GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yvgN in Salinicoccus carnicancri Crm

Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate WP_017549319.1 C792_RS0110070 aldo/keto reductase

Query= SwissProt::O32210
         (276 letters)



>NCBI__GCF_000330705.1:WP_017549319.1
          Length = 283

 Score =  207 bits (526), Expect = 3e-58
 Identities = 115/270 (42%), Positives = 159/270 (58%), Gaps = 7/270 (2%)

Query: 11  LHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVA 70
           L++G + P  GLG   ++        V A  KNGYR IDT+  Y NE  VG  I+ + V 
Sbjct: 9   LNDGTDTPAIGLGTVGLKGARGVGSIVTAIEKNGYRLIDTSTNYDNEGAVGEAIRRTAVP 68

Query: 71  REELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHW--PGKDKYKDTWRALEK 128
           REEL I SK+      Y+  +   ++SL R+ +DY D YLIHW  P + KY + W+AL  
Sbjct: 69  REELIINSKLPGAAHDYDQAIQMIQESLYRIGIDYFDKYLIHWPLPKQGKYVEAWQALID 128

Query: 129 LYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEA 188
             K G I+ IGVSNF   HLE+L+ +  + P  NQ+E HP     EL +  K  GI  EA
Sbjct: 129 ARKFGLIKTIGVSNFLTEHLEKLIDETGVTPATNQIERHPYFNNNELVEDNKRLGIVPEA 188

Query: 189 WSPLMQ--GQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIF 246
           WSP  +    +L+NE +  IA+K+ KS AQ+I+RW++Q+ V+ IPKS       EN D+F
Sbjct: 189 WSPFGREINDVLENETIRGIAQKYGKSPAQIIVRWNVQNDVLVIPKSSSPVHQRENLDVF 248

Query: 247 DFELSQEDMDKIDALNKDER---VGPNPDE 273
           DFELS ED+ +ID+L+K E     G +P+E
Sbjct: 249 DFELSNEDVKEIDSLDKGEEGRVEGQHPNE 278


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: 248
Number of extensions: 12
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: 283
Length adjustment: 26
Effective length of query: 250
Effective length of database: 257
Effective search space:    64250
Effective search space used:    64250
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