GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Sinorhizobium meliloti 1021

Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate SMc01635 SMc01635 oxidoreductase

Query= SwissProt::Q8P3K4
         (300 letters)



>FitnessBrowser__Smeli:SMc01635
          Length = 253

 Score =  152 bits (384), Expect = 8e-42
 Identities = 92/249 (36%), Positives = 138/249 (55%), Gaps = 10/249 (4%)

Query: 57  LQGKRCLITAAGAGIGRESALACARAGAHVIATD--IDAAA--LQALAAESDAITTQLLD 112
           L  +  ++T AG+GIGR  A   AR GAHV+  D  ++AA   + A+AA   +     +D
Sbjct: 3   LNNRIAIVTGAGSGIGRAGAAIMAREGAHVVVVDRSVEAAGDTVAAIAAGGGSAEALAVD 62

Query: 113 VTD----AAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCK 168
           VTD    A  I  ++  HG  D+L N AG    G + + +   + RS+++NV A +   +
Sbjct: 63  VTDDDALADGIADILYRHGRIDILHNHAGAQVAGDLEEVEVAGFDRSWNLNVRAHFMAAR 122

Query: 169 AVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNA 228
            V+P M + GRG I+N SS +S +        Y  TK AVI +++ +A DY   GVR NA
Sbjct: 123 LVMPSMKKAGRGVIVNTSS-SSGVLYDREMIAYTTTKHAVIAMTRQMAGDYAKYGVRVNA 181

Query: 229 ICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTT 288
           +CPG + TP     +  +GG E A+     +R P+GR     EIA+ +++L SD SS+ T
Sbjct: 182 LCPGWVDTPFNEPFIDQMGGRE-AIEAYIRERVPLGRWASVDEIAESILFLVSDRSSYMT 240

Query: 289 GQTHIIDGG 297
           GQ  ++DGG
Sbjct: 241 GQILVVDGG 249


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: 158
Number of extensions: 10
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: 253
Length adjustment: 25
Effective length of query: 275
Effective length of database: 228
Effective search space:    62700
Effective search space used:    62700
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