GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yvgN in Marinobacter adhaerens HP15

Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate GFF854 HP15_833 2,5-diketo-D-gluconic acid reductase B

Query= SwissProt::O32210
         (276 letters)



>FitnessBrowser__Marino:GFF854
          Length = 269

 Score =  171 bits (434), Expect = 1e-47
 Identities = 97/262 (37%), Positives = 154/262 (58%), Gaps = 10/262 (3%)

Query: 17  MPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFI 76
           +P  G+G F+++ GN+A ++VK+A+  GYR IDTA +Y NE  VG GI  SG+ R E+F+
Sbjct: 6   LPKIGMGTFRLK-GNDARDAVKSALSLGYRHIDTAQMYGNEAEVGDGITSSGIPRREIFL 64

Query: 77  TSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPG---KDKYKDTWRALEKLYKDG 133
           T+K+W++       + +   SL RL+ D++DL LIHWP    +   K+   AL    ++G
Sbjct: 65  TTKIWHDQLHASDLINSLHDSLARLKTDHVDLALIHWPSPGDEVPMKEYLGALRDSQREG 124

Query: 134 KIRAIGVSNFQVHHLEE---LLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWS 190
               IG+SNF    ++E   +L D  I    NQVE HP L  +++  + +  GI +  + 
Sbjct: 125 LAEHIGISNFTCAQMDEAKAILGDTPI--FTNQVEVHPFLANRKVVAHAQKLGITVTGYM 182

Query: 191 PLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFEL 250
           PL  G+++++E L +IA + N + AQV + W    GVV IP S +      N +  + EL
Sbjct: 183 PLAVGKVMEDETLQRIAAERNLTPAQVAIAWVASRGVVPIPSSTRPGHQKANLEALEVEL 242

Query: 251 SQEDMDKIDALNKDERVGPNPD 272
           S+E++  ID L+++ER+  NPD
Sbjct: 243 SEEEIRAIDELDRNERIA-NPD 263


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: 173
Number of extensions: 11
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: 276
Length of database: 269
Length adjustment: 25
Effective length of query: 251
Effective length of database: 244
Effective search space:    61244
Effective search space used:    61244
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