P3K4
         (300 letters)



>NCBI__GCF_000299915.1:WP_008486155.1
          Length = 249

 Score =  123 bits (308), Expect = 5e-33
 Identities = 81/249 (32%), Positives = 123/249 (49%), Gaps = 13/249 (5%)

Query: 57  LQGKRCLITAAGAGIGRESALACARAGAHVIAT-------DIDAAALQALAAESDAITTQ 109
           L GKR L+T A  G+G+  AL  A  GA VI         D   A + AL  ++ A+   
Sbjct: 4   LNGKRALVTGASRGLGQAMALGLAENGAEVICASSREGGCDDTVAKILALGGKARALAAD 63

Query: 110 LLDVTDAAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKA 169
           L D     A+     A GP DVL N  G +++ + LD    A+     +N++A +   + 
Sbjct: 64  LGDSQAVQALAEQALAAGPVDVLVNNGGCIYREAALDFPLDAFDAVIKVNLNAAFQLSQL 123

Query: 170 VLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAI 229
           +   M+ +G G I+N++S+ S   G+     Y  +K A+ GL+KA+A ++   G++ NAI
Sbjct: 124 LGRAMVTKGSGKIVNIASMLSYSGGI-RVPAYTASKHAIAGLTKALANEWGQHGIQVNAI 182

Query: 230 CPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTG 289
            PG  +T       QAL  D +        R P GR G+P ++   VV+LAS  S +  G
Sbjct: 183 APGYFRT----DNTQALQDDAERS-SEIEKRIPAGRWGNPDDLKGAVVFLASKASDYVNG 237

Query: 290 QTHIIDGGW 298
               +DGGW
Sbjct: 238 HILAVDGGW 246


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: 147
Number of extensions: 7
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: 249
Length adjustment: 25
Effective length of query: 275
Effective length of database: 224
Effective search space:    61600
Effective search space used:    61600
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