GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Azospirillum brasilense Sp245

Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate AZOBR_RS28175 AZOBR_RS28175 short-chain dehydrogenase

Query= SwissProt::Q8P3K4
         (300 letters)



>FitnessBrowser__azobra:AZOBR_RS28175
          Length = 251

 Score =  147 bits (370), Expect = 3e-40
 Identities = 97/252 (38%), Positives = 139/252 (55%), Gaps = 15/252 (5%)

Query: 55  TRLQGKRCLITAAGAGIGRESALACARAGAHVIATDI-DAAALQAL----AAESDAITTQ 109
           T + G   L+T   +GIGR +ALA A+AGA  I T   +A  L+ +     A   A+  Q
Sbjct: 2   TDMSGGVALVTGGTSGIGRATALAFAKAGATAIVTGRREAEGLETVDLVRQAGGRAVFVQ 61

Query: 110 LLDVTDAAAITALVAA----HGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYY 165
             DV DA  + AL A     HG  D  FN AG     S+ D  E  + R  ++N+  ++ 
Sbjct: 62  A-DVADAEEVAALFARIERDHGRLDYAFNNAGIHFGRSVADTTEADFDRMVAVNIKGVWL 120

Query: 166 TCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVR 225
             K  LP ML +G+G+I++  SV   I G+    VY  +KAAV G+++++A +    GVR
Sbjct: 121 CLKHELPIMLRQGKGAIVSTGSVLGQI-GLAGNSVYSASKAAVEGMTRSVAIEVAKSGVR 179

Query: 226 CNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESS 285
            NA+CP  I+TP       + GG+E AV  +     P+GR+G PRE+A  VV+L SD +S
Sbjct: 180 VNAVCPAIIQTP---MSAGSFGGEE-AVNAALGPLHPVGRVGQPREVADTVVWLCSDAAS 235

Query: 286 FTTGQTHIIDGG 297
           F TGQ+  +DGG
Sbjct: 236 FITGQSINVDGG 247


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: 164
Number of extensions: 6
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: 251
Length adjustment: 25
Effective length of query: 275
Effective length of database: 226
Effective search space:    62150
Effective search space used:    62150
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.

Links

Downloads

Related tools

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