GapMind for catabolism of small carbon sources

 

Alignments for a candidate for udh in Pseudomonas simiae WCS417

Align D-galacturonate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate GFF3392 PS417_17360 NAD-dependent dehydratase

Query= reanno::WCS417:GFF3392
         (274 letters)



>FitnessBrowser__WCS417:GFF3392
          Length = 274

 Score =  562 bits (1448), Expect = e-165
 Identities = 274/274 (100%), Positives = 274/274 (100%)

Query: 1   MTTTPTTPVPFNRLLLTGAAGGLGKVLRERLRPYAQVLRLSDIANMAPAADASEEVQPCD 60
           MTTTPTTPVPFNRLLLTGAAGGLGKVLRERLRPYAQVLRLSDIANMAPAADASEEVQPCD
Sbjct: 1   MTTTPTTPVPFNRLLLTGAAGGLGKVLRERLRPYAQVLRLSDIANMAPAADASEEVQPCD 60

Query: 61  LADKQAVHHLVEGVDAILHFGGVSVERSFEEVLGANISGIFHIYEAARRHGVKRVIFASS 120
           LADKQAVHHLVEGVDAILHFGGVSVERSFEEVLGANISGIFHIYEAARRHGVKRVIFASS
Sbjct: 61  LADKQAVHHLVEGVDAILHFGGVSVERSFEEVLGANISGIFHIYEAARRHGVKRVIFASS 120

Query: 121 NHVIGFYKQGEKLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQ 180
           NHVIGFYKQGEKLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQ
Sbjct: 121 NHVIGFYKQGEKLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQ 180

Query: 181 NRRMMHTWLSFDDLTQLLERALYTPNVGHTVVYGMSDNLDTWWDNRYAAHLGFAPKDSSE 240
           NRRMMHTWLSFDDLTQLLERALYTPNVGHTVVYGMSDNLDTWWDNRYAAHLGFAPKDSSE
Sbjct: 181 NRRMMHTWLSFDDLTQLLERALYTPNVGHTVVYGMSDNLDTWWDNRYAAHLGFAPKDSSE 240

Query: 241 VFRAQVETQPPVSDNDPAKVYQGGAFCAAGPFGD 274
           VFRAQVETQPPVSDNDPAKVYQGGAFCAAGPFGD
Sbjct: 241 VFRAQVETQPPVSDNDPAKVYQGGAFCAAGPFGD 274


Lambda     K      H
   0.319    0.136    0.413 

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: 411
Number of extensions: 8
Number of successful extensions: 1
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: 274
Length of database: 274
Length adjustment: 25
Effective length of query: 249
Effective length of database: 249
Effective search space:    62001
Effective search space used:    62001
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