GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Shewanella oneidensis MR-1

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 201943 SO2813 oxidoreductase, short chain dehydrogenase/reductase family (NCBI ptt file)

Query= metacyc::MONOMER-16230
         (256 letters)



>FitnessBrowser__MR1:201943
          Length = 254

 Score =  129 bits (324), Expect = 6e-35
 Identities = 85/249 (34%), Positives = 134/249 (53%), Gaps = 16/249 (6%)

Query: 6   KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65
           K   V G SRGIG A  +  A +GA V   +  S+   A +  L +E+ A GG AIA+ A
Sbjct: 15  KVAFVQGGSRGIGAAIVKRLASEGAAVAFTYVSSE---AQSQLLVDEVIAQGGKAIAIKA 71

Query: 66  DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYFTV 125
           D+ + ++  + +       G +D++VNNAGI  + S  ++  E + + V TN+   +   
Sbjct: 72  DSTEPEAIRRAIRETKAHLGGLDIVVNNAGILIWDSIENLTLEDWERIVNTNVRSVFVAS 131

Query: 126 QAAARRMKEQGRGGAIIAVSSISA----LVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181
           Q AA  M +   GG II + S +A     VGGA+   Y  +K+ L+ L +  A  LGP  
Sbjct: 132 QEAALHMND---GGRIINIGSTNAERIPFVGGAI---YGMSKSALVGLAKGLARDLGPRA 185

Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241
           I  N + PG + TD+N +   + +  E + +   LGR G+ +++A  + F+A   A Y+T
Sbjct: 186 ITVNNIQPGPVDTDMNPD---NGDSSEPIKAIGVLGRYGKAEEIASFVAFIAGPEAGYIT 242

Query: 242 GASLLVDGG 250
           GASL++DGG
Sbjct: 243 GASLMIDGG 251


Lambda     K      H
   0.319    0.136    0.383 

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: 159
Number of extensions: 9
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: 254
Length adjustment: 24
Effective length of query: 232
Effective length of database: 230
Effective search space:    53360
Effective search space used:    53360
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