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_RS12240 CA265_RS12240 phosphoglycerate dehydrogenase

Query= BRENDA::O66939
         (334 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS12240 CA265_RS12240
           phosphoglycerate dehydrogenase
          Length = 311

 Score =  152 bits (384), Expect = 1e-41
 Identities = 98/325 (30%), Positives = 168/325 (51%), Gaps = 31/325 (9%)

Query: 3   VLFTSVPQEDVPFYQEALKDLSLKIYTTDVSKVPENELKKAELISVFVYDK--LTEELLS 60
           +L  ++ +E +   QE     ++ ++T       ++ L   E+ ++    K  + + L+ 
Sbjct: 6   LLLETIAEEALALLQE-----NVNVFTGYDEAGLKDTLNNVEVHAIITRGKKHIDKTLMD 60

Query: 61  KMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEHTFAMILTLVKRLKRIE 120
             P L++     VG D++D+D    + I V + P  +  ++AEHT A++L L++ + R  
Sbjct: 61  ACPHLEVAARCGVGLDNVDVDEASARKIRVINAPGSNAATIAEHTLALMLMLMRDMHRSV 120

Query: 121 DRVKKLNFSQDSEILARELNRLTLGVIGTGRIGSRVAMYGLAFGMKVLCYDVVKREDLKE 180
           + VK+ N++  ++    ELN  TLG++G G IG RVA  G AFGMKVLC+          
Sbjct: 121 NHVKQNNWNWRNQYAGDELNGKTLGILGLGNIGKRVAKLGDAFGMKVLCW---------S 171

Query: 181 KGCVYTSLDELLKESDVISLHVPYTKETHHMINEERISLMKDGVYLINTARGKVVDTDAL 240
           +      LDE+L++SDV+SLH+P + ET+ +I   +++LMK   +LINTARG ++D  AL
Sbjct: 172 RSVQDLPLDEVLQQSDVVSLHLPLSNETNEIIGASQLALMKPKAFLINTARGALIDHAAL 231

Query: 241 YRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKNLKILELACKDNVIITPHIAYYTD 300
             A   G  +G   DV  DE                 L+ L +    N ++TPH A  T 
Sbjct: 232 LDALNAGTIAGFAADVLPDE---------------PPLQSLAVVQHPNALVTPHAASLTA 276

Query: 301 KSLERIREETVKVVKAFVKGDLEQI 325
            + +++   TV+ V + + G   ++
Sbjct: 277 STYKQMCLLTVRNVLSVLAGQQPEL 301


Lambda     K      H
   0.319    0.138    0.383 

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: 196
Number of extensions: 6
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: 334
Length of database: 311
Length adjustment: 28
Effective length of query: 306
Effective length of database: 283
Effective search space:    86598
Effective search space used:    86598
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 (21.7 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 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