GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Shewanella oneidensis MR-1

Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate 203460 SO4382 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)

Query= SwissProt::A9CES4
         (256 letters)



>FitnessBrowser__MR1:203460
          Length = 241

 Score =  110 bits (274), Expect = 3e-29
 Identities = 86/254 (33%), Positives = 126/254 (49%), Gaps = 19/254 (7%)

Query: 3   LNNKVALITGAARGIGLGFAQAFAAEGAKVIIA-DIDIARATTSAA---AIGPAAKAVKL 58
           +NN+V L+TG++RGIG   A   AA G  + +    + A A  SAA   A+G     +K 
Sbjct: 1   MNNRV-LVTGSSRGIGKAIALKLAAAGHDIALHYHSNQAAADASAAELRALGVNVSLLKF 59

Query: 59  DVTDLAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPINGITEESYERVFDINLKGPMFMM 118
           DV D   + A ++A  E  G    +V NA I        ++E  ++ V   NL G   ++
Sbjct: 60  DVADRVAVRAALEADIEANGAYYGVVLNAGINRDNAFPAMSEAEWDSVIHTNLDGFYNVI 119

Query: 119 KAVSNVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALALVKHGINVN 178
                 M+   +GG+II +AS +G  G      Y ASKA +I AT++ +L L K  I VN
Sbjct: 120 HPCVMPMVQARKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRKITVN 179

Query: 179 AIAPGVVDGEHWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKGLAVFLASAD 238
            IAPG+++ +   V D              K  V + VP+ R   P++I  LA FL S D
Sbjct: 180 CIAPGLIETD--MVADI------------PKDMVEQLVPMRRMGKPNEIAALAAFLMSDD 225

Query: 239 SDYILAQTYNVDGG 252
           + YI  Q  +V+GG
Sbjct: 226 AAYITRQVISVNGG 239


Lambda     K      H
   0.319    0.133    0.376 

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: 114
Number of extensions: 8
Number of successful extensions: 3
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: 256
Length of database: 241
Length adjustment: 24
Effective length of query: 232
Effective length of database: 217
Effective search space:    50344
Effective search space used:    50344
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: 46 (22.3 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