GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Oscillibacter ruminantium GH1

Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_040663927.1 ON16_RS13885 SDR family oxidoreductase

Query= SwissProt::A3LZU7
         (258 letters)



>NCBI__GCF_000307265.1:WP_040663927.1
          Length = 251

 Score =  124 bits (312), Expect = 1e-33
 Identities = 83/249 (33%), Positives = 131/249 (52%), Gaps = 11/249 (4%)

Query: 8   KVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDG--ENNVLTI 65
           +V  ITG   GIG+A A+ MA  GAKVV+     E    + +E+K    +   +   +T 
Sbjct: 6   QVAIITGSTKGIGKATALLMAAEGAKVVIVGTTEEAGNAVVEEIKAAGGEAFFQKTNVTS 65

Query: 66  PGDISLPETGRRIVELAVEKFGEINVFVSNAGVCG-FREFLEITPETLFQTVNINLNGAF 124
             D+        +V  A++++G+I++ V+NAGV G      +IT E   + +  NL   F
Sbjct: 66  AADLDA------LVSAALDQYGKIDILVNNAGVGGSLANMDQITDEEWDKVLATNLTAPF 119

Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKYGI 184
             ++     M K G GG I+ ++S+++   G     YT  K G+L L +  +   G  GI
Sbjct: 120 QVMKRVIPVMEKAG-GGKIVNVASMASTAAGRGGIAYTTAKHGVLGLTRQVSLDHGHAGI 178

Query: 185 RCNAILPGTISTALNEEDLKDPEKRKYMEGRI-PLGRVGDPKDIAGPAIFLASDMSNYVN 243
           R NA+LPG I T +    L  P+    M+ ++ P GR G P+++A   +FLAS+ S+++ 
Sbjct: 179 RVNAVLPGPIDTQMIARVLAMPQHPLNMKIKMSPAGRPGQPEEVAKAILFLASEDSSFIQ 238

Query: 244 GAQLLVDGG 252
           GA L VDGG
Sbjct: 239 GAALAVDGG 247


Lambda     K      H
   0.317    0.136    0.382 

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: 122
Number of extensions: 8
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: 258
Length of database: 251
Length adjustment: 24
Effective length of query: 234
Effective length of database: 227
Effective search space:    53118
Effective search space used:    53118
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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