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_RS23175 CA265_RS23175 phosphoglycerate dehydrogenase

Query= BRENDA::Q9I530
         (329 letters)



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

 Score =  135 bits (341), Expect = 1e-36
 Identities = 81/252 (32%), Positives = 138/252 (54%), Gaps = 8/252 (3%)

Query: 65  AAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAY 124
           AA   + VA   AG +++D   A    + +++ P  +  AV EHA GL+L+L     RA 
Sbjct: 61  AAPNLKFVARAGAGLDNIDDKIAFERNIELINAPEGNCDAVGEHATGLLLSLMNNFRRAD 120

Query: 125 NRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRIQAL 184
              R G +   G  G++L GK+VG+IG G +G++FA+ +AGF  +++AYD Y      A 
Sbjct: 121 IEIRNGVWDREGNRGYELKGKKVGIIGYGFMGQSFAKKLAGFEVDVMAYDKYKTGFSDAF 180

Query: 185 GGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALI 244
             R ++++ ++  SD++SLH PLTA+T+ ++D +     K     INT RG +VN  A++
Sbjct: 181 -AREVSMEEIVKHSDVLSLHIPLTAETKQMVDDEYFYHFKKPIFFINTARGEIVNTPAVL 239

Query: 245 EALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREAL 304
            A+KSG++   GLDV + E    F    +Q   ++    L +   V++T H    T ++ 
Sbjct: 240 NAIKSGKILGAGLDVLQTEK---FPALGEQAWYNE----LKNNDKVILTPHVGGWTFDSY 292

Query: 305 AAIADTTLDNIA 316
             I++   + ++
Sbjct: 293 RKISEVLAEKLS 304


Lambda     K      H
   0.323    0.137    0.402 

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: 264
Number of extensions: 11
Number of successful extensions: 2
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: 329
Length of database: 309
Length adjustment: 28
Effective length of query: 301
Effective length of database: 281
Effective search space:    84581
Effective search space used:    84581
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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, 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