GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gyaR in Pedobacter sp. GW460-11-11-14-LB5

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate CA265_RS23175 CA265_RS23175 phosphoglycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS23175 CA265_RS23175
           phosphoglycerate dehydrogenase
          Length = 309

 Score =  162 bits (411), Expect = 8e-45
 Identities = 101/297 (34%), Positives = 159/297 (53%), Gaps = 27/297 (9%)

Query: 23  YEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNID 82
           YE++   D     R   L+K+++   +      ++D E+   AP LK +A+   G DNID
Sbjct: 23  YEVD---DEPQITRQQTLDKIKDYTGIAVRTKFRIDAEIFAAAPNLKFVARAGAGLDNID 79

Query: 83  IEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLM 142
            + A +R I + N P    DA  + A  LLL++      AD  +R+G W +         
Sbjct: 80  DKIAFERNIELINAPEGNCDAVGEHATGLLLSLMNNFRRADIEIRNGVWDREGNR----- 134

Query: 143 FLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLL 202
             GY LKGK +GI+G+G +GQ+ AK+  GF + ++ Y + +      +  A  V  E ++
Sbjct: 135 --GYELKGKKVGIIGYGFMGQSFAKKLAGFEVDVMAYDKYKT--GFSDAFAREVSMEEIV 190

Query: 203 KESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGA 262
           K SD +SLH+PLT ET  M+ ++     K     INT+RG +V+T A++ A+K G I GA
Sbjct: 191 KHSDVLSLHIPLTAETKQMVDDEYFYHFKKPIFFINTARGEIVNTPAVLNAIKSGKILGA 250

Query: 263 GLDVFE--------EEPYYNEELFKLKN---VVLAPHIGSATHEAREGMAELVAKNL 308
           GLDV +        E+ +YNE    LKN   V+L PH+G  T ++   ++E++A+ L
Sbjct: 251 GLDVLQTEKFPALGEQAWYNE----LKNNDKVILTPHVGGWTFDSYRKISEVLAEKL 303


Lambda     K      H
   0.317    0.137    0.392 

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: 272
Number of extensions: 16
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: 331
Length of database: 309
Length adjustment: 28
Effective length of query: 303
Effective length of database: 281
Effective search space:    85143
Effective search space used:    85143
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: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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