GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Marinobacter adhaerens HP15

Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate GFF846 HP15_825 short-chain dehydrogenase/reductase SDR

Query= SwissProt::Q8P3K4
         (300 letters)



>FitnessBrowser__Marino:GFF846
          Length = 256

 Score =  117 bits (293), Expect = 3e-31
 Identities = 86/251 (34%), Positives = 129/251 (51%), Gaps = 15/251 (5%)

Query: 57  LQGKRCLITAAGAGIGRESALACARAGAHVIATD--ID-----AAALQALAAESDAITTQ 109
           L GK  LIT A  GIG   A   A  GAHVI +   ID     A++++     ++A    
Sbjct: 9   LTGKVALITGASRGIGESIARTLAEYGAHVIVSSRKIDGCEAVASSIRDAGGSAEAYACH 68

Query: 110 LLDVTDAAAITALV-AAHGPFDVLFN-CAGYVHQGSILDCDEPAWRRSFSINVDAMYYTC 167
           + D+    +I A +   HG  D+L N  A   + G + D D  A+ ++  +N+   ++ C
Sbjct: 69  IGDMDQIESIWAHIDQTHGKLDILVNNAAANPYFGPVEDTDLGAFNKTVDVNIRGYFFMC 128

Query: 168 KAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCN 227
                 M + G GSI+N++SV + +     + +Y VTKAAVI ++K+ A +   Q +R N
Sbjct: 129 ARGAQMMKKAGGGSIVNVASV-NGVNPGHYQGIYSVTKAAVISMTKSFAMELGQQKIRVN 187

Query: 228 AICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFT 287
           A+ PG   T    +   AL  +E A+ K      PM R+ DP E+A  V+YL SD SS+T
Sbjct: 188 ALLPGLTDT----KFASALTTNE-AIKKQAMAHIPMKRVADPGEMAGTVLYLVSDASSYT 242

Query: 288 TGQTHIIDGGW 298
           TG     DGG+
Sbjct: 243 TGACINADGGY 253


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: 156
Number of extensions: 12
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: 256
Length adjustment: 25
Effective length of query: 275
Effective length of database: 231
Effective search space:    63525
Effective search space used:    63525
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 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