GapMind for catabolism of small carbon sources

 

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

Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate CA265_RS09010 CA265_RS09010 3-phosphoglycerate dehydrogenase

Query= CharProtDB::CH_091801
         (331 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS09010 CA265_RS09010
           3-phosphoglycerate dehydrogenase
          Length = 315

 Score =  122 bits (306), Expect = 1e-32
 Identities = 85/290 (29%), Positives = 140/290 (48%), Gaps = 34/290 (11%)

Query: 31  TQELLTPETAKLAEGSDSAVVYQQLDYTRETLTALANVGVTNLSLRNVGTDNIDFDAARE 90
           T+ +   + A+  +  D+  V       +E + A+ N+ +  +    VG DNID + AR 
Sbjct: 26  TETVPQDQLAEALKNYDAITVRSATKVRKELIDAVPNIKL--IGRGGVGMDNIDVEYARS 83

Query: 91  FNFNISNVPVYSPNAIAEHSMLQLSRLLR------RTKALDAKIAKRDLRWAPTTGREMR 144
              N+ N P  S  ++AE     L   +R      R   ++      +L+ A   G E+ 
Sbjct: 84  QGINVVNTPAASSLSVAELVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELS 143

Query: 145 MQTVGVIGTGHIGRVAINILKGFGAKVIAYDKYPNAE---LQAEG-------LYVDTLDE 194
            +T+G+IG G IGR    +  G G  V+AYD YP+     L+ +G       +   +LDE
Sbjct: 144 GKTIGIIGFGRIGRATAKVALGLGMNVLAYDLYPSESEITLEFQGGKSVSIPIKTVSLDE 203

Query: 195 LYAQADAISLYVPGVPENHHLINADAIAKMKDGVVIMNAARGNLMDIDAIIDGLNSGKIS 254
           +   +D  SL+ P   +   ++ A+  AKMK+GV I+N +RG  +D  A+ID LNSGK+S
Sbjct: 204 VITGSDFFSLHTPFADKP--ILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKVS 261

Query: 255 DFGMDVYENEVACSMKIGLVKNSPDAKIADLIARENVMITPHTAFYTTKA 304
             G+DV++NE                 +A+++    + +TPH    T +A
Sbjct: 262 FAGLDVFDNE--------------PTPLAEILTHPKISLTPHIGASTNEA 297


Lambda     K      H
   0.317    0.133    0.374 

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: 255
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: 331
Length of database: 315
Length adjustment: 28
Effective length of query: 303
Effective length of database: 287
Effective search space:    86961
Effective search space used:    86961
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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, 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