GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yvgN in Sinorhizobium meliloti 1021

Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate SMa1410 SMa1410 oxidoreductase

Query= SwissProt::O32210
         (276 letters)



>FitnessBrowser__Smeli:SMa1410
          Length = 277

 Score =  156 bits (394), Expect = 5e-43
 Identities = 90/243 (37%), Positives = 134/243 (55%), Gaps = 2/243 (0%)

Query: 21  GLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKV 80
           G G + ++ G     +V+ AI  GYR+ DTA +Y NE   G  + ESG+AR+EL IT+KV
Sbjct: 16  GFGTYPLK-GEPLKAAVREAITVGYRAFDTAQMYGNEAETGEALAESGLARDELCITTKV 74

Query: 81  WNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPG-KDKYKDTWRALEKLYKDGKIRAIG 139
             ++   E  L + E SL+ L++D  D+ ++HWP    +   + R L+K +  G  R IG
Sbjct: 75  HPDNYSEEAFLPSVEASLKALRVDQADVLMLHWPEINGENARSLRLLQKAFDIGLARNIG 134

Query: 140 VSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLD 199
           VSN+    + E     E   + NQVEFHP + Q  L D  +   I L ++  + +G++  
Sbjct: 135 VSNYTAPMMREAQSIVEAPLVTNQVEFHPLIDQSRLLDAAEETKIALSSYCSVARGEVFK 194

Query: 200 NEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKID 259
           + V  +I  ++ K+ AQ +LRW LQ GV     S K   I  N +I DF LS  DM +ID
Sbjct: 195 HPVFAEIGARYGKTAAQTVLRWILQKGVSMNTMSTKPENIRANFEILDFALSPHDMKRID 254

Query: 260 ALN 262
           A+N
Sbjct: 255 AMN 257


Lambda     K      H
   0.316    0.135    0.397 

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: 171
Number of extensions: 6
Number of successful extensions: 2
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: 276
Length of database: 277
Length adjustment: 25
Effective length of query: 251
Effective length of database: 252
Effective search space:    63252
Effective search space used:    63252
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 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