GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS09010
          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.

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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